bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrative metabolomics and network pharmacology to study the preventative impact of dioscin treatment on hyperuricemia
Authors: Yu Donghua , Fu Jiaqi , Wang Yu , Lu Fang , Chen Pingping , Liu Shumin
Published: December 2022

This work aims to combine network pharmacology and metabolomics to explore the mechanism of action of dioscin on hyperuricemia (HUA). The preventative impact of dioscin on HUA and its putative mechanism were examined using network pharmacological analysis and metabonomics. Network pharmacology study further pointed out the potential targets of dioscin after a review of the relevant biomarker pathways discovered by metabolomic analysis. Molecular docking was then used to examine how the active chemicals interacted with the target proteins. The therapeutic effect of dioscin on HUA was shown to be mediated by 13 potentially important metabolites as a result of metabonomic research. Most of these metabolites are regulated after dioscin therapy to help patients recover. Based on network pharmacology, we identified 10 central genes, which is partly in agreement with metabolomics data. Using metabolomics and network pharmacology, this study investigated the primary targets and mechanisms of dioscin in the treatment of HUA. It is advantageous that dioscin has been developed as an additional drug for the treatment of HUA.
Embodied design: A framework for teaching practices focused on the early development of computational thinking
Authors: Deng Wenbo , Guo Xipei , Cheng Weihua , Zhang Wenlan
Published: December 2022

Computational thinking, as an essential competency for the future development of citizens, is an important goal of computer science instruction. Although studies have shown that early exposure to computer programming is beneficial for improving computational thinking, current programming instruction does not systematically consider the factors that influence the development of computational thinking. To promote the early development of computational thinking, we analyzed the main factors that influence the development of computational thinking in terms of learners' cognitive level, instructional content, and technological environment. Therefore, this study proposes a teaching framework for developing computational thinking based on embodied cognitive theory. This teaching framework shows how to choose a suitable technological environment, design the appropriate content and apply adequate methods to effectively promote students' computational thinking development.
Bedside ocular ultrasonography for diagnosing increased intracranial pressure in patients with leptomeningeal metastases from non‐small‐cell lung cancer
Authors: Jiang Cheng , Lin Yongjuan , Li Huiying , Xie Yu , Yu Tingting , Feng Jingyu , Huang Mingmin , Guo Aibin , Shen Haiyun , Zhang YiDan , Yin Zhenyu
Published: December 2022

Objectives

To explore the diagnostic accuracy of ultrasound measurement of optic nerve sheath diameter (ONSD) and optic disc height (ODH) in detecting intracranial hypertension in non‐small‐cell lung cancer (NSCLC) patients with leptomeningeal metastases (LM).

Methods

Seventy‐two patients with NSCLC‐LM and 65 patients with NSCLC were enrolled. The ONSD, ODH, eyeball transverse diameter (ETD), and eyeball vertical diameter (EVD) were measured by ultrasound. Subsequently, lumbar puncture was performed in NSCLC‐LM patients to measure cerebrospinal fluid pressure (CSFP), and intrathecal chemotherapy was regularly implemented. Pearson's correlation analysis was used to analyze the relationship between CSFP and ultrasound findings. The diagnostic accuracy of ONSD, ODH, and combined ONSD and ODH was evaluated by receiver operating characteristic (ROC) curve analysis and the corresponding area under the ROC curve (AUC).

Results

The ONSD, ODH, ONSD/ETD, and ONSD/EVD values were higher in the NSCLC‐LM group (all p < 0.05). The ONSD, ODH, ONSD/ETD, and ONSD/EVD values were all elevated in the abnormally elevated CSFP group (all p < 0.05). ONSD, ODH, ONSD/ETD, and ONSD/EVD were positively correlated with CSFP (r = 0.531, 0.383, 0.534, and 0.535, all p < 0.0001). The AUCs for ONSD, ODH, ONSD/ETD, and ONSD/EVD to detect CSFP >280 mmH2O were 0.787 (95% CI: 0.64–0.93, sensitivity 68.75%, specificity 91.07%), 0.885 (95% CI: 0.81–0.96, sensitivity 100%, specificity 69.64%), 0.765 (95% CI: 0.64–0.89, sensitivity 81.25%, specificity 64.29%), and 0.788 (95% CI: 0.64–0.93, sensitivity 56.25%, specificity 91.07%), respectively. When ONSD was combined with ODH, the AUC was 0.913 (95% CI: 0.83–0.99, sensitivity 87.85%, specificity 85.70%). Furthermore, intrathecal chemotherapy was associated with a downtrend in CSFP and ultrasound findings.

Conclusion

There are important advantages of using bedside ultrasonography for detecting elevated CSFP in NSCLC‐LM patients. Further research should be performed to evaluate the clinical significance of an enlarged ONSD and increased ODH in NSCLC‐LM.
Genomic alterations and clinical outcomes in patients with dedifferentiated liposarcoma
Authors: Jagosky Megan H. , Anderson Colin J. , Symanowski James T. , Steuerwald Nury M. , Farhangfar Carol J. , Baldrige Emily A. , Benbow Jennifer H. , Livingston Michael B. , Patt Joshua C. , Ahrens Will A. , Kneisl Jeffrey S. , Kim Edward S.
Published: December 2022

Purpose

Patients with unresectable dedifferentiated liposarcoma (DDLPS) have poor overall outcomes. Few genomic alterations have been identified with limited therapeutic options.

