bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Methods for Vaccine Effectiveness Studies
Authors: Okoli George N , Cowling Benjamin J 
Published: October 2024

Abstract
Evaluating the impact of public health investments in vaccination programs is crucial for ensuring their efficiency and effectiveness. Vaccine effectiveness (VE) studies, such as those using the test-negative design, are commonly used to confirm the impact of vaccines and guide future improvements. The test-negative design, favored for its simplicity and cost efficiency, mitigates biases common in other epidemiologic study designs. However, its validity can be compromised by inconsistent symptom definitions and retrospective data application. Here we summarize recent findings that (1) highlight the need to address correlated vaccination behaviors when estimating VE, (2) suggest using negative control variables to reduce confounding, and (3) recommend accounting for infection history in VE studies to improve accuracy and reliability. These insights are important for refining VE estimation methods.
Gut microbiota carbon and sulfur metabolisms support Salmonella infections
Authors: Leleiwi Ikaia , Kokkinias Katherine , Kim Yongseok , Baniasad Maryam , Shaffer Michael , Sabag-Daigle Anice , Daly Rebecca A , Flynn Rory M , Wysocki Vicki H , Ahmer Brian M M , Borton Mikayla A , Wrighton Kelly C 
Published: October 2024

Abstract
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for seven members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that support Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.
The Emerging Role of GLP-1 Agonists in Burn Care: What Do We Know?
Authors: Manasyan Artur , Cannata Brigette , Ross Erin , Lasky Sasha , Stanton Eloise W , Malkoff Nicolas , Collier Zachary , Johnson Maxwell B , Gillenwater Timothy Justin 
Published: October 2024

Abstract
Glucagon-like peptide-1 (GLP-1) agonists mimic the action of GLP-1, a hormone that regulates blood glucose levels via stimulation of insulin release and inhibition of glucagon secretion. After the burn, the current literature suggests that the use of GLP-1 agonists results in less insulin dependence with similar glucose control and hypoglycemic events to patients receiving a basal-bolus insulin regimen. Glucagon-like peptide-1 agonists may also promote wound healing through various mechanisms including angiogenesis and improved keratinocyte migration. Despite the potential benefits, GLP-1 agonists reduce gastrointestinal motility which impacts their widespread adoption in burn care. This dysmotility can result in inadequate nutrition delivery, unintentional weight loss, and is a potential aspiration risk. The net impact of these medications on patients with burns is unclear. Given their potential to demonstrate the safety, efficacy, and optimal dosing of various GLP-1 agonists in acute burn management.
Pre-stack seismic inversion based on one-dimensional GRU combined with two-dimensional improved ASPP
Authors: Chen Xiao , Li Shu , Wei Zong , Ning Juan , Yang Xi 
Published: October 2024

Abstract
Pre-stack seismic inversion is essential to detailed stratigraphic interpretation of seismic data. Recently, various deep learning methods have been introduced into pre-stack inversion, effectively capturing the vertical correlations of seismic data. However, existing deep learning methods face challenges such as insufficient feature extraction, poor lateral continuity, and unclear inversion details. We introduce the atrous spatial pyramid pooling (ASPP) module into the pre-stack inversion process, modifying the connection order and mode of its three components. Additionally, we incorporate a triplet attention module to extract features at different scales and utilize a gate recurrent unit (GRU) module to extract global information. During the network training stage, we employ a multi-gather simultaneous inversion method, combining one- and two-dimensional inversions. The proposed method is named IGIT (I for improved ASPP, G for GRU, I for initial model, and T for triplet attention). To verify the feasibility of this network model, we evaluate it using the Marmousi2 model, SEAM model, and field data, comparing the results with other deep learning methods. Experimental results demonstrate that the IGIT not only improves lateral continuity but also delivers accurate and clear inversion details. Notably, the inversion effect for density parameters shows significant enhancement.
Acceptance characterization of electron detector in SEM using stainless steel sphere
Authors: Sekiguchi Takashi , Yao Yuanzhao , Sonoda Ryosuke , Sohda Yasunari 
Published: October 2024

Abstract
Although modern scanning electron microscope (SEM) possesses several electron detectors, it is not clear what kind of information is contained in a SEM image taken by a certain detector. Specifically, the detectors installed in the objective lens are difficult to know their characters. Thus, we propose a simple method to assess the acceptance of electron detector using a stainless steel sphere. After taking images under certain conditions, say electron beam energy, working distance (WD), etc., the image intensity of each pixel point, which is characterized by coordinate (θ, φ), is evaluated. The advantage of this method is the ease of implementation and the whole information of electron emission from the tilted surfaces is contained in the image. Using this information, the acceptance of the detector can be analyzed systematically. In this paper, the traditional Everhart–Thornley (ET) detector is analyzed with this method. It is demonstrated how the sphere image changes according to the measurement condition. The ET image quality is strongly governed by WD but not so much by the electron beam energy. We propose an alternative method to avoid the ambiguity of WD. Using a needle-type specimen stage, the ET image does not vary so much with WD and the reliability of ET image significantly improves.
Improvement of primary Sjögren’s syndrome salivary gland function by Xinfeng capsule and its effect on EGR1-STAT3 signaling pathway
Authors: Zhu Ling , Wang Beijia , Li Pingping , Cheng Gangli , Bu Su , Bian Sijie , Qiu Xiaoting , Liu Jian , Huo Xingxing 
Published: October 2024

