bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profile of the southern corn billbug, Sphenophorus callosus Oliver, an important pest of corn in eastern North Carolina
Authors: Reisig Dominic 
Published: January 2025

Abstract
Southern corn billbug Sphenophorus callosus Oliver, was a historically widespread and damaging pest throughout the southeastern United States. However, it only persists as a major problem in poorly drained corn production areas in eastern North Carolina. Unfortunately, little replicated research has been conducted on this insect in corn since the 1980s. The purpose of this profile is to provide a current, comprehensive resource on the biology and ecology of this pest relative to corn, as well as to provide a description of sampling and management methods. This is a univoltine insect with a narrow host range. The only known cultivated host it will reproduce on is corn, Zea mays L., and yellow nutsedge, Cyperus esculentus L. Injury and damage to corn can be caused by adult feeding on seedlings, or by larval development in the crown. The most effective management tactics for southern corn billbug are cultural management tactics, including crop rotation, tillage, proper fertility, drainage, and effective weed control. Neonicotinoid seed treatments are the most important management tactic for this pest, but their efficacy is declining. Hence, this pest may become more problematic across the southeastern United States. A significant portion of the biological research on this insect needs to be revisited within the context of modern corn production practices. Furthermore, more work should be done to understand the mechanisms for effective cultural management tactics. Finally, novel methods of management should be explored for this insect to expand the range of available management tactics.
Assessing the potential economic impacts of spotted lanternfly (Hemiptera: Fulgoridae) infestations on grape production in New York State
Authors: Pinto Allan F , Eshenaur Brian C , Acevedo Flor E , Calixto Alejandro A , Centinari Michela , Gómez Miguel I 
Published: January 2025

Abstract
Lycorma delicatula, known as the spotted lanternfly, an insect native to Asia, feeds on a broad range of plant species in the United States, including tree of heaven, black walnut, silver and red maple, and grapes. As of early 2024, grape growers in New York State have not reported spotted lanternfly-related issues. In contrast, growers in Pennsylvania experienced significant losses during the early years of infestation, with some vineyards replanting due to vine death caused by spotted lanternfly. Over time, Pennsylvania growers developed management strategies, but the threat remains significant. We hypothesize that New York grape growers, informed by the economic impacts faced by Pennsylvania growers, will adopt a risk-averse approach and will be better prepared to combat spotted lanternfly. This manuscript examines spotted lanternfly biology, life stages, and host plants while estimating potential economic impacts to inform growers, stakeholders, and policymakers about the potential economic losses in New York grape production. If left uncontrolled or if growers are uninformed and unprepared, economic losses in the Lake Erie and Finger Lakes regions could escalate significantly, reaching up to $1.5, $4, and $8.8 million in the first, second, and third years of infestation, respectively. These figures underscore the critical importance of proactive management and preparedness measures to mitigate the impact of spotted lanternfly infestations on agricultural economies. We also discuss the implication of these findings in management and regulatory efforts. Future research should focus on establishing the appropriate economic thresholds and conducting cost–benefit analyses of various pest control measures in grape production in New York.
Where is the Limit? Assessing the Potential of Algorithm-Based Cartel Detection
Authors: Wallimann Hannes , Emmenegger Solange , Pouly Marc , Wegelin Philipp 
Published: January 2025

Abstract
Academic research on cartel detection has primary focused on algorithm-based screening of markets. However, only a few studies have assessed the extent to which competition authorities can generalize from a developed model to new markets. In our paper, we aim to fill this gap by investigating how close a market on which an algorithm is trained has to be to detect cartels in a new market. Our results confirm that when comparable training data are available, the machine-learning-based models are powerful tools to flag cartels. However, we show that the algorithms’ performances are limited when lacking comparable training data from the same industry, leading to the conclusion that practitioners should exercise a great deal of caution when choosing training data from different industries for cartel screening. In addition to our main contribution, we present a way of automated feature engineering and selection based on frequently used hand-crafted screens (descriptive statistics derived from firms’ prices) that are generally used in the recent cartel screening literature of algorithm-based cartel detection. Finally, to overcome the prerequisite of any pre-defined screen, we present the first-time application of various recurrent neural network architectures together with raw price data to flag potential cartels.
Repurposing the familiar: Future treatment options against chronic kidney disease
Authors: Bhadange Rohan , Gaikwad Anil Bhanudas 
Published: January 2025