Experimental Design

Patients treated at Levine Cancer Institute with DDLPS were identified. Next generation sequencing (NGS), immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) testing were performed on tumor tissue collected at diagnosis or recurrence/progression. Confirmation of genomic alterations was performed by orthologous methods and correlated with clinical outcomes. Univariate Cox regression was used to identify genomic alterations associated with clinical outcomes.

Results

Thirty‐eight DDLPS patients with adequate tissue for genomic profiling and clinical data were identified. Patient characteristics included: median age at diagnosis (66 years), race (84.2% Caucasian), and median follow‐up time for the entire cohort was 12.1 years with a range from approximately 3.5 months to 14.1 years. Genes involved in cell cycle regulation, including MDM2 (74%) CDK4 (65%), and CDKN2A (23%), were amplified along with WNT/Notch pathway markers: HMGA2, LGR5, MCL1, and CALR (19%–29%). While common gene mutations were identified, PDE4DIP and FOXO3 were also mutated in 47% and 34% of patients, respectively, neither of which have been previously reported. FOXO3 was associated with improved overall survival (OS) (HR 0.37; p = 0.043) along with MAML2 (HR 0.30; p = 0.040). Mutations that portended worse prognosis included RECQL4 (disease‐specific survival HR 4.67; p = 0.007), MN1 (OS HR = 3.38; p = 0.013), NOTCH1 (OS HR 2.28, p = 0.086), and CNTRL (OS HR 2.42; p = 0.090).

Conclusions

This is one of the largest retrospective reports analyzing genomic aberrations in relation to clinical outcomes for patients with DDLPS. Our results suggest therapies targeting abnormalities should be explored and confirmation of prognostic markers is needed. Dedifferentiated liposarcoma is one of the most common subtypes of soft tissue sarcoma yet little is known of its molecular aberrations and possible impact on outcomes. The work presented here is an evaluation of genetic abnormalities among a population of patients with dedifferentiated liposarcoma and how they corresponded with survival and risk of metastases. There were notable gene mutations and amplifications commonly found, some of which had interesting prognostic implications.
NUPR1 imparts oncogenic potential in bladder cancer
Authors: Zhang Lifeng , Gao Shenglin , Shi Xiaokai , Chen Yin , Wei Shuzhang , Mi Yuanyuan , Zuo Li , Qi Chunjian
Published: December 2022

Background

NUPR1, or p8, is a small chromatin protein that plays a central role in the resistance to treatment and progression of cancer. Nevertheless, the molecular mechanism of NUPR1 in bladder cancer (BLCA) remains unclear.

Methods

We used online databases and immunohistochemistry (IHC) to explore the expression of NUPR1 in BLCA tissues and controls. Lentivirus‐mediated small interfering ribonucleic acid (siRNA) was used to knockdown the expression of NUPR1 in two human BLCA cell lines. We used an in vivo experiment to investigate the effect of NUPR1 knockdown on the growth of BLCA. Moreover, an in silico analysis was conducted to assess the differential expression profile after NUPR1 interference. The CIBERSORT algorithm was utilized to evaluate the effects of tumor‐infiltrating immune cells among BLCA patients.

Results

The expression of NUPR1 in BLCA tissues was significantly higher than in the control. NUPR1 expression was also positively correlated with the stage of BLCA. After lentivirus‐mediated interference, the expression of NUPR1 was significantly down‐regulated in BLCA cell lines. The cell cycle was blocked in G1 phase and the cell proportion of S phase was decreased in both two cell lines. Moreover, in vivo experiment revealed that the tumor growth of BLCA can be delayed by inhibiting the expression of NUPR1. Both in silico analysis and functional experiments revealed that NUPR1 was correlated with epithelial–mesenchymal transition (EMT). We also revealed that macrophages were the most related immune cells associated with the expression of NUPR1 in BLCA.

Conclusions

This study suggests that NUPR1 plays a carcinogenic role in BLCA. NUPR1 lentivirus‐mediated interference could interfere with cycle progression of the BLCA cell, resulting in cell cycle arrest in the G1‐phase. The carcinogenic effect of NUPR1 in BLCA is likely achieved through EMT. NUPR1 is correlated with the M0‐type macrophage markers CD68 and CD11b‐integrin.
Age and the cascade impact on coronary flow reserve (CFR) and discordance of fractional flow reserve and non‐hyperemic pressure ratios (NHPR)
Authors: Kern Morton J.
Published: December 2022

Key Points

CFR decreases with age because hyperemic flow is reduced.

Reduced hyperemic flow affects FFR but not NHPR, contributing to a higher rate of discordance between pressure ratios in the elderly.

