Spatio-temporal composition of aquatic birds communityin Juluapan Lagoon, Colima, Mexican Central Pacific / Composición espacio-temporal de las aves acuáticas en la laguna Juluapan, Colima, en el Pacífico Central Mexicano

Abstract Introduction: Aquatic birds (AB) are usually associated with wetlands, which provide refuge, food, and/or nesting sites for resident and migratory species. Despite their ecological importance, there is little knowledge on AB in some tropical environments, such as those found on the Colima coast. Objective: To investigate the spatial and temporal composition of the AB community in Juluapan Lagoon, Colima, Central Mexican Pacific. Methods: Monthly counts were conducted between June 2017 and May 2018 during low-tide conditions to record habitat use by AB. Species richness and bird counts were obtained to compare sampling areas; mean richness and number of individuals were compared between seasons. Results: We detected 53 species and 5 750 individuals. The highest species richness and relative abundance values were obtained in winter at the lagoon area farthest from the connection with the marine system, where anthropogenic activity is lower. Diversity was greater in zones 2 and 3 in spring, summer, and fall. Muddy flats were the most used environment, and the most frequent activity was resting. Nesting activity was only recorded in the middle of the lagoon at the mangrove during spring. "Shorebirds" and "waders" were the most dominant groups in the bird community of the Juluapan lagoon. Conclusions: This coastal wetland is a site of great biological importance for aquatic birds; thus, conservation measures should be implemented, and there should be a continuous study of the effects of anthropogenic pressure.

Resumen Introducción: Las aves acuáticas (AA) son usualmente relacionadas a los humedales debido a que éstos funcionan como sitios de refugio, alimentación y anidación de diferentes especies residentes y migratorias. Sin embargo, el conocimiento sobre las aves acuáticas en algunos humedales es nulo. Objetivo: Investigar la composición espacio-temporal de la comunidad de AA en la laguna Juluapan, Colima, en el Pacífico Central Mexicano. Métodos: Entre junio de 2017 y mayo de 2018 se llevaron a cabo conteos mensuales en condiciones de marea baja para registrar el uso de hábitat de las AA. Se obtuvieron valores de riqueza de especies y número de individuos para realizar comparaciones entre zonas de muestreo, así como el promedio del número de especies y número de individuos para comparaciones entre temporadas. Resultados: Se registraron un total de 53 especies y 5 750 individuos. Los valores de riqueza de especies y densidad de individuos fueron más altos durante invierno, en la zona más alejada al ambiente marino, donde la actividad antropogénica es menor. La diversidad tuvo valores más altos en la zona 2 y 3, durante primavera, verano y otoño. El ambiente más explotado por las aves fueron las planicies lodosas; y el descanso fue la actividad más frecuente. Asimismo, la actividad de anidación sólo se registró en el manglar de la zona media durante primavera. Las "aves playeras" y "aves zancudas" fueron los grupos más predominantes en la comunidad de aves de la laguna Juluapan. Conclusiones: Este humedal costero es un sitio de gran importancia biológica para aves acuáticas, por lo que resulta necesario la implementación de medidas de conservación, así como el estudio de los efectos por la presión antropogénica.

Psychometric evaluation of the affiliate stigma scale for caregivers of people with mental illness in Uganda.