Abstract

Objectives
Chronic kidney disease (CKD) is a serious health issue with rising morbidity and mortality rates. Despite advances in understanding its pathophysiology, effective therapeutic options are limited, necessitating innovative treatment approaches. Also, current frontline treatments that are available against CKD are not uniformly effective and often come with significant side effects. Therefore, identifying new therapeutic targets or improving existing treatments for CKD is crucial. Drug repurposing is a promising strategy in the drug discovery process that involves screening existing approved drugs for new therapeutic applications.

Key findings
This review discusses the pharmacological mechanisms and clinical evidence that support the efficacy of these repurposed drugs. Various drugs classes such as inodilators, endothelin-1 type A (ET-1A) receptor antagonists, bisphosphonates, mineralocorticoid receptor (MR) antagonists, DNA demethylating agents, nuclear factor erythroid 2-related factor 2 (NRF2) activators, P2X7 inhibitors, autophagy modulators, hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHI) are discussed that could remarkably contribute against CKD.

Summary
The review critically examines the potential for repurposing well-established drugs to slow the progression of CKD and enhance patient outcomes. This review emphasizes the importance of a multidisciplinary approach in advancing the field of drug repurposing, ultimately paving the way for innovative and effective therapies for patients suffering from CKD.
Long-term survival of stage 4 gallbladder cancer after extended radical surgery plus limited chemotherapy: a case report
Authors: Huang Zhengbin , Sun Jian , Li Changsong , Chen Sheng , Jin Tian , Wu Zhengqi 
Published: January 2025

Abstract
Gallbladder cancers (GBC) are insidious, malignant, and associated with poor prognosis, with a 5-year survival rate of 5%. Long-term survival in advanced GBC is rare. Here, we report a case of a 45-year-old female who presented with intermittent right upper quadrant pain for 1 month. A gallbladder mass and two liver masses were identified on a computed tomography (CT) scan of the abdomen and pelvis with intravenous contrast, which was highly suspicious for GBC. The patient underwent extended radical surgery, and a low to moderately differentiated gallbladder adenocarcinoma was diagnosed through pathology. Postoperatively, the patient received chemotherapy with gemcitabine and cisplatin but only tolerated one cycle. The patient has been disease-free for over 7 years, representing an unusually long survival.
DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach
Authors: Wirecki Tomasz K , Lach Grzegorz , Badepally Nagendar Goud , Moafinejad S Naeim , Jaryani Farhang , Klaudel Gaja , Nec Kalina , Baulin Eugene F , Bujnicki Janusz M 
Published: January 2025

Abstract
Designing RNA sequences that form a specific structure remains a challenge. Current computational methods often struggle with the complexity of RNA structures, especially when considering pseudoknots or restrictions related to RNA function. We developed DesiRNA, a computational tool for the design of RNA sequences based on the Replica Exchange Monte Carlo approach. It finds sequences that minimize a multiobjective scoring function, fulfill user-defined constraints and minimize the violation of restraints. DesiRNA handles pseudoknots, designs RNA–RNA complexes and sequences with alternative structures, prevents oligomerization of monomers, prevents folding into undesired structures and allows users to specify nucleotide composition preferences. In benchmarking tests, DesiRNA with a default simple scoring function solved all 100 puzzles in the Eterna100 benchmark within 24 h, outperforming all existing RNA design programs. With its ability to address complex RNA design challenges, DesiRNA holds promise for a range of applications in RNA research and therapeutic development.
The SARS-CoV-2 nucleocapsid protein interferes with the full enzymatic activation of UPF1 and its interaction with UPF2
Authors: Nuccetelli Veronica , Mghezzi-Habellah Makram , Deymier Séverine , Roisin Armelle , Gérard-Baraggia Francine , Rocchi Cecilia , Coureux Pierre-Damien , Gouet Patrice , Cimarelli Andrea , Mocquet Vincent , Fiorini Francesca 
Published: January 2025

