bluuebunny/crossref_metadata_2025_split huggingface dataset:
A widely distributed epifaunal clam, Chama macerophylla, exhibits compensatory responses to ocean warming and acidification
Authors: Kirkland Amanda , Frick Alanna J , Beaulieu Haley R , Granier Mark , Price Bennett H , Wiley John B , Boyle Kelly S , Cox T. Erin 
Published: August 2024

Abstract

Global ocean change can negatively impact bivalves, that serve to increase microhabitat and clarify waters in coastal ecosystems. Although effects of global stressors on commercial bivalves have been studied, predicting effects on non-commercial species is challenging due to species-specific responses and potential for synergistic or antagonistic effects when stressors are combined. We assessed the impact of global ocean change on the leafy jewel box clam, Chama macerophylla, a widely distributed epifaunal species. We focused on clams in the northern Gulf of Mexico, where amplified warming and acidification are anticipated. We hypothesized adult clams would experience heightened physiological stress when exposed to warming and acidification, with synergistic effects to combined stressors. Moderate and extreme stressor(s) used in experiments were seldom to never recorded in clam habitat. Yet, 98% of clams survived a 30-day laboratory exposure to single and combined stressor(s). Shells were bimineralic and no alterations in mineral composition were observed. Initially, clams at ambient carbonate chemistry showed increased respiration with higher temperatures, that were subsequently lower by day 30. Notably, clams, when at a constant ambient temperature, exhibited the highest calcification in the most acidic waters, suggesting a compensatory mechanism. When both stressors were present, respiration did not increase as expected with warmer temperatures, and extreme conditions led to variable calcification. Physiological responses from multi-stressor experiments were not statistically relatable to the stress condition, making it challenging to discern impacts of multi-stressors. This study highlights the importance of understanding adaptive mechanisms and long-term stress on bivalves crucial to benthic-pelagic coupling.
Widespread impact of transposable elements on the evolution of posttranscriptional regulation in the cotton genus Gossypium
Authors: Tian Xuehan , Wang Ruipeng , Liu Zhenping , Lu Sifan , Chen Xinyuan , Liu Fang , Zhang Xianlong , Wang Maojun 
Published: August 2024

Abstract

Transposable element (TE) expansion has long been known to mediate genome evolution and phenotypic diversity in organisms, but its impact on the evolution of posttranscriptional regulation following species divergence remains unclear. To address this issue, we performed long-read direct RNA sequencing, polysome profiling sequencing, and small RNA sequencing in the cotton genus Gossypium, the species of which range more than 3-fold in genome size. We found that TE expansion contributed to the turnover of transcription splicing sites and regulatory sequences, leading to changes in alternative splicing patterns and the expression levels of orthologous genes. We also found that TE-derived uORFs (upstream open reading frames) and microRNAs (miRNAs) served as regulatory elements mediating differences in the translation levels of orthologous genes. We further identified genes that exhibited lineage-specific divergence at the transcriptional (5,694 genes), splicing (5,255 genes) and translational (5,570 genes) levels, and showcased the high flexibility and fluidity of gene expression regulation in the evolutionary process. Our work highlights the significant role of TE in driving posttranscriptional regulation divergence in the cotton genus, and offers insights for deciphering the evolutionary mechanisms of cotton species and the formation of biological diversity.
Vapor pressure deficit control and mechanical vibration techniques to induce self-pollination in strawberry flowers
Authors: Lee Hyein , Cui Meiyan , Lee Byungkwan , Myung Jeesang , Shin Jaewook , Chun Changhoo 
Published: August 2024

