Aggregation/Crystallization-Induced Emission in Naphthyridine-Based Carbazolyl-Modified Donor-Acceptor Boron Dyes Tunable by Fluorine Atoms

Four donor-acceptor boron difluoride complexes based on the carbazole electron donor and the [1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridine acceptor were designed, synthesized, and systematically spectroscopically investigated in solutions, in dye-doped polymer films, and in the solid states. The dyes exhibit an intense blue to red solid-state emission with photoluminescence quantum yields of up to 59 % in pure dye samples and 86 % in poly(methyl methacrylate) films. All boron complexes show aggregation-induced emission and reversible mechanofluorochromism. The optical properties of these dyes and their solid state luminescence can be tuned by substitution pattern, i. e., the substituents at the naphthyridine unit. Exchange of CH3- for CF3-groups does not only increase the intramolecular charge transfer character, but also provides a crystallization-induced emission enhancement.

Transcriptome Profiling of a Salt Excluder Hybrid Grapevine Rootstock 'Ruggeri' throughout Salinity

Salinity is one of the substantial threats to plant productivity and could be escorted by other stresses such as heat and drought. It impairs critical biological processes, such as photosynthesis, energy, and water/nutrient acquisition, ultimately leading to cell death when stress intensity becomes uncured. Therefore, plants deploy several proper processes to overcome such hostile circumstances. Grapevine is one of the most important crops worldwide that is relatively salt-tolerant and preferentially cultivated in hot and semi-arid areas. One of the most applicable strategies for sustainable viticulture is using salt-tolerant rootstock such as Ruggeri (RUG). The rootstock showed efficient capacity of photosynthesis, ROS detoxification, and carbohydrate accumulation under salinity. The current study utilized the transcriptome profiling approach to identify the molecular events of RUG throughout a regime of salt stress followed by a recovery procedure. The data showed progressive changes in the transcriptome profiling throughout salinity, underpinning the involvement of a large number of genes in transcriptional reprogramming during stress. Our results established a considerable enrichment of the biological process GO-terms related to salinity adaptation, such as signaling, hormones, photosynthesis, carbohydrates, and ROS homeostasis. Among the battery of molecular/cellular responses launched upon salinity, ROS homeostasis plays the central role of salt adaptation.

Hyperbaric oxygen alleviates selective domains of cognitive and motor deficits in female 5xFAD mice

Treatment of Alzheimer's disease (AD) has been limited to managing of symptoms or anti-amyloid therapy with limited results and uncertainty. Seeking out new therapies that can reverse the effects of this devastating disease is important. Hyperbaric oxygen (HBO) therapy could be such a candidate as it has been shown to improve brain function in certain neurological conditions. Furthermore, the role sex plays in the vulnerability/resilience to AD remains equivocal. An understanding of what makes one sex more vulnerable to AD could unveil new pathways for therapy development. In this study, we investigated the effects of HBO on cognitive, motor, and affective function in a mouse model of AD (5xFAD) and assessed protein oxidation in peripheral tissues as a safety indicator. The motor and cognitive abilities of 5xFAD mice were significantly impaired. HBO therapy improved cognitive flexibility and associative learning of 5xFAD females but not males, but HBO had no effect other aspects of cognition. HBO also reversed AD-related declines in balance but had no impact on gait and anxiety-like behavior. HBO did not affect body weights or oxidative stress in peripheral tissues. Our study provides further support for HBO therapy as a potential treatment for AD and emphasizes the importance of considering sex as a biological variable in therapeutic development. Further investigations into the underlying mechanisms of HBO's sex-specific responses are warranted, as well as optimizing treatment protocols for maximum benefits.

Accelerating Elastic Property Prediction in Fe-C Alloys through Coupling of Molecular Dynamics and Machine Learning

The scarcity of high-quality data presents a major challenge to the prediction of material properties using machine learning (ML) models. Obtaining material property data from experiments is economically cost-prohibitive, if not impossible. In this work, we address this challenge by generating an extensive material property dataset comprising thousands of data points pertaining to the elastic properties of Fe-C alloys. The data were generated using molecular dynamic (MD) calculations utilizing reference-free Modified embedded atom method (RF-MEAM) interatomic potential. This potential was developed by fitting atomic structure-dependent energies, forces, and stress tensors evaluated at ground state and finite temperatures using ab-initio. Various ML algorithms were subsequently trained and deployed to predict elastic properties. In addition to individual algorithms, super learner (SL), an ensemble ML technique, was incorporated to refine predictions further. The input parameters comprised the alloy's composition, crystal structure, interstitial sites, lattice parameters, and temperature. The target properties were the bulk modulus and shear modulus. Two distinct prediction approaches were undertaken: employing individual models for each property prediction and simultaneously predicting both properties using a single integrated model, enabling a comparative analysis. The efficiency of these models was assessed through rigorous evaluation using a range of accuracy metrics. This work showcases the synergistic power of MD simulations and ML techniques for accelerating the prediction of elastic properties in alloys.

An updated end-to-end ecosystem model of the Northern California Current reflecting ecosystem changes due to recent marine heatwaves

The Northern California Current is a highly productive marine upwelling ecosystem that is economically and ecologically important. It is home to both commercially harvested species and those that are federally listed under the U.S. Endangered Species Act. Recently, there has been a global shift from single-species fisheries management to ecosystem-based fisheries management, which acknowledges that more complex dynamics can reverberate through a food web. Here, we have integrated new research into an end-to-end ecosystem model (i.e., physics to fisheries) using data from long-term ocean surveys, phytoplankton satellite imagery paired with a vertically generalized production model, a recently assembled diet database, fishery catch information, species distribution models, and existing literature. This spatially-explicit model includes 90 living and detrital functional groups ranging from phytoplankton, krill, and forage fish to salmon, seabirds, and marine mammals, and nine fisheries that occur off the coast of Washington, Oregon, and Northern California. This model was updated from previous regional models to account for more recent changes in the Northern California Current (e.g., increases in market squid and some gelatinous zooplankton such as pyrosomes and salps), to expand the previous domain to increase the spatial resolution, to include data from previously unincorporated surveys, and to add improved characterization of endangered species, such as Chinook salmon (Oncorhynchus tshawytscha) and southern resident killer whales (Orcinus orca). Our model is mass-balanced, ecologically plausible, without extinctions, and stable over 150-year simulations. Ammonium and nitrate availability, total primary production rates, and model-derived phytoplankton time series are within realistic ranges. As we move towards holistic ecosystem-based fisheries management, we must continue to openly and collaboratively integrate our disparate datasets and collective knowledge to solve the intricate problems we face. As a tool for future research, we provide the data and code to use our ecosystem model.