Using a dichotomous age cut off of 60 years, the impact of age in patients with discordant physiologic indices is minimal.
Bifunctional Ru‐Cluster‐Decorated Co3B−Co(OH)2 Hybrid Catalyst Synergistically Promotes NaBH4 Hydrolysis and Water Splitting
Authors: Li Huatong , Liu Zhengqi , Wang Lixia , Guo Man , Isimjan Tayirjan Taylor , Yang Xiulin
Published: December 2022

Developing a highly efficient bifunctional catalyst for hydrolysis of metal hydrides and spontaneous hydrogen evolution reaction (HER) is essential for substituting conventional fuels for H2 production. Herein, Ru‐cluster‐modified Co3B−Co(OH)2 supported on nickel foam (Ru/Co3B−Co(OH)2@NF) is constructed by electroless deposition, calcination and chemical reduction. The catalyst exhibits an excellent hydrogen generation rate (HGR) of 4989 mL min−1
and good reusability, superior to most previously reported catalysts. Besides, Ru/Co3B−Co(OH)2@NF displays a prominent hydrogen evolution reaction catalytic capability with a low overpotential of 153.0 mV at 100 mA cm−2 (50.5 mV at 10 mA cm−2), a small Tafel slope of 40.0 mV dec−1 and long‐term stability (100 h@10 mA cm−2) in 1.0 M KOH. The excellent catalytic H2 generation capacity benefits from the rapid charge transfer promoted by metallic Co3B, the synergistic catalytic effect of Co3B−Co(OH)2 and Ru clusters, and the unique composite structure favorable for solute transport and gas emission.
Tweezer‐Based C−H Oxidation Catalysts Overriding the Intrinsic Reactivity of Aliphatic Ammonium Substrates
Authors: Knezevic Melina , Tiefenbacher Konrad
Published: December 2022

The site‐selective C−H oxygenation of alkyl chains as well as deactivated positions remains a great challenge for chemists. Here, we report the synthesis and application of four new supramolecular tweezer‐based oxidation catalysts. They consist of the well‐explored M(pdp/mcp) oxidation moiety and a molecular tweezer capable of binding ammonium salts. All catalysts display preferential oxidation of the strongly deactivated C3/C4 positions, however to different degrees. Furthermore, the best performing catalyst Fe(pdp)Twe was explored with an expanded substrate scope. It was demonstrated that the deactivated positions C3/C4 are also preferentially oxidized in these cases.
The Active Sites and Corresponding Stability Challenges of the M‐N‐C Catalysts for Proton Exchange Membrane Fuel Cell
Authors: Peng Ruolin , Zhao Zhongkun , Sun Hongmin , Yang Yongping , Song Tinglu , Yang Yao , Shao Jiankun , Jin Haibo , Sun Hongtao , Zhao Zipeng
Published: December 2022

Comprehensive Summary

Proton exchange membrane fuel cells (PEMFCs) as promising alternatives to traditional internal combustion engines have attracted massive concerns to promote their wide application in society. However, the biggest challenge to the commercialization of PEMFCs remains the high cost due to the adoption of the platinum group metal (PGM) catalysts in the cathode. Thus, the development of PGM‐free catalysts based on earth‐abundant elements with a much lower cost is considered as the most favorable solution. Although the reported activity of the state‐of‐the‐art PGM‐free catalyst is comparable with that of a typical commercial Pt/C catalyst, the precise structure of active sites on the PGM‐free catalysts is debatable. In addition, the stability of the highly active PGM‐free catalysts still needs improvement. Herein, we reviewed the recent research about the nature of the active sites, the progress in stability improvement, and the degradation mechanisms of active sites on PGM‐free catalysts.
Cardiovascular disease in adolescent and young adult cancer survivors: Impact of sociodemographic and modifiable risk factors
Authors: Berkman Amy M. , Andersen Clark R. , Roth Michael E. , Gilchrist Susan C.
Published: December 2022

Background

There is a growing population of adolescent and young adult (AYA) cancer survivors (ages 15–39 years), and they have an elevated risk of developing cardiovascular disease (CVD). Little is known about the contribution of sociodemographic and modifiable factors to the risk of CVD in AYA survivors and whether these factors differentially modulate their risk compared with that in the general population. The current study sought to fill these gaps.

Methods

Self‐reported data from the US National Health Interview Survey (2009–2018) were used to identify AYA cancer survivors (≥2 years postdiagnosis) and age‐matched and sex‐matched controls. The risk of CVD based on sociodemographic factors (sex, race/ethnicity, income, education) and modifiable risk factors (diabetes, body mass index, smoking, physical activity) was determined within and between survivors and controls using logistic regression models.

Results

In total, 4766 AYA cancer survivors and 47,660 controls were included. The odds of CVD were significantly higher in survivors than in controls by sex, race/ethnicity, income, education, smoking status, and physical activity. An annual household income <$50,000 disproportionately increased the odds of CVD in survivors. One third of survivors reported no moderate‐to‐vigorous–intensity physical activity (MVPA). Performing any MVPA lowered the odds of CVD in survivors (odds ratio, 0.61; 95% CI, 0.450.81) and controls (odds ratio, 0.68; 95% CI, 0.61–0.77).