Abstract

Background
Pollination strategies to supplement or replace insect pollinators are needed to produce marketable strawberry fruits in indoor vertical farms. To ensure the self-pollination of strawberry flowers, we investigated the anther dehiscence and pollen attachment under different vapor pressure deficit (VPD) conditions and external mechanical sine wave vibrations.
Results
The proportion of dehisced anthers was examined under VPDs of 2.06, 1.58, and 0.33 kPa, and the projected area of pollen clumps was assessed under VPDs of 2.06 and 0.33 kPa. After exposing flowers to a VPD of 0.33 kPa, vibrations with various frequency (Hz) and root mean square acceleration (m s−2) combinations were used to evaluate pollination effectiveness. The anthers underwent complete dehiscence at VPDs of 2.06, 1.58, and 0.33 kPa. The projected area of the pollen clump was larger at a VPD of 0.33 than that at 2.06 kPa. Pollen clump detachment was effective at 100 and 800 Hz with 40 m s−2, while pollen attachment to the stigma was most effective at 100 Hz.
Conclusions
These findings suggest that environmental control strategies and specific vibration characteristics can successfully aid strawberry flower pollination. This study provides fundamental insights into mechanical vibration pollination systems for fruit production in indoor vertical farming.
Leading anti-tick vaccine targets are variably conserved in cattle fever ticks
Authors: Busch Joseph D. , Stone Nathan E. , Pemberton Grant L. , Roberts Mackenzie L. , Turner Rebekah E. , Thornton Natalie B. , Sahl Jason W. , Lemmer Darrin , Buckmeier Greta , Davis Sara K. , Guerrero-Solorio Roberto I. , Karim Shahid , Klafke Guilherme , Thomas Donald B. , Olafson Pia U. , Ueti Massaro , Mosqueda Juan , Scoles Glen A. , Wagner David M. 
Published: August 2024

Abstract

Background
Rhipicephalus (Boophilus) microplus causes significant cattle production losses worldwide because it transmits Babesia bovis and B. bigemina causative agents of bovine babesiosis. Control of these ticks primarily has relied on treatment of cattle with chemical acaricides, but frequent use, exacerbated by the one-host life cycle of these ticks, has led to high-level resistance to multiple classes of acaricides. Consequently, new approaches for control, such as anti-tick vaccines, are critically important. Key to this approach is targeting highly conserved antigenic epitopes to reduce the risk of vaccine escape in heterologous tick populations.
Methods
We evaluated amino acid conservation within 14 tick proteins across 167 R. microplus collected from geographically diverse locations in the Americas and Pakistan using PCR amplicon sequencing and in silico translation of exons.
Results
We found that amino acid conservation varied considerably across these proteins. Only one target, the voltage-dependent anion channel, was fully conserved in all 167 R. microplus samples (protein similarity 1.0). Five other proteins were highly conserved: the aquaporin RmAQP1 (0.989), vitellogenin receptor (0.985), serpin-1 (0.985), and subolesin (0.981). In contrast, the glycoprotein protease Bm86 was one of the least conserved (0.889). The Bm86 sequence used in the original Australian TickGARD vaccine carried many amino acid replacements compared to the R. microplus populations examined here, supporting the hypothesis that this vaccine target is not optimal for use in the Americas. By mapping amino acid replacements onto predicted 3D protein models, we also identified amino acid changes within several small peptide vaccines targeting portions of the aquaporin RmAQP2, chitinase, and Bm86.
Conclusions
These findings emphasize the importance of thoroughly analyzing protein variation within anti-tick vaccine targets across diverse tick populations before selecting candidate vaccine antigens. When considering protein conservation alone, RmAQP1, vitellogenin receptor, serpin-1, subolesin, and especially the voltage-dependent anion channel rank as high priority anti-tick vaccine candidates for use in the Americas and perhaps globally.
Interrogating Data-Independent Acquisition LC-MS/MS for affinity proteomics
Authors: Tabb David L. , Kaniyar Mohammed Hanzala , Bringas Omar Rosas , Shin Heaji , Stefano Luciano , Taylor Martin S. , Xie Shaoshuai , Yilmaz Omer H. , LaCava John 
Published: August 2024