Abstract
The nonsense-mediated mRNA decay (NMD) pathway triggers the degradation of defective mRNAs and governs the expression of mRNAs with specific characteristics. Current understanding indicates that NMD is often significantly suppressed during viral infections to protect the viral genome. In numerous viruses, this inhibition is achieved through direct or indirect interference with the RNA helicase UPF1, thereby promoting viral replication and enhancing pathogenesis. In this study, we employed biochemical, biophysical assays and cellular investigations to explore the interplay between UPF1 and the nucleocapsid (Np) protein of SARS-CoV-2. We evaluated their direct interaction and its impact on inhibiting cellular NMD. Furthermore, we characterized how this interaction affects UPF1’s enzymatic function. Our findings demonstrate that Np inhibits the unwinding activity of UPF1 by physically obstructing its access to structured nucleic acid substrates. Additionally, we showed that Np binds directly to UPF2, disrupting the formation of the UPF1/UPF2 complex essential for NMD progression. Intriguingly, our research also uncovered a surprising pro-viral role of UPF1 and an antiviral function of UPF2. These results unveil a novel, multi-faceted mechanism by which SARS-CoV-2 evades the host’s defenses and manipulates cellular components. This underscores the potential therapeutic strategy of targeting Np-UPF1/UPF2 interactions to treat COVID-19.
Cold suppresses virus accumulation and alters the host transcriptomic response in the turnip mosaic virus–Arabidopsis halleri system
Authors: Honjo Mie N , Emura Naoko , Kamitani Mari , Kudoh Hiroshi 
Published: January 2025

Abstract
Since plant viruses cause lifelong infections, virus–plant interactions are exposed to large temperature fluctuations in evergreen perennials. In such circumstances, virus–plant interactions are expected to change significantly between the warm and cold seasons. However, few studies have investigated the effects of cold temperatures on virus–plant interactions. Here, we show that in a persistent infection system of the turnip mosaic virus (TuMV)–Arabidopsis halleri, cold temperatures lead to slow viral replication/spreading within the host, attenuated host symptoms, and cold-specific transcriptomic responses. Many differentially expressed genes (DEGs) were detected between virus-inoculated and mock-inoculated plants under warm and cold conditions; however, the sets of DEGs and response timings were temperature-dependent. At cold temperatures, the expression of photosynthesis-related genes decreased in the early stages of infection. However, it recovered to the same level as that in uninfected plants in the later stages. In contrast, the transcriptomic changes under warm conditions suggest that viral infections cause auxin signaling disruption. These responses coincided with the inhibition of host growth. We identified 6 cold- and 38 warm-specific DEGs, which changed their expression in response to TuMV infection under more than half of the conditions for either cold or warm temperatures. Further validation of the putative relationships between transcriptomic and phenotypic responses of the host is required. Our findings on temperature-dependent host responses at both symptomatic and transcriptomic levels help us understand how warm and cold temperatures affect virus–plant interactions in seasonal environments.
A novel classifier of radiographic knee osteoarthritis for use on knee DXA images is predictive of joint replacement in UK Biobank
Authors: Beynon Rhona A , Saunders Fiona R , Ebsim Raja , Faber Benjamin G , Jung Mijin , Gregory Jennifer S , Lindner Claudia , Aspden Richard M , Harvey Nicholas C , Cootes Timothy , Tobias Jonathan H 
Published: January 2025

Abstract

Objectives
DXA scans may offer a novel means of evaluating radiographic knee OA (rKOA) in large population studies and through opportunistic screening. We aimed to develop and apply a semi-automated method for assessing rKOA using ≈20 000 knee DXA images from UK Biobank (UKB) and assess its face validity by checking for expected relationships with clinical outcomes.

Methods
Right knee DXA scans were manually annotated for osteophytes to derive corresponding grades. Joint space narrowing (JSN) grades in the medial joint compartment were determined from automatically measured minimum joint space width. Overall rKOA grade (0–4) was determined by combining osteophyte and JSN grades. Logistic regression was employed to investigate the associations of osteophyte, JSN and rKOA grades with knee pain and hospital-diagnosed KOA. Cox proportional hazards modelling was used to examine the associations of these variables with risk of subsequent total knee replacement (TKR).