BACKGROUND: Affiliate stigma is common among caregivers of people with mental illness and impacts negatively on the caregivers' quality of life and their ability to care for the patients. Although there is evidence of affiliate stigma in sub-Saharan Africa, the psychometric properties of commonly used tools are not available in the African context. The aim of this analysis was to evaluate the factor structure of the affiliate stigma scale among caregivers of people with mental illness in southwestern Uganda. Having a validated method to assess affiliate stigma in the Ugandan setting helps to appropriately evaluate affiliate stigma among caregivers of people with mental illnesses, which could inform the development of interventions to support such caregivers. METHOD: A total of 385 caregivers of people with mental illness attending outpatient psychiatry clinics in selected tertiary hospitals in southwestern Uganda were enrolled in the study. The affiliate stigma and depression were assessed using the affiliate stigma scale and the patient health questionnaire (PHQ-9) respectively. We conducted exploratory and confirmatory factor analysis to determine the factor structure, reliability and validity of the affiliate stigma scale. We also evaluated the convergent validity of the affiliate stigma scale by determining the correlation between affiliate stigma scale scores and the PHQ-9. RESULT: More than half of participants were male (55.06%) and majority of caregivers were living in rural areas (80.26%). The sample size was adequate, as evidenced by the KMO of 0.91 and the inter-correlation was sufficient to conduct the factor analysis, according to the Bartlett test. Confirmatory factor analysis revealed four factors and all 22 items were retained as all of them had a factor loading > 0.4. The internal consistency of the total scale was excellent (alpha = 0.92). The affiliate stigma score correlated with depression which has been hypothesized to be associated with the stigma of mental illness. CONCLUSION: The study findings show the affiliate stigma scale as a valid measure of affiliate stigma among the caregivers of patients with mental illness in southwestern Uganda. Therefore, this scale provides an opportunity to mental health care providers to assess affiliate stigma and develop interventions aimed at prevention stigma among caregivers and improve outcomes among people with mental illness.

How word meaning structure relates to executive functioning and theory of mind in children with developmental language disorder: A multiple case study.

Background and aims: Many children with developmental language disorder (DLD) have difficulties in executive functioning (EF) and theory of mind (ToM). These difficulties might be explained by the theory that children's conceptual understanding changes over five stages of word meaning structure, from concrete and context-dependent to abstract and precise. We present a multiple case study examining how word meaning structure relates to EF and ToM in children with DLD. Methods: Participants were five children with DLD aged 9-12 and five typically developing children matched for age, gender, and nonverbal intelligence. Word meaning structure was assessed using new dynamic test. EF was assessed using the Zoo Map Task and Behavioral Rating Inventory for EF. ToM was assessed using the ToM test, Frith-Happé Animations, and Bermond-Vorst Alexithymia Questionnaire. Behavioral problems were measured using the Child Behavior Checklist. Anamnestic interviews with the parents were conducted to describe the case histories. Results: For the children with DLD, lower scores in the word meaning structure task were observed compared to those observed for their matched peers, with no statistical test applied. Word meaning structure related positively to EF and ToM, but not to behavioral problems. Instances in which word meaning structure dissociates from EF and ToM are discussed in individual case descriptions. Conclusions: By linking language to conceptual development, variations in word meaning structure may explain some EF and ToM difficulties in children with DLD. Implications: The present study offers a basis for future research on the relationships among word meaning structure, EF, and ToM.

Analysis of influence mechanism of CO2-water coupling fracturing sandstone.

The existence of hard rock layers has a serious impact on coal seam mining, in order to explore the acidification and crushing mechanism of hard sandstone rock layers, this paper adopts the self-developed CO2-water-rock coupling test device to carry out the testing of mechanical properties and internal structural characteristics of rock samples before and after the coupling action of the three sandstones, and analyzes the influencing factors of sandstone CO2 coupling crushing. The study shows that: the lower the temperature of CO2-water-rock coupling, the higher the pore pressure, the higher the volume fraction of CO2 in the coupling fracturing fluid, and the longer the coupling time, the greater the decrease in the mechanical strength of the rock samples, and the more complicated the splitting damage pattern is, and the CO2-water-rock coupling makes the pore and fracture volume fraction and fractal dimension of three kinds of sandstone samples increase to varying degrees, whereas the volume fraction of minerals and the fractal dimension decrease, and the CO2-water-rock coupling results in a decrease in the volume fraction of minerals and fractal dimension, and a decrease in the volume fraction of minerals and fractal dimension. The pore volume fraction and fractal dimension of the three sandstone samples increased to different degrees, while the mineral volume fraction and fractal dimension decreased, and the pore volume fraction and fractal dimension of the three sandstone samples decreased. The damage pattern of sandstone samples after coupling is affected by both chemical and mechanical damages. When using coupling fracturing fluid with 8 % CO2, the degree of mineral dissolution and dissolution is the largest, and the dissolution effect is larger than the precipitation effect, which has the most significant effect on the morphology type and connectivity of microscopic pore cracks, and the study in this paper has certain theoretical and practical value for the chemical softening of sandstone.