Conclusions

Sociodemographic and modifiable risk factors increased the odds of CVD in AYA survivors, in some cases disproportionately, compared with controls. Understanding health behavior trajectories among different sociodemographic populations is needed to identify opportunities to lower the risk of CVD. Performing any MVPA is particularly important for AYA survivors.
Pharmacokinetic, Safety, and Tolerability Evaluations of Gepotidacin (GSK2140944) in Healthy Japanese Participants
Authors: Barth Aline , Hossain Mohammad , Perry Caroline R. , Gross Annette S. , Ogura Hirofumi , Shabbir Shaila , Thomas Sebin , Dumont Etienne F. , Brimhall Darin B. , Srinivasan Meenakshi , Swift Brandon
Published: December 2022

Gepotidacin is a novel, bactericidal, first‐in‐class triazaacenaphthylene antibiotic in late‐phase development for uncomplicated urinary tract infection and uncomplicated urogenital gonorrhea. Two clinical studies were conducted to assess the pharmacokinetics (PK) and interethnic comparisons of oral gepotidacin (free‐base and to‐be‐marketed mesylate formulations) administered as single doses ranging from 1500 to 3000 mg in fed and fasted states, and as 2 × 3000‐mg doses given 12 hours apart under fed conditions in healthy participants of Japanese ancestry. Dose proportionality was observed in plasma exposures, and comparable area under the concentration‐time curve (AUC) and maximum concentration were observed in fed and fasted states. Interethnic comparisons for Japanese versus non‐Japanese participant data showed slightly higher plasma maximum concentration (7%‐30%) yet similar plasma AUCs; slightly lower urine AUCs (11%‐18%) were observed. The slightly higher plasma exposures in healthy Japanese versus White participants in the same study were attributed to lower mean body weights (64 kg versus ≈80 kg). Adverse events were primarily gastrointestinal, and when administered with food, gastrointestinal tolerability was improved. Overall, the gepotidacin PK and safety‐risk profiles in healthy Japanese support potential evaluation of the global clinical doses in future studies.
A Simple and Low‐Tech Heat‐Shock Method to Increase Genome Editing Efficiency in Plants
Authors: Blomme Jonas , Ribera Júlia Arraiza , Develtere Ward , Jacobs Thomas B.
Published: December 2022

CRISPR/Cas is now the standard technique to generate novel plant genotypes. However, optimizing the efficiency of the system continues to be an aspect of research and development. One of the improvements for increasing mutagenesis efficiency in different species is the application of heat stress. However, many experimental setups are limited by the requirement of using dedicated climate chambers to impose heat stress and by difficulties in the phenotyping of soil‐grown plants. Here, we describe a simplified heat stress assay for in vitro–grown plants that can be completed in 6 days using commonly available laboratory equipment. We show that three 24‐hr heat shocks (3×HS) at 37°C alternated with 24 hr of recovery at 21°C efficiently increases indel rates of LbCas12a and Cas9. We illustrate how visual mutant phenotypes (pds3 and gl1) can assist in quantifying genome editing efficiency, and describe how to quantify genome editing efficiency using genotyping by Sanger sequencing. We also provide a support protocol to efficiently clone a CRISPR expression vector in a single step. Together, our methods allow researchers to increase CRISPR‐induced mutations using a low‐tech setup in plants. © 2022 Wiley Periodicals LLC.

Basic Protocol 1: 3×HS protocol

Basic Protocol 2: Genotyping by Sanger sequencing

Support Protocol: One‐step cloning of a CRISPR expression vector
Targeted Protein Degradation: Design Considerations for PROTAC Development
Authors: Tran Nathan L. , Leconte Georges A. , Ferguson Fleur M.
Published: December 2022

Targeted protein degradation has recently gained widespread interest as both a novel therapeutic strategy and a useful tool in biomedical research. Targeted protein degraders are often sub‐stoichiometric and do not require strong binding affinity for their targets, enabling access to previously inaccessible targets. Proteolysis‐targeting chimeras (PROTACs) are one class of targeted protein degraders that promote degradation by recruiting a target protein to an E3‐ligase complex via a heterobifunctional molecule. The modular nature of PROTACs allows for their rational design and systematic optimization. Here we suggest resources and methodologies for developing PROTAC degraders for researchers that may be new to the field. © 2022 Wiley Periodicals LLC.
Deformation characteristics and novel strain criteria of strainbursts induced by low‐frequency cyclic disturbance
Authors: Hu Lihua , Ju Minghe , Zhao Peng , Li Xiaozhao
Published: December 2022

Strainbursts induced by cyclic disturbance with low frequency (termed as cyclic‐induced strainbursts) are major dynamic disasters during deep excavation and mining. There is currently no quantitative criterion available for the prediction of such disastrous events. In this study, based on true triaxial experiments, we analyzed the deformation characteristics, established two novel strain criteria for the cyclic‐induced strainbursts, and explained the physical meaning of these criteria. Characteristic strains for the cyclic‐induced strainbursts were defined, including the control strain εctr, the strain caused by the combined dynamic and static loading εsd, and the ultimate strain εu after strainbursts. As indicated by the results, the deformation evolution of the cyclic‐induced strainbursts shows remarkable fatigue characteristics, which resemble that of rock subjected to cyclic loading and unloading. In other words, there are three stages during deformation evolution, namely, initial rapid growth, uniform velocity growth after several periods of disturbance, and sudden sharp growth preceding the burst. The ultimate strain εu is insensitive to the tangential static stress and disturbance amplitude, but it changes nonlinearly with disturbance frequency. From the perspective of deformation, the occurrence of a cyclic‐induced strainburst is controlled by the control strain εctr. Thus, a control strain criterion is proposed; that is, when the stain εsd is larger than the control strain εctr, a strainburst will be induced by cyclic disturbance. Moreover, based on the statistical results, a strain ratio criterion is proposed; that is, when the strain ratio εsd/εu is greater than 30%, a cyclic‐induced strainburst will be induced.
High thermal tolerance in high‐elevation species and laboratory‐reared colonies of tropical bumble bees
Authors: Gonzalez Victor H. , Oyen Kennan , Aguilar Marlene L. , Herrera Andres , Martin Ruben D. , Ospina Rodulfo
Published: December 2022