Development and Performance Evaluation of a Novel Solar Dryer Integrated with Thermal Energy Storage System for Drying of Agricultural Products

Passive solar dryers play a crucial role in reducing postharvest losses in fruits and vegetables, especially in regions like sub-Saharan Africa with low electrification rates and limited financial resources. However, the intermittent nature of solar energy presents a significant challenge for these dryers. Passive solar dryers integrated with thermal energy storage (TES) can reduce intermittence and improve the drying efficiency. Currently, phase change materials (PCMs) are popular heat storage materials in dryers, and paraffin wax dominates. The main problem with the use of PCMs is that it is necessary to closely constrain the temperature range of the process during charging and discharging. This can be a difficult condition to meet in simple solar dryers due to the variable availability of solar radiation. Instead, solid-phase materials, such as sand and rocks, are often used. Soapstone is one of the natural rocks with good thermal properties, but it has yet to be used as a TES material in solar dryers for drying agricultural products. Therefore, the main objective of the present study was to develop a novel solar dryer integrated with soapstone as a TES material and evaluate its performance. The proximate analysis to examine the quality of dried products using the developed technology was also carried out. The comparative experiments for the developed dryer were conducted in two modes: dryer with TES materials and without TES materials, and the results were compared with open sun drying (OSD) by drying 50 kg of fresh pineapple and carrot at different times. The drying times for pineapples in the dryer with TES, without TES, and OSD were 13, 24, and 52 h, respectively. However, the drying times for carrots in the dryer with TES, without TES, and OSD were 12, 23, and 50 h, respectively. Notably, the dryer integrated with TES materials could supply heat for around 3-4 h after sunset. The thermal efficiency of the dryer, collector efficiency, and storage efficiency of TES materials were calculated and found to be 45, 43, and 74.5%, respectively. Proximate analysis indicated that the dryer integrated with TES materials effectively maintained the quality of the dried products compared to OSD. Solar dryer integrated with soapstone showed great promise as sustainable and efficient solutions for reducing postharvest losses and enhancing food security in resource-constrained regions like sub-Saharan Africa.

Handheld Ultra-Fast Duplex Polymerase Chain Reaction Assays and Lateral Flow Detection and Identification of Leishmania Parasites for Cutaneous Leishmaniases Diagnosis

Early and accurate detection of infectious diseases is a key step for surveillance, epidemiology and control, notably timely disease diagnosis, patient management and follow-up. In this study, we aimed to develop handheld ultra-fast duplex PCR assays coupled to amplicon detection by lateral flow (LF) immunoassay to deliver a rapid and simple molecular diagnostic test for concomitant detection and identification of the main Leishmania parasites encountered in Tunisia. We selected two DNA targets to amplify L. major/L. tropica and L. infantum/L. tropica groups of species DNAs, respectively. We optimized the experimental conditions of a duplex ultra-fast PCR. The amplification is performed using a portable Palm convection PCR machine within 18 min, and the products are detected using an LF cassette within 10 min. The test allows the identification of the infecting species according to the position and number of test lines revealed. Tested on a selection of DNAs of representative Leishmania strains of the three studied species (N = 37), the ultra-fast duplex PCR-LF showed consistent, stable and reproducible results. The analytical limit of detection of the test was 0.4 pg for L. major, 4 pg for L. infantum and 40 pg for L. tropica.

Facilitated Adsorption of Mercury(II) and Chromium(VI) Ions over Functionalized Carbon Nanotubes

By considering the importance of water and its purity, herein, a powerful adsorbent has been developed for the adsorption of two toxic contaminants that commonly exist in water, viz., divalent mercury and hexavalent chromium. The efficient adsorbent, CNTs-PLA-Pd, was prepared by covalent grafting polylactic acid to carbon nanotubes and subsequent deposition of palladium nanoparticles. The CNTs-PLA-Pd could adsorb Hg(II), and Cr(VI) entirely exists in water. The adsorption rate for Hg(II) and Cr(VI) was rapid at initial stage, followed by gradual decrease, and attained the equilibrium. The Hg(II) and Cr(VI) adsorption was perceived within 50 min and 80 min, respectively with CNTs-PLA-Pd,. Further, experimental data for Hg(II) and Cr(VI) adsorption was analyzed, and kinetic parameters were estimated using pseudo-first and second-order models. The adsorption process of Hg(II) and Cr(VI) followed the pseudo-second-order kinetics, and the rate-limiting step in the adsorption was chemisorption. The Weber-Morris intraparticle pore diffusion model revealed that the Hg(II) and Cr(VI) adsorption over CNTs-PLA-Pd occurs through multiple phases. The experimental equilibrium parameters for the Hg(II) and Cr(VI) adsorption were estimated by Langmuir, Freundlich, and Temkin isotherms models. All three models were well suited and demonstrated that Hg(II) and Cr(VI) adsorption over CNTs-PLA-Pd transpires through monolayer molecular covering and chemisorption.