Influence of IoT implementation on Resource management in construction.

The desire to increase resource management efficacy in the construction sector is expanding because of measures to reduce costs, boost productivity, and minimize environmental impact. The Internet of Things (IoT) has the potential to alter resource management in the construction sector by delivering real-time data and insights that may assist decision-makers in optimizing resource allocation and usage. Incorporating Internet of Things (IoT) technology into the construction sector will be investigated in this study to discover how resource management is affected. The aim of the study is to identify the essential aspects that promote optimal IoT integration and to investigate how IoT may influence resource management. The relations between variables and their fundamental elements are investigated using structural equation modelling (SEM). In the context of building projects, the study analyses how IoT integration influences resource allocation and utilization, real-time monitoring, and proactive maintenance. The building sector in Malaysia provides concepts on IoT in resource management. Based on this research's outcomes, there is a distinct association between the utilization of IoT technology and effective resource management in the construction sector. IoT adoption is affected by a multiplicity of issues, including data analytics, data security and privacy, integration and interoperability, scalability, and flexibility. This study contributes to addressing considerable gaps in the corpus of information on IoT technology integration in the construction sector. It analyses how IoT may effect resource management, emphasizing how IoT technology may enhance the efficacy of human, mechanical, and material resources.

Association of chronotype with language and episodic memory processing in children: implications for brain structure.

Introduction: Chronotype refers to individual preference in circadian cycles and is associated with psychiatric problems. It is mainly classified into early (those who prefer to be active in the morning and sleep and wake up early) and late (those who prefer to be active in the evening and sleep and wake up late) chronotypes. Although previous research has demonstrated associations between chronotype and cognitive function and brain structure in adults, little is known regarding these associations in children. Here, we aimed to investigate the relationship between chronotype and cognitive function in children. Moreover, based on the significant association between chronotype and specific cognitive functions, we extracted regions-of-interest (ROI) and examined the association between chronotype and ROI volumes. Methods: Data from 4,493 children (mean age of 143.06 months) from the Adolescent Brain Cognitive Development Study were obtained, wherein chronotype (mid-sleep time on free days corrected for sleep debt on school days) was assessed by the Munich Chronotype Questionnaire. Subsequently, the associations between chronotype, cognitive function, and ROI volumes were evaluated using linear mixed-effects models. Results: Behaviorally, chronotype was negatively associated with vocabulary knowledge, reading skills, and episodic memory performance. Based on these associations, the ROI analysis focused on language-related and episodic memory-related areas revealed a negative association between chronotype and left precentral gyrus and right posterior cingulate cortex volumes. Furthermore, the precentral gyrus volume was positively associated with vocabulary knowledge and reading skills, while the posterior cingulate cortex volume was positively associated with episodic memory performance. Discussion: These results suggest that children with late chronotype have lower language comprehension and episodic memory and smaller brain volumes in the left precentral gyrus and right posterior cingulate cortex associated with these cognitive functions.

Shallow tillage mitigates plant competition by increasing diversity and altering plant community assembly process.

Introduction: Understanding how human activities affect biodiversity is needed to inform systemic policies and targets for achieving sustainable development goals. Shallow tillage to remove Artemisia ordosica is commonly conducted in the Mu Us Desert. However, the impacts of shallow tillage on plant community species diversity, phylogenetic structure, and community assembly processes remain poorly understood. Methods: This study explores the effects of shallow tillage on species diversity including three a-diversity and two b-diversity indicators, as well as phylogenetic structure [phylogenetic diversity (PD), net relatedness index (NRI), and nearest taxon index (NTI)]. Additionally, this research analyzes the effects of shallow tillage on the community assembly process. Results and discussion: The results showed that the a-diversity index, b-diversity index, and PD of the shallow tillage (ST) communities were significantly higher than those of the non-shallow tillage (NT) communities, and the phylogenetic structures of both the ST and NT communities tended to be differentiated, with competitive exclusion being the main mechanism of plant assembly. However, shallow tillage increased the relative importance of the stochastic processes dominated by dispersal limitation, mitigating plant competition in the communities. This conclusion was supported by the Raup-Crick difference index-based analysis. Conclusion: Therefore, for the ecological restoration of the Mu Us Desert, species with adaptability and low niche overlap should be selected to increase the utilization efficiency of the environmental resources. The results of this study provide a foundation for policy development for ecosystem management and restoration in the Mu Us Desert.