Bumble bees are key pollinators with some species reared in captivity at a commercial scale, but with significant evidence of population declines and with alarming predictions of substantial impacts under climate change scenarios. While studies on the thermal biology of temperate bumble bees are still limited, they are entirely absent from the tropics where the effects of climate change are expected to be greater. Herein, we test whether bees' thermal tolerance decreases with elevation and whether the stable optimal conditions used in laboratory‐reared colonies reduces their thermal tolerance. We assessed changes in the lower (CTMin) and upper (CTMax) critical thermal limits of four species at two elevations (2600 and 3600 m) in the Colombian Andes, examined the effect of body size, and evaluated the thermal tolerance of wild‐caught and laboratory‐reared individuals of Bombus pauloensis. We also compiled information on bumble bees' thermal limits and assessed potential predictors for broadscale patterns of variation. We found that CTMin decreased with increasing elevation, while CTMax was similar between elevations. CTMax was slightly higher (0.84°C) in laboratory‐reared than in wild‐caught bees while CTMin was similar, and CTMin decreased with increasing body size while CTMax did not. Latitude is a good predictor for CTMin while annual mean temperature, maximum and minimum temperatures of the warmest and coldest months are good predictors for both CTMin and CTMax. The stronger response in CTMin with increasing elevation, and similar CTMax, supports Brett's heat‐invariant hypothesis, which has been documented in other taxa. Andean bumble bees appear to be about as heat tolerant as those from temperate areas, suggesting that other aspects besides temperature (e.g., water balance) might be more determinant environmental factors for these species. Laboratory‐reared colonies are adequate surrogates for addressing questions on thermal tolerance and global warming impacts.
Fertilization modes and the evolution of sperm characteristics in marine fishes: Paired comparisons of externally and internally fertilizing species
Authors: Ito Takeshi , Morita Masaya , Okuno Seiya , Inaba Kazuo , Shiba Kogiku , Munehara Hiroyuki , Koya Yasunori , Homma Mitsuo , Awata Satoshi
Published: December 2022

Fertilization mode may affect sperm characteristics, such as morphology, velocity, and motility. However, there is little information on how fertilization mode affects sperm evolution because several factors (e.g., sperm competition) are intricately intertwined when phylogenetically distant species are compared. Here, we investigated sperm characteristics by comparing seven externally and four internally fertilizing marine fishes from three different groups containing close relatives, considering sperm competition levels. The sperm head was significantly slenderer in internal fertilizers than in external fertilizers, suggesting that a slender head is advantageous for swimming in viscous ovarian fluid or in narrow spaces of the ovary. In addition, sperm motility differed between external and internal fertilizers; sperm of external fertilizers were only motile in seawater, whereas sperm of internal fertilizers were only motile in an isotonic solution. These results suggest that sperm motility was adapted according to fertilization mode. By contrast, total sperm length and sperm velocity were not associated with fertilization mode, perhaps because of the different levels of sperm competition. Relative testis mass (an index of sperm competition level) was positively correlated with sperm velocity and negatively correlated with the ratio of sperm head length to total sperm length. These findings suggest that species with higher levels of sperm competition have faster sperm with longer flagella relative to the head length. These results contradict the previous assumption that the evolution of internal fertilization increases the total sperm length. In addition, copulatory behavior with internal insemination may involve a large genital morphology, but this is not essential in fish, suggesting the existence of various sperm transfer methods. Although the power of our analyses is not strong because of the limited number of species, we propose a new scenario of sperm evolution in which internal fertilization would increase sperm head length, but not total sperm length, and change sperm motility.
Maladaptive nest‐site selection and reduced nest survival in female sage‐grouse following wildfire
Authors: Dudley Ian F. , Coates Peter S. , Prochazka Brian G. , Davis Dawn M. , Gardner Scott C. , Delehanty David J.
Published: December 2022

Increased wildfire frequency and associated replacement of sagebrush (Artemisia spp.) with invasive annual grasses contribute to declines of greater sage‐grouse (Centrocercus urophasianus; hereafter, sage‐grouse) populations across the Great Basin. However, little is known about wildfire effects on sage‐grouse nest‐site selection and nest survival, which can influence population persistence. The primary objective of this study was to evaluate the effects of the Rush Fire on sage‐grouse nest survival using before (2007–2009) and after (2015–2018) data collected from a population of sage‐grouse occupying the border of northeastern California and northwestern Nevada. We employed a before–after–control–impact (BACI) experimental design to account for spatiotemporal heterogeneity in the system and to derive estimates of relative change in survival parameters. Sage‐grouse nest survival decreased after the Rush Fire but decreased more in the burned area relative to the unburned area. Although female sage‐grouse continued to occupy burned areas, nest survival was reduced from 52% to 19%. Using a BACI ratio approach we found that nest survival decreased approximately 51% in the burned area, relative to the unburned area, following wildfire. Habitat analyses were restricted to the postfire period and found that female sage‐grouse that nested within unburned areas selected for wider nesting substrate, taller perennial grass height, and greater low sagebrush canopy cover. Conversely, female sage‐grouse that nested in burned areas used shorter sagebrush canopy cover than what was available across the entire study area but showed stronger selection for perennial grass height than their unburned counterparts. Strong nest‐site fidelity in sage‐grouse may explain the continued use of suboptimal habitat in wildfire‐altered landscapes, resulting in a reproductive cost, and overall reproduction well below replacement rate. Results suggest that fire suppression or rapid postfire habitat restoration, especially within nesting habitat, may be essential to conserving robust sage‐grouse populations into the future.
Fence types influence pronghorn movement responses
Authors: DeVoe Jesse D. , Proffitt Kelly M. , Millspaugh Joshua J.
Published: December 2022