Abstract

Data-Independent Acquisition (DIA) LC-MS/MS is an attractive partner for co-immunoprecipitation (co-IP) and affinity proteomics in general. Reducing the variability of quantitation by DIA could increase the statistical contrast for detecting specific interactors versus what has been achieved in Data-Dependent Acquisition (DDA). By interrogating affinity proteomes featuring both DDA and DIA experiments, we sought to evaluate the spectral libraries, the missingness of protein quantity tables, and the CV of protein quantities in six studies representing three different instrument manufacturers. We examined four contemporary bioinformatics workflows for DIA: FragPipe, DIA-NN, Spectronaut, and MaxQuant. We determined that (1) identifying spectral libraries directly from DIA experiments works well enough that separate DDA experiments do not produce larger spectral libraries when given equivalent instrument time; (2) experiments involving mock pull-downs or IgG controls may feature such indistinct signals that contemporary software will struggle to quantify them; (3) measured CV values were well controlled by Spectronaut and DIA-NN (and FragPipe, which implements DIA-NN for the quantitation step); and (4) when FragPipe builds spectral libraries and quantifies proteins from DIA experiments rather than performing both operations in DDA experiments, the DIA route results in a larger number of proteins quantified without missing values as well as lower CV for measured protein quantities.
Jan Sjödin faba bean mutation collection: status and molecular characterization
Authors: Khazaei Hamid , Carlson-Nilsson Ulrika , Schulman Alan H. 
Published: August 2024

Abstract

Background
Plant mutagenesis creates novel alleles that increase genetic diversity and enhance crop resilience, productivity, and sustainability. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We phenotyped and genotyped a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934–2023) over half a century ago. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays.
Results
In this study, we used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genetically characterize 52 mutant lines along with the background line, cv. Primus. A range of flowers, seeds, leaves, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype.
Conclusions
Given the high marker density, our findings support the power of SPET for faba bean genotyping. Our results will be useful for breeding and genetic studies in faba bean.
From Image to Insight: Deep Learning Solutions for Accurate Identification and Object Detection of Acorus Species Slices
Authors: Liu Yinghui , Liu Haitao , Li Linlan , Ding Ying 
Published: August 2024

Abstract

Given the morphological similarity and medicinal efficacy differences between Acorus tatarinowii Rhizoma and Acorus calamus Rhizoma, both belonging to the Acorus rhizome slices, as well as the phenomenon of their mixed use in the market, this study aims to achieve high-precision classification and rapid object detection of these two Acorus Species Slices using deep learning technology, thus enhancing the accuracy and efficiency of Traditional Chinese Medicine (TCM) identification. The study constructed a high-quality dataset consisting of 1,928 rigorously preprocessed and annotated images of Acorus tatarinowii Rhizoma and Acorus calamus Rhizoma specimens. The ResNet50 model was employed for classifying to improve classification accuracy. Furthermore, the YOLOv8 algorithm was utilized for object detection. Experimental results indicate that the ResNet50 model can accurately distinguish between Acorus tatarinowii Rhizoma and Acorus calamus Rhizoma decoction pieces, achieving a test set accuracy of 92.8%, thereby realizing precise classification. Meanwhile, the YOLOv8 algorithm achieved rapid object detection in mixed states of the two, with a detection accuracy of 98.6% and a detection frame rate of 22fps. This study successfully applied deep learning technology to the classification and object detection of TCM decoction pieces, providing an effective means for intelligent identification and management of Chinese medicinal materials.
A Linear Transconductance Cell with a Tunable Control Voltage for Variable Gain Amplifiers
Authors: Akbari Meysam 
Published: August 2024

Abstract

This paper proposes a highly linear transconductance cell with a widely tunable control voltage based on a bulk-driven technique. The transconductance is configured using a self-biasing structure to achieve high linear operation under control-voltage variations. In addition, the transistors of the input differential pair are driven from the bulk terminal to increase the input dynamic range and provide a low-voltage structure. A reference voltage is embedded to control the transistors' DC currents and balance the circuit's operation under unwanted variations such as corner cases. The proposed cell is simulated via 180-nm CMOS technology under a supply of 0.5 V. The simulation results show that the DC gain changes from 0 dB to 14.2 dB for control-voltage variations in the range of 0–0.5 V. Moreover, the common mode input voltage can change from 0.125 V to 0.375 V without any degeneration in linearity, which results in a 0.25 V input dynamic range. The proposed cell consumes only 250 nW of power, which is suitable for ultralow-power applications.
Biodegradation of PAHs in drilling wastes from oil-contaminated soil using an isolated halotolerant bacterial consortium
Authors: Jaafarzadeh Neamatollah , Talepour Nastaran , Montazeri Effat Abbasi , Seyedali Seyed Rasoul , Ayalwar Sara , Pourabdi Nazanin , Ganjiazad Ehsan , chaghazardi Zahra , Mirzavand Morteza , pachelak Zahra Hatami , Veysi Zahra , Kaydi Neda , Noveiri Hoda , Jafarzadeh Zahra 
Published: August 2024