Impact of Bone Mineral Density and Bone Structural Properties on Postmenopausal Women With Rheumatoid Arthritis in Japan: A Cross-Sectional Study.

Introduction There has been no study on bone structural properties in postmenopausal women with rheumatoid arthritis (RA) in Japan. This study investigated bone mineral density (BMD) and bone structural properties in Japanese postmenopausal women with RA. Methods The study had a cross-sectional design and included 119 postmenopausal women aged 50-80 years with RA symptoms for more than five years. BMD, trabecular bone score (TBS), and results of hip structure analysis (HSA) were measured on dual-energy X-ray absorptiometry scans. The control group consisted of 288 women aged 50-80 years without RA. The RA group and control group using bisphosphonates were compared after propensity score matching for age, body mass index, and fracture history. Women in the RA group were also compared according to the use of glucocorticoids (GCs). Results After the propensity matching score, there were no other significant differences in BMD, TBS, and HSA parameters between the RA group and the control group. In the RA group, the TBS was lower in patients on GCs than those not on GCs (1.272 vs 1.313, p=0.008). There were no other significant differences in BMD and HSA parameters between patients in the RA group according to the use of GCs. Conclusion Although there were no differences in BMD, the TBS was lower in patients on GCs than those not on GCs in the RA group. It is thus important for physicians who administer GCs to treat patients with RA to be aware of not only BMD but also TBS.

Genetic diversity and population structure of Plenodomus biglobosus on flixweed (Descurainia sophia) in northwestern China.

Plenodomus biglobosus (Pb), a causal agent of blackleg of rapeseed, is composed of several subspecies, including 'australensis' (Pba), 'brassicae' (Pbb) and 'canadensis' (Pbc). Besides rapeseed, Pb can infect many wild cruciferous plants (WCPs), such as flixweed (Descurainia sophia) and pennycress (Thlaspi arvense), which may become the infection source for blackleg of rapeseed. However, Pb on WCPs has not been well investigated in China. This study identified the blackleg fungi on two WCPs in Sayram Lake and Zhaosu County in Xinjiang of China: flixweed (15 isolates) and pennycress (1 isolate) as well as on rapeseed (971 isolates). They belonged to Pba (11), Pbb (18) and Pbc (958). Pba occurred on flixweed (10) and pennycress (1) only in Sayram Lake, whereas Pbb and Pbc occurred on flixweed (1 and 4 isolates, respectively) and rapeseed (17 and 954 isolates, respectively) in Zhaosu County. Then, virulence of 16 isolates from flixweed and pennycress was determined on rapeseed. Their genomes were sequenced and used to identify the mating-type idiomorphs and to analyze population genetic structure. Results showed that all of the 16 isolates were virulent to rapeseed. Only MAT1-1 was detected in 11 Pba isolates, implying that Pba may lack sexual reproduction. The 16 isolates from two WCPs were divided into four genetic groups: Group I for Pbc (4 isolates), Group II for Pbb (1 isolate), and Group III (3 isolates) and IV (8 isolates) for Pba. The findings about the single mating-type in Pba and its limited geographic distribution provided a case showing the importance of sexual reproduction in epidemics of Pb. To the best of our knowledge, this is the first report of Pba, Pbb and Pbc on flixweed, and Pba on pennycress in China.

Tricyanomethane or Dicyanoketenimine - Silylation makes the Difference.