Results
Of the 19 595 participants included (mean age 63.7 years), 19.5% had rKOA grade ≥1 (26.1% female, 12.5% male). Grade ≥1 osteophytes and grade ≥1 JSN were associated with knee pain, hospital-diagnosed KOA and TKR. Higher rKOA grades were linked to stronger associations with these clinical outcomes, with the most pronounced effects observed for TKR. Hazard ratios for the association of rKOA grades with TKR were 3.28, 8.75 and 28.63 for grades 1, 2 and 3–4, respectively.

Conclusions
Our DXA-derived measure of rKOA demonstrated a progressive relationship with clinical outcomes. These findings support the use of DXA for classifying rKOA in large epidemiological studies and in future population-based screening.
Hearing loss occurs prior to thrombocytopenia in both mice and humans with DFNA1
Authors: Kurasawa Shunkou , Ganaha Akira , Ayabe Shinya , Yoshiki Atsushi , Kawama Fumiya , Kitayama Shota , Tabuchi Keiji , Yamashita Kouhei , Ueyama Takehiko 
Published: January 2025

AbstractDFNA1 (deafness, nonsyndromic autosomal dominant 1), initially identified as nonsyndromic sensorineural hearing loss, has been associated with an additional symptom: macrothrombocytopenia. However, the timing of the onset of hearing loss (HL) and thrombocytopenia has not been investigated, leaving it unclear which occurs earlier. Here, we generated a knock‐in (KI) DFNA1 mouse model, diaphanous‐related formin 1 (DIA1)KIΔv3/KIΔv3, in which Aequorea coerulescens green fluorescent protein (AcGFP)‐tagged human DIA1(p.R1213X) was knocked into the ATG site of Dia1. Additionally, the exon 7 of Dia1 was deleted using genome editing to knock out (KO) Dia1‐v3, a specific variant of Dia1. AcGFP‐DIA1(p.R1213X) expression and endogenous DIA1 KO were confirmed in cochleae and platelets. Hearing function in DIA1KIΔv3/KIΔv3, but not DIA1KIΔv3/+ mice, evaluated by auditory brainstem response, was significantly worse at low frequencies compared to wild‐type (WT) mice starting at 3 months of age (3M), with progressive deterioration. Using confocal microscopy and scanning electron microscopy, various stereociliary deformities were identified in the cochleae of DIA1KIΔv3/KIΔv3 mice. Platelet counts in DIA1KIΔv3/KIΔv3, but not DIA1KIΔv3/+ mice, were significantly lower than those in WT mice at 12M, but not at 6M. Furthermore, in a cohort of eight patients with DFNA1 harboring the p.R1213X mutation, HL preceded thrombocytopenia in three individuals. Thus, in both mice and humans, though HL and thrombocytopenia are progressive, HL manifests earlier than thrombocytopenia. Unlike myosin heavy chain 9 (MYH9)‐related diseases, thrombocytopenia cannot be a predictive marker for HL in DFNA1. Nevertheless, monitoring platelet counts could provide insights into the progression of the hearing impairments in patients with DFNA1.
Aerobic exercise regulates gut microbiota profiles and metabolite in the early stage of Alzheimer's disease
Authors: Wei Cuilan , Wu Xiaojing , Li Chuikun , Zhang Yeting , Yuan Qiongjia , Huang Rui 
Published: January 2025