Abstract

Objectives
The study was aimed to investigate the effects of Xinfeng capsule (XFC) on tissue morphology, and gland function of the salivary gland (SG) in a primary Sjögren’s syndrome (pSS) mouse model.

Methods
An animal model of pSS was established by inducing SG protein in C57BL/6 mice. SG tissues were collected for tissue sequencing and subsequent experiments to detect the expression of cholinergic receptor muscarinic 3(M3R), early growth response factor 1 (EGR1) and target genes in the SG before and after XFC intervention, with in vitro validation.

Results
Downstream targets of the EGR1 gene were predicted and analyzed using data analysis. EGR1 showed high expression and was selected for subsequent experiments. Administration of XFC significantly increased saliva production (P &lt; 0.001) and reduced the extent of lymphatic infiltration observed in SG. Furthermore, the expression of EGR1 was increased in the model group with statistical significance in contrast with the control group but decreased after administration of XFC (P &lt; 0.05). Data analysis predicted the downstream target of EGR1 as signal transducer and activator of transcription 3 (STAT3), which was validated in SG tissues of mice (P &lt; .05).

Conclusions
XFC demonstrated a significant improvement in the salivary secretion function of the SG in pSS mice. EGR1 can serve as a biomarker and therapeutic target for pSS.
Gastric tube-preserving pancreaticoduodenectomy for ampullary adenocarcinoma after Lewis-Santy esophagectomy: a case report and literature review
Authors: Nachtergaele Sylvie , Mattart Laurine , Vindevogel Christophe , Francart David , Herman Dominique , Brescia Lionel 
Published: October 2024

Abstract
Pancreaticoduodenectomy after esophagectomy is a challenging procedure given the need to preserve the vascularization of the gastric plasty. We describe a case of a modified Longmire III procedure in a 68-year-old patient who underwent an esophagectomy with gastric conduit reconstruction in 2019 for esophageal adenocarcinoma. Two years later, an adenocarcinoma of the ampulla of Vater was diagnosed, necessitating pancreaticoduodenectomy with preservation of the gastric conduit. The patient presented no postoperative complications. Hepatic recurrence was observed 13 months after surgical resection. At 24 months follow-up, new liver metastases were observed. Preservation of the gastroduodenal and right gastric arteries was achieved, enabling conservation of the gastric plasty. Given the limitations of lymphadenectomy, the indication for this surgery must always be carefully considered. In the context of complex surgery, a complete preoperative workup to precisely determine the vascular anatomy as well as any anatomical variations is essential to establish the best operative strategy.
Niclosamide attenuates erectile dysfunction and corporal fibrosis via reversal of Smad signaling in diabetic rat model
Authors: Engin Seçkin , Barut Elif Nur , Kaya Yaşar Yeşim , Işık Semanur , Kerimoğlu Gökçen , Burnett Arthur L , Sezen Sena F 
Published: October 2024

Abstract

Background
Diabetes mellitus-induced erectile dysfunction (DMED) is a common urological complication of diabetes, and current drugs often fail to provide an effective treatment. Smad2/3 signaling-mediated corporal fibrosis has a critical role in the molecular basis of DMED.

Aim
We investigated the effect of Niclosamide (Nic), an antihelmintic drug with antifibrotic effects, on erectile function in a rat DMED model.

Methods
Male Sprague Dawley rats were injected intraperitoneally (i.p) with streptozotocin (75 mg/kg) to induce diabetes. At week 8, both diabetic and nondiabetic rats were treated with Nic (10 mg·kg−1/day; i.p) or vehicle for 4 weeks. At week 12, erectile function was evaluated as intracavernous pressure (ICP) response to the electrical stimulation of the cavernous nerve (CN). Penile tissues were harvested for Masson’s trichrome staining or western blotting to determine corporal fibrosis and Smad2/3 pathway-related protein expression, respectively.

Outcomes
At the end of the experimental protocol, in vivo erectile function was assessed by measuring the ratio of ICP/ mean arterial pressure (MAP) and total ICP following CN stimulation. Smooth muscle content and collagen fibers were evaluated by Masson’s trichrome staining of the penile tissues. The expressions of fibrosis-related proteins (Smad2, Smad3, fibronectin) were determined using western blotting in the penile tissues.