Pseudohalides such as tricyanomethanide, [C(CN)3]-, are well known in chemistry, biochemistry and industrial chemistry. The protonated species HC(CN)3, a classic hydrogen pseudohalide Brønsted acid, is a very strong acid with a pKa value of -5. However, HC(CN)3 is difficult to handle as it tends to decompose rapidly or, more precisely, to oligo- and polymerize. Therefore, silylated pseu-dohalide compounds with the [Me3Si]+ as the "big organometallic proton" have become interesting, exhibiting similar chemical properties but better kinetic protection. Here, the stepwise silylation of the pseudohalide anion [C(CN)3]- is reported, forming the heavier homologue of HC(CN)3, namely [Me3Si][C(CN)3], and in presence of two additional [Me3Si]+ cations even the dicationic species [(Me3Si-NC)3C]2+ as stable [B(C6F5)4]- salt. Surprisingly, in contrast to HC(CN)3, in which the proton is bound to the central carbon atom of [C(CN)3]-, silylation of the [C(CN)3]- anion occurs at one of the three terminal nitrogen atoms, thus forming the long-sought dicyano-ketenimine [Me3Si-NC-C(CN)2]. All further silylation steps take place exclusively on the terminal N atoms of the three CN groups and not on the central carbon atom, until the intriguing, highly symmetrical dication, [(Me3Si-NC)3C]2+, is finally generated. The experimental data are supported by quantum-chemical calculations in terms of thermodynamics and chemical bonding.

Leveraging Entropy and Crystal Structure Engineering in Prussian Blue Analogue Cathodes for Advancing Sodium-Ion Batteries.

The synergistic engineering of chemical complexity and crystal structures has been applied to Prussian blue analogue (PBA) cathodes in this work. More precisely, the high-entropy concept has been successfully introduced into two structure types of identical composition, namely, cubic and monoclinic. Through the utilization of a variety of complementary characterization techniques, a comprehensive investigation into the electrochemical behavior of the cubic and monoclinic PBAs has been conducted, providing nuanced insights. The implementation of the high-entropy concept exhibits crucial selectivity toward the intrinsic crystal structure. Specifically, while the overall cycling stability of both cathode systems is significantly improved, the synergistic interplay of crystal structure engineering and entropy proves particularly significant. After optimization, the cubic PBA demonstrates structural advantages, showcasing good reversibility, minimal capacity loss, high thermal stability, and unparalleled endurance even under harsh conditions (high specific current and temperature).

Multiview learning with twin parametric margin SVM.

Multiview learning (MVL) seeks to leverage the benefits of diverse perspectives to complement each other, effectively extracting and utilizing the latent information within the dataset. Several twin support vector machine-based MVL (MvTSVM) models have been introduced and demonstrated outstanding performance in various learning tasks. However, MvTSVM-based models face significant challenges in the form of computational complexity due to four matrix inversions, the need to reformulate optimization problems in order to employ kernel-generated surfaces for handling non-linear cases, and the constraint of uniform noise assumption in the training data. Particularly in cases where the data possesses a heteroscedastic error structure, these challenges become even more pronounced. In view of the aforementioned challenges, we propose multiview twin parametric margin support vector machine (MvTPMSVM). MvTPMSVM constructs parametric margin hyperplanes corresponding to both classes, aiming to regulate and manage the impact of the heteroscedastic noise structure existing within the data. The proposed MvTPMSVM model avoids the explicit computation of matrix inversions in the dual formulation, leading to enhanced computational efficiency. We perform an extensive assessment of the MvTPMSVM model using benchmark datasets such as UCI, KEEL, synthetic, and Animals with Attributes (AwA). Our experimental results, coupled with rigorous statistical analyses, confirm the superior generalization capabilities of the proposed MvTPMSVM model compared to the baseline models. The source code of the proposed MvTPMSVM model is available at https://github.com/mtanveer1/MvTPMSVM.

Investigation of heat-induced pork batter quality detection and change mechanisms using Raman spectroscopy coupled with deep learning algorithms.

Pork batter quality significantly affects its product. Herein, this study explored the use of Raman spectroscopy combined with deep learning algorithms for rapidly detecting pork batter quality and revealing the mechanisms of quality changes during heating. Results showed that heating increased ß-sheet content (from 26.38 to 41.42%) and exposed hidden hydrophobic groups, which formed aggregates through chemical bonds. Dominant hydrophobic interactions further cross-linked these aggregates, establishing a more homogeneous and denser network at 80 °C. Subsequently, convolutional neural networks (CNN), long short-term memory neural networks (LSTM), and CNN-LSTM were comparatively used to predict gel strength and whiteness in batters based on the Raman spectrum. Thereinto, CNN-LSTM provided the optimal results for gel strength (Rp = 0.9515, RPD = 3.1513) and whiteness (Rp = 0.9383, RPD = 3.0152). Therefore, this study demonstrated the potential of Raman spectroscopy combined with deep learning algorithms as non-destructive tools for predicting pork batter quality and elucidating quality change mechanisms.