Development of the RF-MEAM Interatomic Potential for the Fe-C System to Study the Temperature-Dependent Elastic Properties

One of the major impediments to the computational investigation and design of complex alloys such as steel is the lack of effective and versatile interatomic potentials to perform large-scale calculations. In this study, we developed an RF-MEAM potential for the iron-carbon (Fe-C) system to predict the elastic properties at elevated temperatures. Several potentials were produced by fitting potential parameters to the various datasets containing forces, energies, and stress tensor data generated using density functional theory (DFT) calculations. The potentials were then evaluated using a two-step filter process. In the first step, the optimized RSME error function of the potential fitting code, MEAMfit, was used as the selection criterion. In the second step, molecular dynamics (MD) calculations were employed to calculate ground-state elastic properties of structures present in the training set of the data fitting process. The calculated single crystal and poly-crystalline elastic constants for various Fe-C structures were compared with the DFT and experimental results. The resulting best potential accurately predicted the ground state elastic properties of B1, cementite, and orthorhombic-Fe7C3 (O-Fe7C3), and also calculated the phonon spectra in good agreement with the DFT-calculated ones for cementite and O-Fe7C3. Furthermore, the potential was used to successfully predict the elastic properties of interstitial Fe-C alloys (FeC-0.2% and FeC-0.4%) and O-Fe7C3 at elevated temperatures. The results were in good agreement with the published literature. The successful prediction of elevated temperature properties of structures not included in data fitting validated the potential's ability to model elevated-temperature elastic properties.

Silver Nanocoating of LiNi0.8Co0.1Mn0.1O2 Cathode Material for Lithium-Ion Batteries

Surface coating has become an effective approach to improve the electrochemical performance of Ni-rich cathode materials. In this study, we investigated the nature of an Ag coating layer and its effect on electrochemical properties of the LiNi_0.8Co_0.1Mn_0.1O₂ (NCM811) cathode material, which was synthesized using 3 mol.% of silver nanoparticles by a facile, cost-effective, scalable and convenient method. We conducted structural analyses using X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy, which revealed that the Ag nanoparticle coating did not affect the layered structure of NCM811. The Ag-coated sample had less cation mixing compared to the pristine NMC811, which could be attributed to the surface protection of Ag coating from air contamination. The Ag-coated NCM811 exhibited better kinetics than the pristine one, which is attributed to the higher electronic conductivity and better layered structure provided by the Ag nanoparticle coating. The Ag-coated NCM811 delivered a discharge capacity of 185 mAh·g^-1 at the first cycle and 120 mAh·g^-1 at the 100th cycle, respectively, which is better than the pristine NMC811.

Bifurcation analysis of motoneuronal excitability mechanisms under normal and ALS conditions

Introduction

Bifurcation analysis allows the examination of steady-state, non-linear dynamics of neurons and their effects on cell firing, yet its usage in neuroscience is limited to single-compartment models of highly reduced states. This is primarily due to the difficulty in developing high-fidelity neuronal models with 3D anatomy and multiple ion channels in XPPAUT, the primary bifurcation analysis software in neuroscience.

Methods

To facilitate bifurcation analysis of high-fidelity neuronal models under normal and disease conditions, we developed a multi-compartment model of a spinal motoneuron (MN) in XPPAUT and verified its firing accuracy against its original experimental data and against an anatomically detailed cell model that incorporates known MN non-linear firing mechanisms. We used the new model in XPPAUT to study the effects of somatic and dendritic ion channels on the MN bifurcation diagram under normal conditions and after amyotrophic lateral sclerosis (ALS) cellular changes.

Results

Our results show that somatic small-conductance Ca2+-activated K (SK) channels and dendritic L-type Ca2+ channels have the strongest effects on the bifurcation diagram of MNs under normal conditions. Specifically, somatic SK channels extend the limit cycles and generate a subcritical Hopf bifurcation node in the V-I bifurcation diagram of the MN to replace a supercritical node Hopf node, whereas L-type Ca2+ channels shift the limit cycles to negative currents. In ALS, our results show that dendritic enlargement has opposing effects on MN excitability, has a greater overall impact than somatic enlargement, and dendritic overbranching offsets the dendritic enlargement hyperexcitability effects.

Discussion

Together, the new multi-compartment model developed in XPPAUT facilitates studying neuronal excitability in health and disease using bifurcation analysis.

Current and lagged climate affects phenology across diverse taxonomic groups

The timing of life events (phenology) can be influenced by climate. Studies from around the world tell us that climate cues and species' responses can vary greatly. If variation in climate effects on phenology is strong within a single ecosystem, climate change could lead to ecological disruption, but detailed data from diverse taxa within a single ecosystem are rare. We collated first sighting and median activity within a high-elevation environment for plants, insects, birds, mammals and an amphibian across 45 years (1975-2020). We related 10 812 phenological events to climate data to determine the relative importance of climate effects on species' phenologies. We demonstrate significant variation in climate-phenology linkage across taxa in a single ecosystem. Both current and prior climate predicted changes in phenology. Taxa responded to some cues similarly, such as snowmelt date and spring temperatures; other cues affected phenology differently. For example, prior summer precipitation had no effect on most plants, delayed first activity of some insects, but advanced activity of the amphibian, some mammals, and birds. Comparing phenological responses of taxa at a single location, we find that important cues often differ among taxa, suggesting that changes to climate may disrupt synchrony of timing among taxa.

Why don't we share data and code? Perceived barriers and benefits to public archiving practices

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

A knowledge graph representation learning approach to predict novel kinase-substrate interactions

The human proteome contains a vast network of interacting kinases and substrates. Even though some kinases have proven to be immensely useful as therapeutic targets, a majority are still understudied. In this work, we present a novel knowledge graph representation learning approach to predict novel interaction partners for understudied kinases. Our approach uses a phosphoproteomic knowledge graph constructed by integrating data from iPTMnet, protein ontology, gene ontology and BioKG. The representations of kinases and substrates in this knowledge graph are learned by performing directed random walks on triples coupled with a modified SkipGram or CBOW model. These representations are then used as an input to a supervised classification model to predict novel interactions for understudied kinases. We also present a post-predictive analysis of the predicted interactions and an ablation study of the phosphoproteomic knowledge graph to gain an insight into the biology of the understudied kinases.