Impediments that constrain animal movements across spatiotemporally heterogeneous landscapes can result in reduced or complete loss of access to critical resources. Across their range in North America, pronghorn (Antilocapra americana) are exposed to fences that can affect their ability to permeate the landscape, access critical resources, and respond to climatic variations. Understanding pronghorn movement responses to fences is essential for improving landscape permeability; however, prior studies provide only limited insight due to lack of information on fence characteristics and small sample sizes. Our study used hourly collar locations from adult female pronghorn in six herds in Montana, USA, and identified encounters with mapped fences to evaluate three movement responses (i.e., probability of an unaltered initial response, probability of crossing following an altered initial response, and passage time following an altered initial response) as a function of fence and landscape attributes. Based on 5581 encounters identified from movement pathways of 265 collared pronghorn and 979 km of mapped fences, we found that variability in pronghorn fence response was correlated with fence type. Woven wire fences substantially reduced unaltered initial and crossing responses and increased passage times as compared with low (i.e., average lowest wire height <41 cm) or high (i.e., average lowest wire height ≥41 cm) strand fences. Both low and high strand fences elicited similar responses of being relatively permeable at the initial encounter with reduced permeability thereafter. Fence crossing probabilities following altered initial responses increased through time modestly for strand fences but only negligibly for woven wire fences, with passage times averaging approximately 14 h. Pronghorn knowledge of and fidelity to specific permeable locations along fences, which may be due to inconsistent fence and landscape characteristics along the fence stretch, likely allow some woven wire fences and most strand fences, regardless of the average lowest wire height, to be permeable. Improving landscape permeability for pronghorn should focus on removing woven wire fences, replacing woven wire fences with strand fences, and incorporating variation in the lowest wire heights into new fence designs or modifications of existing fences.
Geo‐ecological functions provided by coral reef fishes vary among regions and impact reef carbonate cycling regimes
Authors: Perry Chris T. , Salter Michael A. , Lange Ines D. , Kochan David P. , Harborne Alastair R. , Graham Nicholas A. J.
Published: December 2022

Coral reef fishes perform essential and well‐documented ecological functions on reefs, but also contribute important geo‐ecological functions, which influence reef carbonate cycling regimes. These functions include reef framework modification (through bioerosion and breakage), and the production, reworking, and transport of reefal sediments. To explore how these functions vary across reefs and regions, we compiled a dataset of available taxa‐specific function rates and applied these to fish census data from sites in the Pacific Ocean (PO), Indian Ocean (IO), and Greater Caribbean (GC), each region displaying a gradient in fish biomass. The highest overall function rates occur at the highest fish biomass sites in the PO (Kingman Reef) and IO (Chagos Archipelago), where bioerosion dominates framework modification and sediment generation (up to 7 kg m−2 year−1). At the lowest biomass PO and IO sites, framework modification and sediment generation are driven mainly by breakage and occur at lower rates (~2 kg m−2 year−1). Sediment reworking rates are high across all PO and IO sites (~1–5 kg m−2 year−1) and higher than other function rates at low biomass sites. Geo‐ecological function rates are generally low across the GC sites, despite total fish biomass being comparable to, or even exceeding, some PO and IO sites, with sediment reworking (up to ~1 kg m−2 year−1) being the dominant function. These site‐level differences partly reflect total fish biomass, but fish assemblage size structure and species identity are critical, with a few fish families (and species) underpinning the highest function rates and regulating the “health” of the fish‐driven carbonate cycling regime. Reefs with high fish‐driven framework modification, sediment production and reworking rates define one end of this spectrum, while at lower biomass sites little new sediment is produced and sediment reworking dominates. While additional species‐level rate data are urgently needed to better constrain function rates, these transitions align with ideas about the progressive shutdown of carbonate production regimes on ecologically perturbed reefs, with important implications for reef‐building, shoreline sediment supply, and sediment carbon and nutrient cycling.
In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary
Authors: Fulford R. S. , Houghton K. , James J. , Russell M.
Published: December 2022