Abstract

Petroleum contaminants and fossil fuel activities contribute significantly to environmental pollution, especially in regions involved in oil production. Polyaromatic hydrocarbons (PAHs) in petroleum products are hazardous to the environment and human health because of their intricate chemical makeup and cancer-causing characteristics. In this study, we isolated and characterized bacterial strains from oil-contaminated soil using 16S rRNA analysis to evaluate their potential for degrading PAHs commonly found in drilling wastes. We also analyzed the PAH content in drilling cuttings and assessed the effectiveness of PAH biodegradation by the isolated bacterial consortium on real oil-drilled cutting samples. Additionally, a bioremediation consortium comprising Pseudomonas stutzeri, Pseudomonas aeruginosa, and Bacillus subtilis was used to remediate PAHs. This study suggests that indigenous bacteria contribute favorably to the process of PAH biodegradation. We observed that benzo(a)anthracene exhibited the fastest degradation rate among the tested compounds, while fluorene showed slower degradation than the other tested compounds. Importantly, the efficiency of all tested scenarios surpassed 97%, highlighting the efficacy of the bioremediation approach in reducing PAH contamination. These results underscore the potential of utilizing bacterial consortia for effective PAH remediation, contributing to the development of sustainable strategies for environmental remediation.
Modeling and application of urban waterlogging resilience assessment based on PSR–NES framework and analysis of driving mechanisms
Authors: Gao Yuqin , Xu Mengqi , Zheng Hang , Liu Yunping , Xu Jing 
Published: August 2024

ABSTRACT

Extreme weather events are escalating globally, intensifying urban waterlogging disasters and endangering inhabitants and assets while hindering socio-economic progress. This study explores factors hindering cities' waterlogging disaster mitigation using urban resilience theory. It introduces a pressure–state–response (PSR)–natural–economic–social (NES) assessment model to evaluate urban waterlogging resilience, focusing on Nanjing as a key city in flood control. Flood scenarios are simulated using the MIKE model for different rainstorm recurrence periods. Urban flooding resilience is assessed with a hybrid approach. Geodetector analysis identifies primary resilience drivers. Results validate the PSR–NES composite resilience index, showing complex resilience patterns across the study area. High-resilience areas are mainly in the east and southeast, while low-resilience areas cluster along roads and low-lying communities. Key resilience indicators include waterlogging duration, inundation depth, warning capacity, economic density, and road accessibility. These factors interact with nonlinear enhancements and synergies. The study's insights can identify urban management or flood defense infrastructure deficiencies, guiding tailored flood defense strategies for stakeholders.
To Explore Potential Natural Inhibitors of Cysteine Proteases to Combat Human African Trypanosomiasis and Chagas Disease
Authors: Saha Aloke , Pushpa  , Bagchi Soumya Ranjan , Samadder Asmita , Nandi Sisir 
Published: August 2024

Background:
Human African Trypanosomiasis (HAT), also known as sleeping
sickness, and Chagas disease are neglected tropical diseases caused by Trypanosoma brucei
and Trypanosoma cruzi, respectively. These diseases present significant challenges in treatment
due to the toxicity, low efficacy, and drug-resistant strains associated with current therapies.

Introduction:
Cysteine proteases play vital roles in the life cycles of these parasites, making
them potential targets for therapeutic intervention. Natural inhibitors sourced from plants, marine
organisms, and microorganisms show promise for developing novel therapies.

Methods:
This review surveys the potential of natural inhibitors as therapeutic agents against
HAT and Chagas disease. It compiles PubMed and PubChem information from various studies to
provide an overview of their activities and characteristics, including their ability to inhibit cysteine
proteases, modulate the host immune response, and interfere with other parasite proteins.