Results
Erectile function, as determined by the maximum ICP/MAP and total ICP/MAP ratios, was drastically decreased in diabetic rats. Corporal tissues of diabetic rats were severely fibrotic with a significant increase in collagen fibers and a marked reduction in smooth muscle content. Also, the protein expressions of phosphorylated (p-)Smad2, p-Smad3 and fibronectin were significantly increased in the penis of diabetic rats. Both functional and molecular alterations in DMED were effectively reversed by Nic-treated diabetic rats without a glycemic alteration.

Clinical Implications
Nic could be a promising candidate for the treatment of DMED due to its antifibrotic effects.

Strengths and Limitations
The present study provides the first evidence that Nic has beneficial effect on erectile dysfunction by attenuating corporal fibrosis in a rat model of DMED. The effect of Nic on penile endothelial function and the other potential underlying mechanisms needs to be further elucidated.

Conclusions
Nic improved erectile function in DMED rats possibly suppressing penile fibrosis by inhibiting Smad2/3 signaling. These results suggest a potential therapeutic repurposing of Nic as an adjuvant treatment in DMED.
Representation of migrant workers in Chinese newspapers: combining topic modeling and critical discourse analysis
Authors: Pang Nana , Sun Meng , Zhu Haoran 
Published: October 2024

Abstract
Chinese migrant workers have contributed greatly to the industrialization and urbanization of China and have thus long been a popular topic in news reports. Most previous studies on the news about this group have been qualitative or quantitative analyses based on small-scale datasets, with few based on large-scale corpus data. This study combined topic modeling and critical discourse analysis (CDA) to analyze 186,180 reports of migrant workers published by 906 Chinese newspapers between 2001 and 2021. We identified seventeen topics in the news that fell into five categories: “work and labor,” “support and care,” “rights and interests,” “homecoming,” and “social emergencies.” Overall, news reports on the group have become increasingly diverse, with various diachronic changes in the proportions of topic categories and specific topics. In addition, we found three major types of representation of migrant workers: as a disadvantaged group, as outsiders, and as a group vulnerable to risks. These negative representations might be closely related to government policies, ideology, media stance, and social reality (the broader societal context in which these individuals are situated).
Nonconventional Imaging for Viable Bacteria Detection: A Review
Authors: Gimenez Yilbert , Vandenkoornhuyse Philippe 
Published: October 2024

Abstract
The first attempts of bacteria observation started with the use of glass lenses to generate magnified images of specimens. This technique is constrained by the principal limit to the resolution of any optical system. Besides optical microscopy, other imaging techniques emerged to reveal more levels of details. The more the achievable resolution, the more complex the imaging systems, and at the same time, the more potentially cell-killing or DNA-damaging they may become. This article provides a state of the art of nonconventional sensor techniques that have been used in applications related to bacteria imaging, for the purpose of comparing the information they provide and determine their suitability or find out if their combination can yield new results without compromising the ability to keep the cells alive.
KK is Wrong Because We Say So
Authors: Goldstein Simon , Hawthorne John 
Published: October 2024

Abstract
This paper offers a new argument against the KK thesis, which says that if you know p, then you know that you know p. We argue that KK is inconsistent with the fact that anyone denies the KK thesis: imagine that Dudley says he knows p but that he does not have 100 iterations of knowledge about p. If KK were true, Dudley would know that he has 100 iterations of knowledge about p, and so he wouldn’t deny that he did. We consider several epicycles, and also explore whether the argument type also challenges other structural conditions on knowledge, such as closure under deduction.
Unexpected stratification in the equivalent-duration distributions of flare stars
Authors: Yoldaş E , Dal H A 
Published: October 2024

ABSTRACT
In this study, the results obtained from the statistical models of flares observed with ground-based telescopes and TESS observations for the UV Ceti-type stars AD Leo and V1005 Ori are presented. The distribution of flare equivalent duration versus total flare duration for the flares of both stars, observed with different telescopes, has been modelled using the one-phase exponential association (OPEA) model. Although no bifurcation was observed in the models derived with the flare data of V1005 Ori, the OPEA model exhibited bifurcation in almost all observation data of AD Leo. While many similar studies have shown that such models derived for a star do not vary over time and exhibit a single distribution in the same observation season, the stratification in AD Leo’s distributions and consequently in its model is an unexpected result.
Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa
Authors: Srikant Thanvi , Gonzalo Adrián , Bomblies Kirsten 
Published: October 2024