Degree and direction of overlap between social vulnerability and community resilience measurements

An ongoing debate in academic and practitioner communities, centers on the measurement similarities and differences between social vulnerability and community resilience. More specifically, many see social vulnerability and community resilience measurements as conceptually and empirically the same. Only through a critical and comparative assessment can we ascertain the extent to which these measurement schemas empirically relate to one another. This paper uses two well-known indices—the social vulnerability index (SoVI) and the Baseline Resilience Indicators for Communities (BRIC) to address the topic. The paper employs spatio-temporal correlations to test for differences or divergence (negative associations) and similarities or convergence (positive associations), and the degree of overlap. These tests use continental U.S. counties, two timeframes (2010 and 2015), and two case study sub-regions (to identify changes in measurement associations going from national to regional scales given the place-based nature of each index). Geospatial analytics indicate a divergence with little overlap between SoVI and BRIC measurements, based on low negative correlation coefficients (around 30%) for both time periods. There is some spatial variability in measurement overlap, but less than 2% of counties show hot spot clustering of correlations of more than 50% in either year. The strongest overlap and divergence in both years occurs in few counties in California, Arizona, and Maine. The degree of overlap in measurements at the regional scale is greater in the Gulf Region (39%) than in the Southeast Atlantic region (21% in 2010; 28% in 2015) suggesting more homogeneity in Gulf Coast counties based on population and place characteristics. However, in both study areas SoVI and BRIC measurements are negatively associated. Given their inclusion in the National Risk Index, both social vulnerability and resilience metrics are needed to interpret the local community capacities in natural hazards risk planning, as a vulnerable community could be highly resilient or vice versa.

Prioritizing nursing home staff and leadership consistency to improve quality

This Editorial comments on the article by Zheng et al. in this issue.

Electrochemically Prepared Polyaniline as an Alternative to Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) for Inverted Perovskite Solar Cells

The goal of this work is to substitute the conventional high-cost poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) in inverted perovskite solar cells (PSCs) with an efficient and conducting polyaniline (PANI) polymer. The reported use of PANI in PSCs involves a chemical synthesis method which is prone to contamination with impurities as it requires several materials for polymerization and adhesion improvement with substrates, contributing to low device efficiencies. This work mitigates this issue using an electrochemical method that is low cost, less time consuming, and capable of producing thin films of PANI with excellent adhesion to substrates. Results demonstrated that the power conversion efficiency of the electrochemically synthesized PANI-based PSC is 16.94% versus 15.11% for the PEDOT:PSS-based device. It was observed that the work function of PANI was lower compared to that of PEDOT:PSS which decreased V _OC but enhanced hole extraction at the hole transport layer/perovskite interface, thus increasing J _SC. Doping electrolyte solution with lithium bis(trifluoromethanesulfonyl)imide LiTFSI increased the work function of PANI, thus increasing V _OC from 0.87 to 0.93 V. This method enables simple and scalable synthesis of PANI as a competitive hole transport material to replace rather expensive PEDOT:PSS, thus enabling an important step toward low-cost inverted perovskite photovoltaic devices.

A general pattern of trade-offs between ecosystem resistance and resilience to tropical cyclones

Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are predicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from n = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants). We observed a repeated pattern of trade-offs between resistance and resilience across analyses. These patterns are likely the outcomes of evolutionary adaptation, they conform to disturbance theories, and they indicate that consistent rules may govern ecosystem susceptibility to tropical cyclones.

Change in beak overhangs of cliff swallows over 40 years: Partly a response to parasites?

Some birds exhibit a maxillary overhang, in which the tip of the upper beak projects beyond the lower mandible and may curve downward. The overhang is thought to help control ectoparasites on the feathers. Little is known about the extent to which the maxillary overhang varies spatially or temporally within populations of the same species. The colonial cliff swallow (Petrochelidon pyrrhonota) has relatively recently shifted to almost exclusive use of artificial structures such as bridges and highway culverts for nesting and consequently has been exposed to higher levels of parasitism than on its ancestral cliff nesting sites. We examined whether increased ectoparasitism may have favored recent changes in the extent of the maxillary overhang. Using a specimen collection of cliff swallows from western Nebraska, USA, spanning 40 years and field data on live birds, we found that the extent of the maxillary overhang increased across years in a nonlinear way, peaking in the late 2000’s, and varied inversely with cliff swallow colony size for unknown reasons. The number of fleas on nestling cliff swallows declined in general over this period. Those birds with perceptible overhangs had fewer swallow bugs on the outside of their nest, but they did not have higher nesting success than birds with no overhangs. The intraspecific variation in the maxillary overhang in cliff swallows was partly consistent with it having a functional role in combatting ectoparasites. The temporal increase in the extent of the overhang may be a response by cliff swallows to their relatively recent increased exposure to parasitism. Our results demonstrate that this avian morphological trait can change rapidly over time.

Determinants of vaccine coverage and timeliness in a northern Pakistani village

The incidence of vaccine preventable disease in Pakistan remains high despite a long-standing Expanded Program on Immunization (EPI). We describe vaccine completeness, timeliness and determinants of coverage from a remote rural cohort (2012–2014). Vaccination histories were taken from EPI records. Vaccination was complete if all doses were received according to the EPI schedule and timely if doses were not ≥3 days early or ≥ 28 days late. Three models are presented: a multivariable logistic regression of household demographic and socioeconomic factors associated with complete vaccination, a multivariable mixed effects logistic regression assessing whether or not the vaccine was administered late (versus on-time), and a mixed effects multivariable Poisson regression model analysing the interval (in days) between vaccine doses. Of 959 enrolled children with full vaccination histories, 88.2 and 65.1% were fully vaccinated following either the pentavalent or DPT/HBV schedules if measles was excluded; coverage dropped to 50.0 and 27.1% when both doses of measles were included. Sixty-four (6.7%) were unvaccinated. Coverage and timeliness declined with subsequent doses. Migrating into the village after 1995 (95%CI 1.88 to 5.17) was associated with late vaccination. Being male, having an older father, and having parents with at least some formal education reduced the likelihood of a late dose. The interval between doses was consistent at 5 weeks (compared with the 4 weeks recommended by EPI). None of the socio-demographic variables were related to the likelihood of receiving full coverage. Vaccine coverage in Oshikhandass was higher than national averages. Measles vaccine coverage and timeliness were low; special consideration should be paid to this vaccine. The local vaccination schedule differed from the EPI, but the consistency suggests good local administration.