AbstractAerobic exercise (AE) has been shown to offer significant benefits for Alzheimer's disease (AD), potentially influencing the gut microbiota. However, the impact of changes in intestinal flora in early Alzheimer's disease induced by aerobic exercise on metabolic pathways and metabolites is not well understood. In this study, 3‐month‐old APP/PS1 and C57BL/6 mice were divided into two groups each: a control group (ADC for APP/PS1 and WTC for C57BL/6) and an aerobic exercise group (ADE for APP/PS1 and WTE for C57BL/6). The exercise groups underwent a 20‐week aerobic training program on a motorized treadmill before the behavioral test (both the Morris water maze experiment (MWM) and the eight‐arm maze test). Fecal samples were collected to analyze gut microbiota profiles via 16S rRNA gene sequencing. At the same time, the metabolic pathway analysis and the detection of metabolites were carried out. At the phylum level, the ADE group exhibited a significant reduced in the relative abundance of Bacteroidetes compared to the ADC group. At the genus level, both Ileibacterium and Faecalibaculum were found to be more abundant in the ADE group than in the ADC group. Additionally, PICRUSt analysis revealed that lipid metabolism and bile acid metabolism pathways were significantly enriched in the cecal microbiota of mice in the ADE group. The metabolites detected further confirmed the changes in the metabolic pathways mentioned above. Aerobic exercise may modify gut microbiota profiles and metabolites in APP/PS1 mice, thereby potentially playing a beneficial role in delaying cognitive impairment associated with early‐stage Alzheimer's disease.
TRAF6 promotes abdominal aortic aneurysm development by activating macrophage pyroptosis via the NLRP3/Caspase1/GSDMD pathway
Authors: Cai Huoying , Li Huaming , Xiao Xiaoyong , Wang Siwen , Liu Ruiming , Qin Yuansen , Zhou Yu , Yao Chen 
Published: January 2025

AbstractAbdominal aortic aneurysm represents a critical pathology of the aorta that currently lacks effective pharmacological interventions. TNF receptor‐associated factor 6 (TRAF6) has been established to be involved in cardiovascular diseases such as atherosclerosis, hypertension, and heart failure. However, its role in abdominal aortic aneurysm (AAA) remains unclear. This study aimed to explore the role of TRAF6 on AAA formation and its underlying mechanisms. Single‐cell RNA sequencing of human AAA tissues demonstrated that TRAF6 was significantly upregulated in aortic macrophages. Moreover, overexpression of TRAF6 promotes AAA formation in elastase‐induced C57BL/6 mice, while TRAF6 pharmacological inhibition could attenuate AAA development. Consistently, inhibition of TRAF6 in macrophages through in vitro methods notably limits their pyroptosis, while also diminishing proinflammatory responses in these cells. Mechanistically, TRAF6 can modulate macrophage pyroptosis through the NLRP3/Caspase1/GSDMD signaling pathway. Our study highlights the crucial role of the TRAF6/NLRP3/Caspase1/GSDMD axis in macrophage pyroptosis and AAA, offering potential biomarkers and therapeutic targets for AAA.
m6A demethylase Fto inhibited macrophage activation and glycolysis in diabetic nephropathy via m6A/Npas2/Hif‐1α axis
Authors: Zhu Sai , Jiang Ling , Liu Xinran , Chen Chaoyi , Luo Xiaomei , Jiang Shan , Yin Jiuyu , Liu Xueqi , Wu Yonggui 
Published: January 2025

AbstractMacrophage infiltration and activation is a key factor in the progression of diabetic nephropathy (DN). However, aerobic glycolysis induced by m6A methylation modification plays a key role in M1‐type activation of macrophages, but the specific mechanism remains unclear in DN. In this study, the expression of m6A demethylase Fto in bone marrow derived macrophages and primary kidney macrophages from db/db mice. Loss and gain‐of‐function analysis of Fto were performed to assess the role of Fto in DN. Transcriptome and MeRIP‐seq association analysis was performed to identified the target gene was Npas2. In this study, we found that demethylase Fto exhibits low expression in type 2 DN m6A modification of Npas2 mediated by Fto regulates macrophages M1‐type activation and glucose metabolism reprogramming to participate in the process of DN. Furthermore, Fto reduces the m6A modification level of Npas2 in macrophages through a Prrc2a‐dependent mechanism, and decreasing its stability. This process mediates inflammation and glycolysis in M1 macrophages by regulating the Hif‐1α signaling pathway. Fto may act as a suppressor of M1 macrophages inflammation and glycolysis in DN through the m6A/Npas2/Hif‐1α axis. This findings providing a new basis for the prevention and treatment of DN.