Introns with branchpoint-distant 3' splice sites: Splicing mechanism and regulatory roles.

The two transesterification reactions of pre-mRNA splicing require highly complex yet well-controlled rearrangements of small nuclear RNAs and proteins (snRNP) in the spliceosome. The efficiency and accuracy of these reactions are critical for gene expression, as almost all human genes pass through pre-mRNA splicing. Key parameters that determine the splicing outcome are the length of the intron, the strengths of its splicing signals and gaps between them, and the presence of splicing controlling elements. In particular, the gap between the branchpoint (BP) and the 3' splice site (ss) of introns is a major determinant of the splicing efficiency. This distance falls within a small range across the introns of an organism. The constraints exist possibly because BP and 3'ss are recognized by BP-binding proteins, U2 snRNP and U2 accessory factors (U2AF) in a coordinated manner. Furthermore, varying distances between the two signals may also affect the second transesterification reaction since the intervening RNA needs to be accurately positioned within the complex RNP machinery. Splicing such pre-mRNAs requires cis-acting elements in the RNA and many trans-acting splicing regulators. Regulated pre-mRNA splicing with BP-distant 3'ss adds another layer of control to gene expression and promotes alternative splicing.

Characterization of a pectin in fig fruit: Structure and anti-inflammatory activity.

Fig fruit is widely accepted in warm and tropical regions due to the sweet taste and health benefits. The polysaccharides in fig fruit are responsible for the health benefits. However, information regarding polysaccharide structure remains limited. In this study, the water-soluble polysaccharides (FFP) were extracted from fig fruit with a yield of 15.3 mg/g. Anion exchange chromatography and gel permeation chromatography were used for purification. A leading polysaccharide was purified and characterized as below. The monosaccharide composition of FFP included arabinose (Ara), galactose (Gal), galacturonic acid (GalA) and rhamnose (Rha). The glycosidic linkages were revealed to be L-Ara-(1→, →5)-L-Ara-(1→, →2,4)-L-Rha-(1→, →2)-L-Rha-(1→, →4)-D-Gal-(1→ and D-Gal-(1 â†’ . Nuclear magnetic resonnance (NMR) spectra revealed that FFP had →4)-α-D-GalpA-(1 â†’ 2)-α-L-Rhap-(1→ as backbone. The side chains included Galp-ß-D-(1 â†’ 4)-Galp-ß-D-(1 â†’ 4)-Galp-ß-D-(1 â†’ 4)-Galp-ß-D-(1→ and α-L-Araf-(1 â†’ 5)-α-L-Araf-(1 â†’ . They were linked to C-4 of Rhap. FFP inhibited the production of NO, IL-6 and IL-1ß levels induced by LPS. IL-6 and IL-1ß levels were returned to normal. These information are helpful to understand this functional fruit.

Self-hybridization structures of BiOBr0.5Cl0.5: An ultra-high capacity anode material for half/full potassium-ion batteries.

Potassium-ion batteries (PIBs) are gaining attention among emerging technologies for their cost-effectiveness and the abundance of resources they utilize. Within this context, bismuth oxyhalides (BiOX) have emerged as exceptional candidates for anode materials in PIBs due to their unique structural and superior electrochemical properties. However, challenges such as structural instability and low electronic conductivity remain to be addressed. In this study, a flower-like BiOBr0.5Cl0.5/rGO composite anode material was synthesized, demonstrating outstanding K+ storage performance. The self-hybridized structure enhances ion adsorption and diffusion, which in turn improves charge and discharge efficiency as well as long-term stability. In situ X-ray diffraction (XRD) tests confirmed the gradual release and alloying potassium storage mechanism of Bi metal, which occurs through the intermediate KxBiOBr0.5Cl0.5 phase within the BiOBr0.5Cl0.5 anode. This composite exhibited a high specific capacity of 246.4 mAh/g at 50 A/g and maintained excellent capacity retention after 2400 cycles at 5 A/g. Additionally, in full battery tests, it showed good rate performance and long cycle life, maintaining a discharge specific capacity of 119.6 mAh/g at a high current density of 10 A/g. Comprehensive characterizations revealed insights into the structural, electrochemical, and kinetic properties, advancing high-performance PIBs.