Spectroscopy and Theoretical Modeling of Phonon Vibration Modes and Band Gap Energy of Cu2ZnSn(S x Se1-x )4 Bulk Crystals and Thin Films

Semiconductor Cu2ZnSn(S x Se1-x )4 (CZTSSe) solid solution is considered as a perspective absorber material for solar cells. However, during its synthesis or deposition, any modification in the resulting optical properties is hardly predicted. In this study, experimental and theoretical analyses of CZTSSe bulk crystals and thin films are presented based on Raman scattering and absorption spectroscopies together with compositional and morphological characterizations. CZTSSe bulk and thin films are studied upon a change in the x = S/(S + Se) aspect ratio. The morphological study is focused on surface visualization of the solid solutions, depending on x variation. It has been discovered for the first time that the surface of the bulk CZTSSe crystal with x = 0.35 has pyramid-like structures. The information obtained from the elemental analysis helps to consider the formation of a set of possible intrinsic lattice defects, including vacancies, self-interstitials, antisites, and defect complexes. Due to these results and the experimentally obtained values of the band gap within 1.0-1.37 eV, a deviation from the calculated band gap values is estimated in the range of 1.0-1.5 eV. It is suggested which defects can have an influence on such a band gap change. Also, on comparing the experimental Raman spectra of CZTSSe with the theoretical modeling results, an excellent agreement is obtained for the main Raman bands. The proposed theoretical approach allows to estimate the values of concentration of atoms (S or Se) for CZTSSe solid solution directly from the experimental Raman spectra. Thus, the visualization of morphology and the proposed theoretical approach at various x values will help for a deeper understanding of the CZTSSe structure to develop next-generation solar cells.

Chitosan Treatment of E-11 Cells Modulates Transcription of Nonspecific Immune Genes and Reduces Nodavirus Capsid Protein Gene Expression

This study explores whether crustacean products inhibit viral infections in aquaculture. Chitosan (CHT) was extracted from waste products of Parapenaeus longirostris. Biochemical composition, viscosity measurement, molecular weight, structure and cytotoxicity tests were used to characterize the extracted chitosan. Cultures of E-11 cells derived from snakehead Ophicephalus striatus were inoculated with 106.74 TCID50 of an isolate of betanodavirus genotype RGNNV (redspotted grouper nervous necrosis virus) after being treated with solutions of 0.3% CHT for 1 h at room temperature. The antiviral effect of CHT was assessed by comparing the ability of RGNVV to replicate and produce cytopathic effects on CHT-treated cell cultures. The change in RNA expression levels of the nodavirus capsid protein gene and three mediator genes in infected cells with or without CHT treatment was evaluated by qPCR. Changes in gene expression compared to control groups were monitored at 6, 24, 48 and 71 h post treatment in all target gene transcripts. The CCR3 expression in CHT treated cells showed a significant increase (p < 0.05) until day 3. On the other hand, the expression of TNF-α decreased significantly (p < 0.05) in CHT treated cells throughout the experimental period. Likewise, the expression of the IL-10 gene showed a significant downregulation in CHT treated cells at all time points (p ≤ 0.05). As further evidence of an antiviral effect, CHT treatment of cells produced a reduction in virus load as measured by a reduced expression of the viral capsid gene and the increase in RQ values from 406 ± 1.9 at hour 1 to 695 ± 3.27 at 72 h post inoculation. Statistical analysis showed that the expression of the viral capsid gene was significantly lower in cells treated with chitosan (p ≤ 0.05). These results improve our knowledge about the antiviral activity of this bioactive molecule and highlight its potential use in fish feed industry.

Examining the relationships between early childhood experiences and adolescent and young adult health status in a resource-limited population: A cohort study

BACKGROUND

Adolescence is a critical point in the realization of human capital, as health and educational decisions with long-term impacts are made. We examined the role of early childhood experiences on health, cognitive abilities, and educational outcomes of adolescents followed up from a longitudinal cohort study in Pakistan, hypothesizing that early childhood experiences reflecting poverty would manifest in reduced health and development in adolescence.

METHODS AND FINDINGS

Adolescents/young adults previously followed as children aged under 5 years were interviewed. Childhood data were available on diarrhea, pneumonia, and parental/household characteristics. New data were collected on health, anthropometry, education, employment, and languages spoken; nonverbal reasoning was assessed. A multivariable Bayesian network was constructed to explore structural relationships between variables. Of 1,868 children originally enrolled, 1,463 (78.3%) were interviewed as adolescents (range 16.0-29.3 years, mean age 22.6 years); 945 (65%) lived in Oshikhandass. While 1,031 (70.5%) of their mothers and 440 (30.1%) of their fathers had received no formal education, adolescents reported a mean of 11.1 years of education. Childhood diarrhea (calculated as episodes/child-year) had no association with nonverbal reasoning score (an arc was supported in just 4.6% of bootstrap samples), health measures (with BMI, 1% of bootstrap samples; systolic and diastolic blood pressure, 0.1% and 1.6% of bootstrap samples, respectively), education (0.7% of bootstrap samples), or employment (0% of bootstrap samples). Relationships were found between nonverbal reasoning and adolescent height (arc supported in 63% of bootstrap samples), age (84%), educational attainment (100%), and speaking English (100%); speaking English was linked to the childhood home environment, mediated through maternal education and primary language. Speaking English (n = 390, 26.7% of adolescents) was associated with education (100% of bootstrap samples), self-reported child health (82%), current location (85%) and variables describing childhood socioeconomic status. The main limitations of this study were the lack of parental data to characterize the home setting (including parental mental and physical health, and female empowerment) and reliance on self-reporting of health status.

CONCLUSIONS

In this population, investments in education, especially for females, are associated with an increase in human capital. Against the backdrop of substantial societal change, with the exception of a small and indirect association between childhood malnutrition and cognitive scores, educational opportunities and cultural language groups have stronger associations with aspects of human capital than childhood morbidity.