Estuaries provide a suite of ecosystem services to people but are also under heavy stress from human development including excess nutrient loading and alterations in benthic habitat that affect nutrient cycling. Here we examine the interaction of two important and common ecosystem management priorities in estuaries: limiting eutrophication and restoration of submerged aquatic vegetation (SAV). Rates of benthic nitrogen processing can vary by habitat type and there is need for more complete data on the contribution of SAV to overall nitrogen cycling in estuaries, as well as a need to examine nitrogen cycling in situ to better characterize the role of SAV areal coverage in mediating estuarine eutrophication. We compare nitrogen cycling between two common and adjacent habitat types (SAV and adjacent bare sediment [BS]) in an index coastal estuary using an in situ chamber‐based approach to better capture realized habitat differences. We also examined genomic community structure of sediment bacteria and archaea to identify biological indicators of nitrogen exchange. Both mean sediment–water exchange of dissolved N2 and microbial functional community structure differed between SAV and BS. Habitat differences were more consistent with lower variability at locations with low salinity and when sediment organic content was highest, which aligns with findings in other studies. Habitat types differed significantly in microbial composition, including functional groups and genes, like nifH, that may contribute to observed differences in nitrogen cycling. Overall, habitat type appeared most important to nitrogen cycling near the river mouth where sediment nitrogen was higher, and this information has implications for integrated management of habitat restoration/conservation and nutrient loading.
Behavioral cues enable native fishes to exit a California floodplain while leaving non‐native fishes behind
Authors: Ogaz Mollie H. , Rypel Andrew L. , Lusardi Robert A. , Moyle Peter B. , Jeffres Carson A.
Published: December 2022

Floodplains are highly productive environments that provide critical rearing habitat and increased growth for diverse native fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Yet, stranding during the flood recession is a potential negative outcome in restored ecosystems where environmental cues are not always present as they were under historical conditions. Outmigration cues of native and non‐native fishes from a restored floodplain were evaluated along the Cosumnes River, CA, USA. This river is the only remaining major unregulated river in the Sierra Nevada that flows into the Central Valley. It remains unclear how native and non‐native fishes utilize spatiotemporally heterogeneous habitats in the Cosumnes River; however, a better understanding of these dynamics could yield insight into how degraded river ecosystems in the region could be rehabilitated to benefit native fishes. In 2018 and 2019, daily fyke net surveys of fish assemblages were conducted within the floodplain and in outmigration corridors, along with the collection of environmental data to identify possible cues. Bayesian modeling showed that temperature increases, along with the rate of floodplain drawdown and the average flow over a rolling seven‐day period, were important triggers for cuing native fishes to exit the floodplain. We conclude that the numerous benefits to the aquatic food web and growth of native fishes justify the risk of stranding that floodplain restoration poses, particularly when supplemented with outmigration cues.
Identifying individual and spatial drivers of heterogeneous transmission and virulence of malaria in Caribbean anoles
Authors: Toohey John M. , Otero Luisa , Flores Siaca Ian G. , Acevedo Miguel A.
Published: December 2022

Heterogeneous distributions are a fundamental principle of ecology, manifesting as natural variability within ecological levels of organization from individuals to ecosystems. In disease ecology, variability in biotic and abiotic factors can result in heterogeneous patterns of transmission and virulence—broadly defined here as the negative consequences of infection. Still, our classic theoretical understanding of disease dynamics comes from models that assume homogeneous transmission and virulence. Here, we test this assumption by assessing the contribution of various sources of individual and spatial heterogeneity to patterns of transmission and sublethal measurements of virulence in two lizard–malaria systems: a three‐parasite assemblage (Plasmodium floridense,Plasmodium leukocytica, andPlasmodium azurophilum) infecting the lizardAnolis gundlachiin the rainforest of Puerto Rico and a single‐parasite system (P. floridense–Anolis sagrei) in Florida. Using a Bayesian model selection framework, we evaluated whether individual host differences (i.e., body size and sex) or spatial variability (i.e., habitat type and local‐scale host spatial structure) drive heterogeneity in the probability of infection or its associated health costs (i.e., body condition, blood chemistry). We found that the probability of infection increases with increasing lizard body size in both systems. However, in Florida, we found the relationship to be subdued in deforested habitats compared to the adjacent urban hydric forests. Furthermore, infection was spatially clustered within sampling sites, with “hot” and “cold” spots across the landscape. Nevertheless, we found no clear evidence of costs of infection on lizard health in any of the measures assessed and hence no grounds for inference regarding heterogeneous virulence. Ultimately, the consistency of our results across systems suggests prominent roles of individual and spatial heterogeneities as driving factors of transmission of vector‐borne diseases.
β‐diversity in temperate grasslands is driven by stronger environmental filtering of plant species with large genomes
Authors: Zhang Hai‐Yang , Lü Xiao‐Tao , Wei Cun‐Zheng , Powell Jeff R. , Wang Xiao‐Bo , Xing Ding‐Liang , Xu Zhu‐Wen , Li Huan‐Long , Han Xing‐Guo
Published: December 2022

Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS) has long been hypothesized to potentially affect species' capacity to tolerate environmental stress and might therefore help drive community assembly. However, its role in driving β‐diversity (i.e., spatial variability in species composition) remains unclear. We measured GS for 161 plant species and community composition across 52 sites spanning a 3200‐km transect in the temperate grasslands of China. By correlating the turnover of species composition with environmental dissimilarity, we found that resource filtering (i.e., environmental dissimilarity that includes precipitation, and soil nitrogen and phosphorus concentrations) affected β‐diversity patterns of large‐GS species more than small‐GS species. By contrast, geographical distance explained more variation of β‐diversity for small‐GS than for large‐GS species. In a 10‐year experiment manipulating levels of water, nitrogen, and phosphorus, adding resources increased plant biomass in species with large GS, suggesting that large‐GS species are more sensitive to the changes in resource availability. These findings highlight the role of GS in driving community assembly and predicting species responses to global change.
A Biomass‐Ligand‐Based Ru(III) Complex as a Catalyst for Cycloaddition of CO2 and Epoxides to Cyclic Carbonates and a Study of the Mechanism
Authors: Mao Haifang , Guo Manli , Fu Hongqing , Yin Kun , Jin Miaomiao , Wang Chaoyang , Zhao Yun , Dong Zhenbiao , Liu Jibo
Published: December 2022