Abstract
Polyploids arise from whole-genome duplication (WGD) events, which have played important roles in genome evolution across eukaryotes. WGD can increase genome complexity, yield phenotypic novelty, and influence adaptation. Neo-polyploids have been reported to often show seemingly stochastic epigenetic and transcriptional changes, but this leaves open the question whether these changes persist in evolved polyploids. A powerful approach to address this is to compare diploids, neo-polyploids, and evolved polyploids of the same species. Arabidopsis arenosa is a species that allows us to do this—natural diploid and autotetraploid populations exist, while neo-tetraploids can be artificially generated. Here, we use ATAC-seq to assay local chromatin accessibility, and RNA-seq to study gene expression on matched leaf and petal samples from diploid, neo-tetraploid and evolved tetraploid A. arenosa. We found over 8,000 differentially accessible chromatin regions across all samples. These are largely tissue specific and show distinct trends across cytotypes, with roughly 70% arising upon WGD. Interestingly, only a small proportion is associated with expression changes in nearby genes. However, accessibility variation across cytotypes associates strongly with the number of nearby transposable elements. Relatively few genes were differentially expressed upon genome duplication, and ∼60% of these reverted to near-diploid levels in the evolved tetraploid, suggesting that most initial perturbations do not last. Our results provide new insights into how epigenomic and transcriptional mechanisms jointly respond to genome duplication and subsequent evolution of autopolyploids, and importantly, show that one cannot be directly predicted from the other.
A symbiotic oyster in a shrimp burrow: phylogenetic position of Anomiostrea within the Ostreidae (Bivalvia)
Authors: Goto Ryutaro , Garzia Matteo , Oliver P Graham , Paulay Gustav , Salvi Daniele 
Published: October 2024

ABSTRACT
The ostreid genus Anomiostrea Habe & Kosuge, 1966, is monotypic for A. coralliophila Habe, 1975, which is known as a symbiont inhabiting the burrow of the ghost shrimp Neocallichirus jousseaumei (Nobili, 1904), but despite this unusual habit among oysters its phylogenetic position within the Ostreidae remained unknown. Using specimens collected from two distant localities of the Indo-Pacific, Oman and Japan, we compared shell morphology of these specimens with the holotype and assessed their phylogenetic relationships based on DNA sequence data from two mitochondrial and two nuclear genes. The genetic distance in cytochrome c oxidase subunit I between the specimens from Japan and Oman was 5.5%, indicating substantial geographic differentiation. Our molecular phylogenetic results suggest that A. coralliophila is sister to Ostrea algoensis G. B. Sowerby II, 1871, an oyster from rocky shores in South Africa, and both are closely related to other Ostrea species. This confirms assignment of Anomiostrea to Ostreinae and suggests that this burrow-wall symbiont evolved from typical rocky-shore oysters. Moreover, A. coralliophila was not monophyletic with another symbiotic ostreid Ostrea permollis G. B. Sowerby II, 1871, nor with other symbiotic oysters, indicating that the symbiotic habit evolved multiple times in the Ostreinae.
Evolution of left–right asymmetry in side-resting (pleurothetic) bivalves: a test of genes as leaders or followers
Authors: Palmer A Richard 
Published: October 2024

ABSTRACT
Side-resting (pleurothetic) lifestyles evolved independently many times across the Bivalvia in free-lying, byssally attached and cementing lineages. Within some species individuals lie indifferently on either their right or left side (randomly pleurothetic), whereas in others they lie consistently on one side (left-pleurothetic or right-pleurothetic). Morphological differences between valves (asymmetries) typically accompany this behaviour, so it can be studied widely across living and fossil bivalves. Because direction of asymmetry is rarely inherited in cases of random asymmetry, any evolutionary transition from randomly pleurothetic to fixed (left or right) qualifies as a case of ‘genes as followers’. Origins of left-pleurothetic or right-pleurothetic taxa directly from upright (orthothetic) ancestors would represent examples of ‘genes as leaders’. I therefore surveyed pleurothetic lifestyles across the Bivalvia. By mapping pleurothetic states onto a comprehensive phylogenetic tree that included both living and fossil families, I assessed the prevalence of these alternate modes of evolution. Various lines of evidence were also used to hypothesize phylogenetic relations within the Chamidae—the only living bivalve family exhibiting all three pleurothetic states. Randomly pleurothetic forms (direction not inherited) arose from orthothetic ancestors about half as often as fixed pleurothetic forms (direction is inherited). Unlike many other animal groups, fixed pleurothetic forms rarely arose from randomly pleurothetic ancestors, suggesting a ‘genes as leaders’ mode of evolution was most prevalent. However, many fascinating examples of randomly pleurothetic forms among Upper Ordovician and Silurian bivalves suggest that evolutionary transitions from random to fixed may have been more common. Also, randomly pleurothetic forms were short-lived in some fossil lineages, which would reduce the likelihood of them being detected. Hopefully, this preliminary analysis will motivate further study of (1) phylogenetic relations of key groups like the Chamidae, and basal Limida, Ostreida and Pterioidea, and (2) morphological variation among early members of other pleurothetic bivalve groups.