Fire-induced loss of the world's most biodiverse forests in Latin America

Fire plays a dominant role in deforestation, particularly in the tropics, but the relative extent of transformations and influence of fire frequency on eventual forest loss remain unclear. Here, we analyze the frequency of fire and its influence on postfire forest trajectories between 2001 and 2018. We account for ~1.1% of Latin American forests burnt in 2002-2003 (8,465,850 ha). Although 40.1% of forests (3,393,250 ha) burned only once, by 2018, ~48% of the evergreen forests converted to other, primarily grass-dominated uses. While greater fire frequency yielded more transformation, our results reveal the staggering impact of even a single fire. Increasing fire frequency imposes greater risks of irreversible forest loss, transforming forests into ecosystems increasingly vulnerable to degradation. Reversing this trend is indispensable to both mitigate and adapt to climate change globally. As climate change transforms fire regimes across the region, key actions are needed to conserve Latin American forests.

A Rapid Assessment of Disaster Preparedness Needs and Resources during the COVID-19 Pandemic

Background: This year has seen the emergence of two major crises, a significant increase in the frequency and severity of hurricanes and the COVID-19 pandemic. However, little is known as to how each of these two events have impacted the other. A rapid qualitative assessment was conducted to determine the impact of the pandemic on preparedness and response to natural disasters and the impact of past experiences with natural disasters in responding to the pandemic. Methods: Semi-structured interviews were conducted with 26 representatives of 24 different community-based programs in southern Louisiana. Data were analyzed using procedures embedded in the Rapid Assessment Procedure-Informed Community Ethnography methodology, using techniques of immersion and crystallization and focused thematic analysis. Results: The pandemic has impacted the form and function of disaster preparedness, making it harder to plan for evacuations in the event of a hurricane. Specific concerns included being able to see people in person, providing food and other resources to residents who shelter in place, finding volunteers to assist in food distribution and other forms of disaster response, competing for funds to support disaster-related activities, developing new support infrastructures, and focusing on equity in disaster preparedness. However, several strengths based on disaster preparedness experience and capabilities were identified, including providing a framework for how to respond and adapt to COVID and integration of COVID response with their normal disaster preparedness activities. Conclusions: Although prior experience has enabled community-based organizations to respond to the pandemic, the pandemic is also creating new challenges to preparing for and responding to natural disasters.

Grain and dietary fiber intake and bladder cancer risk: a pooled analysis of prospective cohort studies

BACKGROUND

Higher intakes of whole grains and dietary fiber have been associated with lower risk of insulin resistance, hyperinsulinemia, and inflammation, which are known predisposing factors for cancer.

OBJECTIVES

Because the evidence of association with bladder cancer (BC) is limited, we aimed to assess associations with BC risk for intakes of whole grains, refined grains, and dietary fiber.

METHODS

We pooled individual data from 574,726 participants in 13 cohort studies, 3214 of whom developed incident BC. HRs, with corresponding 95% CIs, were estimated using Cox regression models stratified on cohort. Dose-response relations were examined using fractional polynomial regression models.

RESULTS

We found that higher intake of total whole grain was associated with lower risk of BC (comparing highest with lowest intake tertile: HR: 0.87; 95% CI: 0.77, 0.98; HR per 1-SD increment: 0.95; 95% CI: 0.91, 0.99; P for trend: 0.023). No association was observed for intake of total refined grain. Intake of total dietary fiber was also inversely associated with BC risk (comparing highest with lowest intake tertile: HR: 0.86; 95% CI: 0.76, 0.98; HR per 1-SD increment: 0.91; 95% CI: 0.82, 0.98; P for trend: 0.021). In addition, dose-response analyses gave estimated HRs of 0.97 (95% CI: 0.95, 0.99) for intake of total whole grain and 0.96 (95% CI: 0.94, 0.98) for intake of total dietary fiber per 5-g daily increment. When considered jointly, highest intake of whole grains with the highest intake of dietary fiber showed 28% reduced risk (95% CI: 0.54, 0.93; P for trend: 0.031) of BC compared with the lowest intakes, suggesting potential synergism.

CONCLUSIONS

Higher intakes of total whole grain and total dietary fiber are associated with reduced risk of BC individually and jointly. Further studies are needed to clarify the underlying mechanisms for these findings.

Invisible oil beyond the Deepwater Horizon satellite footprint

Major oil spills are catastrophic events that immensely affect the environment and society, yet determining their spatial extent is a highly complex task. During the Deepwater Horizon (DWH) blowout, ~149,000 km² of the Gulf of Mexico (GoM) was covered by oil slicks and vast areas of the Gulf were closed for fishing. Yet, the satellite footprint does not necessarily capture the entire oil spill extent. Here, we use in situ observations and oil spill transport modeling to examine the full extent of the DWH spill, focusing on toxic-to-biota (i.e., marine organisms) oil concentration ranges. We demonstrate that large areas of the GoM were exposed to invisible and toxic oil that extended beyond the boundaries of the satellite footprint and the fishery closures. With a global increase in petroleum production-related activities, a careful assessment of oil spills' full extent is necessary to maximize environmental and public safety.

Serum dioxin and DNA methylation in the sperm of operation ranch hand veterans exposed to Agent Orange

BACKGROUND

Exposure to the herbicide Agent Orange during the Vietnam War was widespread and is associated with numerous adverse health outcomes. A continuing concern of veterans is the possibility that exposure to the dioxin-containing herbicide might induce adverse reproductive outcomes. We sought to assess whether exposure to Agent Orange in Vietnam was associated with changes in DNA methylation in sperm in a subset of Vietnam veterans who participated in the Air Force Health Study (AFHS).

METHODS

We studied 37 members of the AFHS chosen to have no, low, medium or high exposure to Agent Orange, based upon serum dioxin levels obtained during a series of examinations. DNA from stored semen was extracted and DNA methylation assessed on the Illumina 450 K platform.