Transcriptome data are insufficient to control false discoveries in regulatory network inference.

Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data suffers notoriously from false positives. Approaches to control the false discovery rate (FDR), for example, via permutation, bootstrapping, or multivariate Gaussian distributions, suffer from several complications: difficulty in distinguishing direct from indirect regulation, nonlinear effects, and causal structure inference requiring "causal sufficiency," meaning experiments that are free of any unmeasured, confounding variables. Here, we use a recently developed statistical framework, model-X knockoffs, to control the FDR while accounting for indirect effects, nonlinear dose-response, and user-provided covariates. We adjust the procedure to estimate the FDR correctly even when measured against incomplete gold standards. However, benchmarking against chromatin immunoprecipitation (ChIP) and other gold standards reveals higher observed than reported FDR. This indicates that unmeasured confounding is a major driver of FDR in TRN inference. A record of this paper's transparent peer review process is included in the supplemental information.

Concerted deletions eliminate a neutralizing supersite in SARS-CoV-2 BA.2.87.1 spike.

BA.2.87.1 represents a major shift in the BA.2 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is unusual in having two lengthy deletions of polypeptide in the spike (S) protein, one of which removes a beta-strand. Here we investigate its neutralization by a variety of sera from infected and vaccinated individuals and determine its spike (S) ectodomain structure. The BA.2.87.1 receptor binding domain (RBD) is structurally conserved and the RBDs are tightly packed in an "all-down" conformation with a small rotation relative to the trimer axis as compared to the closest previously observed conformation. The N-terminal domain (NTD) maintains a remarkably similar structure overall; however, the rearrangements resulting from the deletions essentially destroy the so-called supersite epitope and eliminate one glycan site, while a mutation creates an additional glycan site, effectively shielding another NTD epitope. BA.2.87.1 is relatively easily neutralized but acquisition of additional mutations in the RBD could increase antibody escape allowing it to become a dominant sub-lineage.

Silver nanoparticles alter planktonic community structure and promote ecosystem respiration in freshwater mesocosms.

The widespread use of silver nanoparticles (AgNPs) has resulted in their release into the aquatic environment, which threatens the health of aquatic ecosystems. Although the ecotoxicological effects of AgNPs have been widely reported at individual and population levels, the impact of long-term exposure to AgNPs on community structure and ecosystem function in aquatic ecosystems remains poorly understood. Herein, the present study investigated the effects of long-term exposure (28 d) to environmentally relevant concentrations (1 µg/L and 10 µg/L) of AgNPs on the community structure and function of freshwater ecosystems by artificially constructed 28 mesocosms freshwater ecosystem in experimental greenhouses, using plastic water tanks and food web manipulation. The results showed that long-term exposure to AgNPs significantly altered the community structure of zooplankton, phytoplankton, and bacterioplankton in the aquatic ecosystem. Exposure to 10 µg/L AgNPs significantly reduced the zooplankton density (70.3%, p < 0.05) and increased the phytoplankton biomass and bacterial richness and diversity via a "top-down effect." With regards to ecosystem function, AgNPs exposure significantly increased the respiration in freshwater ecosystems but did not have a significant effect on decomposition. The partial least squares path modeling (PLS-PM) further revealed that AgNPs may have a negative impact on ecosystem functions by reducing zooplankton community density and thus increasing phytoplankton biomass. This study is the first to show that long-term exposure to environmentally relevant concentrations of AgNPs leads to alterations in plankton community structure and promotes respiration in freshwater ecosystems. It emphasizes the need for assessing the environmental risk of long-term exposure to AgNPs at the ecosystem level.