Aiming highly efficient conversion of greenhouse gas CO2 to cyclic carbonates, a biomass Ru(III) Schiff base complex catalyst (SalRu) was constructed by employing a derivative of Lignin degradation (5‐aldehyde vanillin). The SalRu catalyst had a remarkable conversion for epoxides into corresponding cyclic carbonates even at atmospheric pressure of CO2 without the presence of co‐catalyst. As the condition at 120 °C and 2 MPa CO2 the conversion reached to 94 % with selectivity at 99 % after 8 h. 32 % cyclic carbonate production was obtained even under 0.2 MPa CO2 pressure. The epoxide activation and ring opening, CO2 insertion and cyclic carbonate formation were illuminated explicitly through the of characteristic absorption peaks changing, which further providing direct and visual evidence for the mechanism proposing. This study has important theoretical significance for the comprehensive utilization of environmental pollutants and energy.
Methods for large‐scale single mediator hypothesis testing: Possible choices and comparisons
Authors: Du Jiacong , Zhou Xiang , Clark‐Boucher Dylan , Hao Wei , Liu Yongmei , Smith Jennifer A. , Mukherjee Bhramar
Published: December 2022

Mediation hypothesis testing for a large number of mediators is challenging due to the composite structure of the null hypothesis, (: effect of the exposure on the mediator after adjusting for confounders; : effect of the mediator on the outcome after adjusting for exposure and confounders). In this paper, we reviewed three classes of methods for large‐scale one at a time mediation hypothesis testing. These methods are commonly used for continuous outcomes and continuous mediators assuming there is no exposure‐mediator interaction so that the product has a causal interpretation as the indirect effect. The first class of methods ignores the impact of different structures under the composite null hypothesis, namely, (1) ; (2) ; and (3) . The second class of methods weights the reference distribution under each case of the null to form a mixture reference distribution. The third class constructs a composite test statistic using the three p values obtained under each case of the null so that the reference distribution of the composite statistic is approximately . In addition to these existing methods, we developed the Sobel‐comp method belonging to the second class, which uses a corrected mixture reference distribution for Sobel's test statistic. We performed extensive simulation studies to compare all six methods belonging to these three classes in terms of the false positive rates (FPRs) under the null hypothesis and the true positive rates under the alternative hypothesis. We found that the second class of methods which uses a mixture reference distribution could best maintain the FPRs at the nominal level under the null hypothesis and had the greatest true positive rates under the alternative hypothesis. We applied all methods to study the mediation mechanism of DNA methylation sites in the pathway from adult socioeconomic status to glycated hemoglobin level using data from the Multi‐Ethnic Study of Atherosclerosis (MESA). We provide guidelines for choosing the optimal mediation hypothesis testing method in practice and develop an R package medScan available on the CRAN for implementing all the six methods.
Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis
Authors: von Berlin Leonie , Westholm Jakub Orzechowski , Ratz Michael , Frisén Jonas
Published: December 2022

Hippocampal adult neural stem cells emerge from progeny of the neuroepithelial lineage during murine brain development. Hippocampus development is increasingly well understood. However, the clonal relationships between early neuroepithelial stem cells and postnatal neurogenic cells remain unclear, especially at the single‐cell level. Here we report fate bias and gene expression programs in thousands of clonally related cells in the juvenile hippocampus based on single‐cell RNA‐seq of barcoded clones. We find evidence for early fate restriction of neuroepithelial stem cells to either neurogenic progenitor cells of the dentate gyrus region or oligodendrogenic, non‐neurogenic fate supplying cells for other hippocampal regions including gray matter areas and the Cornu ammonis region 1/3. Our study provides new insights into the phenomenon of early fate restriction guiding the development of postnatal hippocampal neurogenesis.
The indirect solar dryers with innovative solar air heaters designs: A review article
Authors: Jobair Hussein K. , Nima Mohammed A.
Published: December 2022

The drying process is considered an effective technique for preserving foods and agricultural products from spoilage. Moreover, the drying process lessens the products' weight, volume, and packaging, which prompts a reduction in the products' transportation costs. The drying technique with solar energy represents an ancient method, still alluring due to solar energy abundance and cost‐effectiveness. In this article, the previous manuscripts concerned with studying and analyzing indirect solar dryer systems that utilize innovative solar air heaters (SAHs) are reviewed. The results and conclusions are discussed intensively to clarify the significance of utilizing this type of drying technique. The effect of many parameters on the thermal performance and efficiency of the dryer systems has been investigated. The investigated parameters included the incident solar radiation, air flow rates, outlet solar air heater temperature, absorber plate material, moisture content of the agricultural products, and the shape and configuration of the SAH. Moreover, the manuscript outlines the drying rate mathematical models that were used to validate the experimental findings. Based on the review, it is found that solar dryer systems with modified SAHs designs rather than flat plate SAH have considerable effects on enhancing thermal performance and efficiency.