RESULTS

Initial epigenome-wide analysis returned no loci that survived control for false discovery. However, the TEAD3 gene had four different CpG sites that showed loss of DNA methylation associated with dioxin exposure. Analysis assessing regional DNA methylation changes revealed 36 gene regions, including the region of the imprinted gene H19 to have altered DNA methylation associated with high exposure compared to the low exposure group. Additional comparison of our data with sperm DNA methylation data from Russian boys exposed to dioxin found an additional 5 loci that were altered in both studies and exhibited a consistent direction of association.

CONCLUSIONS

Studying a small number of sperm samples from veterans enrolled in the AFHS, we did not find evidence of significant epigenome-wide alterations associated with exposure to Agent Orange. However, additional analysis showed that the H19 gene region is altered in the sperm of Agent Orange-exposed Ranch Hand veterans. Our study also replicated several findings of a prior study of dioxin-exposed Russian boys. These results provide additional candidate loci for further investigation and may have implications for the reproductive health of dioxin-exposed individuals.

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.

Precipitation and temperature drive continental-scale patterns in stream invertebrate production

Secondary production, the growth of new heterotrophic biomass, is a key process in aquatic and terrestrial ecosystems that has been carefully measured in many flowing water ecosystems. We combine structural equation modeling with the first worldwide dataset on annual secondary production of stream invertebrate communities to reveal core pathways linking air temperature and precipitation to secondary production. In the United States, where the most extensive set of secondary production estimates and covariate data were available, we show that precipitation-mediated, low-stream flow events have a strong negative effect on secondary production. At larger scales (United States, Europe, Central America, and Pacific), we demonstrate the significance of a positive two-step pathway from air to water temperature to increasing secondary production. Our results provide insights into the potential effects of climate change on secondary production and demonstrate a modeling framework that can be applied across ecosystems.

Reproductive life history of sablefish (Anoplopoma fimbria) from the U.S. Washington coast

Sablefish (Anoplopoma fimbria) is a marine groundfish that supports valuable fisheries in the North Pacific Ocean and holds promise for marine aquaculture. Limited information is available, however, about its reproductive biology. This study aimed to characterize the complete reproductive cycle, including seasonal changes in gonadal development (macroscopic and histological), plasma sex steroid levels (17β-estradiol -E2-, and 11-ketotestosterone -11KT-), gonadosomatic and hepatosomatic indices (GSI, and HSI), and condition factor (K) of female and male sablefish captured off the Washington coast. Adult fish (209 females, 159 males) were caught by longline monthly from August 2012 to August 2013. Early signs of recruitment of ovarian follicles into secondary growth, indicated by oocytes containing small yolk granules and cortical alveoli, were first observed in March. Oogenesis progressed during spring and summer, and fully vitellogenic follicles were first observed in July. Vitellogenic growth was correlated with increases in plasma E2, GSI, HSI and K. Periovulatory females, indicated by fully-grown oocytes with migrating germinal vesicles and hydrated oocytes, were found from November to February. At this stage, plasma E2 and GSI reached maximal levels. In males, proliferating cysts containing spermatocytes were first observed in April. Testicular development proceeded during spring and summer, a period during which all types of male germ cells were found. The first clusters of spermatozoa appeared in July, concomitant with a 5.2-fold increase in GSI. Spermiating males were observed from November to April; at this time, spermatids were absent or greatly reduced, and testis lobules were filled with spermatozoa. The highest levels of plasma 11KT were found in males at this stage. Postspawning ovaries and testes, and basal steroids levels were found in fish captured from February to April. These results suggest that sablefish in coastal Washington initiate their reproductive cycle in March/April and spawn primarily in January/February.

The RhoJ-BAD signaling network: An Achilles' heel for BRAF mutant melanomas

Genes and pathways that allow cells to cope with oncogene-induced stress represent selective cancer therapeutic targets that remain largely undiscovered. In this study, we identify a RhoJ signaling pathway that is a selective therapeutic target for BRAF mutant cells. RhoJ deletion in BRAF mutant melanocytes modulates the expression of the pro-apoptotic protein BAD as well as genes involved in cellular metabolism, impairing nevus formation, cellular transformation, and metastasis. Short-term treatment of nascent melanoma tumors with PAK inhibitors that block RhoJ signaling halts the growth of BRAF mutant melanoma tumors in vivo and induces apoptosis in melanoma cells in vitro via a BAD-dependent mechanism. As up to 50% of BRAF mutant human melanomas express high levels of RhoJ, these studies nominate the RhoJ-BAD signaling network as a therapeutic vulnerability for fledgling BRAF mutant human tumors.

BRAF^V600E is the most common mutation in human melanomas, and kinase inhibitors that block BRAF^V600E signaling can rapidly induce tumor regression but only modestly improve melanoma long-term survival. In this study, we identify a novel therapeutic vulnerability for BRAF mutant melanoma tumors. Targeting RhoJ signaling with existing PAK inhibitors was more efficient at blocking the progression of BRAF mutant tumors in vivo when compared to kinase inhibitors currently used to treat melanoma. Approximately half of all human BRAF mutant melanoma tumors express high levels of RhoJ, identifying the RhoJ-BAD pathway as a novel target for melanoma.

Bmal1 function in skeletal muscle regulates sleep

Sleep loss can severely impair the ability to perform, yet the ability to recover from sleep loss is not well understood. Sleep regulatory processes are assumed to lie exclusively within the brain mainly due to the strong behavioral manifestations of sleep. Whole-body knockout of the circadian clock gene Bmal1 in mice affects several aspects of sleep, however, the cells/tissues responsible are unknown. We found that restoring Bmal1 expression in the brains of Bmal1-knockout mice did not rescue Bmal1-dependent sleep phenotypes. Surprisingly, most sleep-amount, but not sleep-timing, phenotypes could be reproduced or rescued by knocking out or restoring BMAL1 exclusively in skeletal muscle, respectively. We also found that overexpression of skeletal-muscle Bmal1 reduced the recovery response to sleep loss. Together, these findings demonstrate that Bmal1 expression in skeletal muscle is both necessary and sufficient to regulate total sleep amount and reveal that critical components of normal sleep regulation occur in muscle.