Results:
Several natural inhibitors, such as berberine, curcumin, and tannins, have been identified
and characterized. These inhibitors have demonstrated encouraging outcomes in both in
vitro and in vivo experiments, indicating their potential as therapeutic agents for HAT and
Chagas disease.

Conclusion:
Natural inhibitors of cysteine proteases offer a promising avenue for developing
novel therapies against HAT and Chagas disease. Further research is needed to identify additional
natural inhibitors and optimize their efficacy and safety for human use. The significance
of this study lies in its potential to contribute to the discovery of effective, safe, and affordable
treatments for these neglected tropical diseases.
Exploring the Therapeutic Potential of Tyrosol and Its Derivatives: A Comprehensive Review
Authors: DK Gokul Raj , Milan KL , Ramkumar Kunka Mohanram 
Published: August 2024

Abstract:
Tyrosol (Ty) and its derivatives have gathered considerable attention in recent
years due to their diverse pharmacological properties and potential therapeutic applications.
This comprehensive review aims to summarize the current understanding of the
therapeutic potential of Ty and its derivatives in combating various diseases, including
cancer, cardiovascular disease (CVD), neurodegenerative diseases, diabetes, and obesity.
This review highlights the multifaceted properties of Ty, including its pharmacokinetic
profile and pharmacological actions, which contribute to its efficacy against these prevalent
health conditions. Moreover, the antimicrobial and wound-healing effects of Ty
are explored, elucidating its potential for broader therapeutic utilization. While existing
studies provide evidence supporting the beneficial effects of Ty, gaps remain in our understanding
of its molecular mechanisms of action and the exploration of novel derivatives.
Future research efforts are thus critical for unraveling the full therapeutic potential
of Ty and its derivatives. Moreover, the synthesis of novel derivatives with enhanced efficacy
and improved bioavailability shows potential for addressing unmet medical
needs. This review emphasizes the necessity for ongoing research into Ty and its derivatives,
providing valuable insights into their potential as essential therapeutic agents for
addressing diverse health conditions.
Rosmanol Alleviates Myocardial Ischemia-Reperfusion Injury by Enhancing the Myocardial miR-126/VEGF/PI3K/AKT Signaling in STZ-Induced Diabetic Rats
Authors: Wu Menghai , Qi Huaxin , Li Jun , Velu Periyannan , Han Xia 
Published: August 2024

Background:
A major factor in type 1 diabetes mortality is Ischemic Heart Disease
(IHD). In order to treat IHD, blood flow must be restored to the heart, which results in myocardial
ischemia-reperfusion (MI/R) damage. While rosmanol inhibits MI/R damage, its role in diabetic-
MI/R (D-MI/R) injury remains unclear. Both microRNA (miR) 126 and the PI3K/AKT
signaling pathway have been linked to preventing MI/R damage.

Objective:
The objective of the present study was to investigate whether rosmanol inhibits DMI/
R-injury in diabetic rats and whether miR-126-phosphatidylinositol 3-kinase (PI3K)/ protein
kinase B axis (miR-126-PI3K/AKT) is implicated in this protective effect.

Methods:
For 30 days, diabetic rats received either distilled water or the drug rosmanol (40
mg/kg, orally) before being subjected to MI/R.

Results:
The findings from the current study demonstrated how rosmanol reduced MI/R damage
in rats with diabetes caused by streptozotocin (STZ). Using spectrophotometry, it was possible
to measure the decrease in myocardial enzyme levels, the rise in cardiac viability, the inhibition
of myocardial oxidative stress, the increase in cardiac function, and the detection of these
changes using a hemodynamic monitoring system. In addition, rosmanol augmented the miR-
126-PI3K/AKT in the hearts of ischemic rats. After stimulating the myocardial miR-126-
PI3K/AKT axis, our results showed that rosmanol protected the heart against MI/R in STZinduced
diabetic rats.

Conclusion:
According to the most recent research, rosmanol may be a useful tool in the therapy
of diabetic IHD since it is an effective agent against D-MI/R damage.