Alternative futures of dissolved inorganic nitrogen export from the Mississippi River Basin: influence of crop management, atmospheric deposition, and population growth

Nitrogen (N) export from the Mississippi River Basin contributes to seasonal hypoxia in the Gulf of Mexico (GOM). We explored monthly dissolved inorganic N (DIN) export to the GOM for a historical year (2002) and two future scenarios (year 2022) by linking macroeonomic energy, agriculture market, air quality, and agriculture land management models to a DIN export model. Future scenarios considered policies aimed at encouraging bioenergy crop production and reducing atmospheric N-emissions, as well as the effect of population growth and the states' infrastructure plans on sewage fluxes. Model-derived DIN export decreased by about 9% (from 279 to 254 kg N km-2 year-1) between 2002 and 2022 due to a 28% increase in area planted with corn, 24% improvement in crop N-recovery efficiency (NRE, to 0.52), 22% reduction in atmospheric N deposition, and 23% increase in sewage inputs. Changes in atmospheric and sewage inputs had a relatively small effect on DIN export and the effect of bioenergy crop production depended on nutrient management practices. Without improved NRE, increased production of corn would have increased DIN export by about 14% (to 289 kg N km-2 year-1) between 2002 and 2022. Model results suggest that meeting future crop demand while reducing the areal extent of hypoxia could require aggressive actions, such improving basin-level crop NRE to 0.62 or upgrading N-removal capabilities in waste water treatment plants beyond current plans. Tile-drained cropland could contribute up to half of DIN export; thus, practices that reduce N losses from tile drains could also have substantial benefit.

Whale, Whale, Everywhere: Increasing Abundance of Western South Atlantic Humpback Whales (Megaptera novaeangliae) in Their Wintering Grounds

The western South Atlantic (WSA) humpback whale population inhabits the coast of Brazil during the breeding and calving season in winter and spring. This population was depleted to near extinction by whaling in the mid-twentieth century. Despite recent signs of recovery, increasing coastal and offshore development pose potential threats to these animals. Therefore, continuous monitoring is needed to assess population status and support conservation strategies. The aim of this work was to present ship-based line-transect estimates of abundance for humpback whales in their WSA breeding ground and to investigate potential changes in population size. Two cruises surveyed the coast of Brazil during August-September in 2008 and 2012. The area surveyed in 2008 corresponded to the currently recognized population breeding area; effort in 2012 was limited due to unfavorable weather conditions. WSA humpback whale population size in 2008 was estimated at 16,410 (CV = 0.228, 95% CI = 10,563-25,495) animals. In order to compare abundance between 2008 and 2012, estimates for the area between Salvador and Cabo Frio, which were consistently covered in the two years, were computed at 15,332 (CV = 0.243, 95% CI = 9,595-24,500) and 19,429 (CV = 0.101, 95% CI = 15,958-23,654) whales, respectively. The difference in the two estimates represents an increase of 26.7% in whale numbers in a 4-year period. The estimated abundance for 2008 is considered the most robust for the WSA humpback whale population because the ship survey conducted in that year minimized bias from various sources. Results presented here indicate that in 2008, the WSA humpback whale population was at least around 60% of its estimated pre-modern whaling abundance and that it may recover to its pre-exploitation size sooner than previously estimated.

A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts

PURPOSE

This study was performed to investigate the genetic determinants of autosomal recessive congenital cataracts in large consanguineous families.

METHODS

Affected individuals underwent a detailed ophthalmological examination and slit-lamp photographs of the cataractous lenses were obtained. An aliquot of blood was collected from all participating family members and genomic DNA was extracted from white blood cells. Initially, a genome-wide scan was performed with genomic DNAs of family PKCC025 followed by exclusion analysis of our familial cohort of congenital cataracts. Protein-coding exons of CRYBB1, CRYBB2, CRYBB3, and CRYBA4 were sequenced bidirectionally. A haplotype was constructed with SNPs flanking the causal mutation for affected individuals in all four families, while the probability that the four familial cases have a common founder was estimated using EM and CHM-based algorithms. The expression of Crybb3 in the developing murine lens was investigated using TaqMan assays.

RESULTS

The clinical and ophthalmological examinations suggested that all affected individuals had nuclear cataracts. Genome-wide linkage analysis localized the causal phenotype in family PKCC025 to chromosome 22q with statistically significant two-point logarithm of odds (LOD) scores. Subsequently, we localized three additional families, PKCC063, PKCC131, and PKCC168 to chromosome 22q. Bidirectional Sanger sequencing identified a missense variation: c.493G>C (p.Gly165Arg) in CRYBB3 that segregated with the disease phenotype in all four familial cases. This variation was not found in ethnically matched control chromosomes, the NHLBI exome variant server, or the 1000 Genomes or dbSNP databases. Interestingly, all four families harbor a unique disease haplotype that strongly suggests a common founder of the causal mutation (p<1.64E-10). We observed expression of Crybb3 in the mouse lens as early as embryonic day 15 (E15), and expression remained relatively steady throughout development.

CONCLUSION

Here, we report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin.

There is no fitness but fitness, and the lineage is its bearer

Inclusive fitness has been the cornerstone of social evolution theory for more than a half-century and has matured as a mathematical theory in the past 20 years. Yet surprisingly for a theory so central to an entire field, some of its connections to evolutionary theory more broadly remain contentious or underappreciated. In this paper, we aim to emphasize the connection between inclusive fitness and modern evolutionary theory through the following fact: inclusive fitness is simply classical Darwinian fitness, averaged over social, environmental and demographic states that members of a gene lineage experience. Therefore, inclusive fitness is neither a generalization of classical fitness, nor does it belong exclusively to the individual. Rather, the lineage perspective emphasizes that evolutionary success is determined by the effect of selection on all biological and environmental contexts that a lineage may experience. We argue that this understanding of inclusive fitness based on gene lineages provides the most illuminating and accurate picture and avoids pitfalls in interpretation and empirical applications of inclusive fitness theory.