bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public willingness to receive chlamydia, gonorrhea, syphilis, and trichomoniasis vaccines: a scoping review
Authors: Valleroy T. , Garon Colin , Perroud Janamarie , Wagner Abram L. 
Published: November 2023

Abstract
Background
Sexually transmitted infections (STIs) like chlamydia, gonorrhea, syphilis, and trichomoniasis contribute significantly to global morbidity and mortality. Researchers are pursuing vaccines for these STIs, and a clinical trial is currently underway for a chlamydia vaccine. However, there is little research available on individuals’ willingness to receive chlamydia, gonorrhea, syphilis, and trichomoniasis vaccines. The purpose of this analysis was to map the existing literature we have on individuals’ willingness to receive these bacterial/parasitic STI vaccines and understand what information on vaccine acceptability is still needed.

Methods
We searched seven databases for literature on STI vaccine acceptability, then conducted title/abstract and full-text reviews to assess eligibility. All reviews and abstractions were conducted blindly by two reviewers, with discrepancies settled by discussion or the input of a third reviewer.

Results
Eight of the original 2,259 texts of interest met inclusion criteria. After data abstraction, we found that gonorrhea was the most commonly examined, followed by chlamydia and syphilis. Trichomoniasis vaccine acceptability was not reported. Most texts reported high acceptability, but there did not appear to be data describing how vaccine characteristics affect acceptability. Similarly, while the literature covers a variety of populations, most of the study populations were based out of the United States or Canada and were patrons of healthcare facilities or participants from a larger health intervention study. Therefore, more information is needed on populations outside North America, and on groups with lower healthcare access and utilization.

Conclusion
As the incidence of bacterial and parasitic STIs increase, and as we grow nearer vaccines for these illnesses, understanding how likely the public is to accept and receive these vaccines is crucial to their success. While the existing literature describes STI vaccine acceptability in a variety of populations, their overall number is small. More research into STI vaccine acceptability outside of North America, and especially examining how factors like number of doses, timing, and cost influence vaccine acceptability is needed to ensure effective future vaccine rollouts.
Benchmarking MicrobIEM – a user-friendly tool for decontamination of microbiome sequencing data
Authors: Hülpüsch Claudia , Rauer Luise , Nussbaumer Thomas , Schwierzeck Vera , Bhattacharyya Madhumita , Erhart Veronika , Traidl-Hoffmann Claudia , Reiger Matthias , Neumann Avidan U. 
Published: November 2023

Abstract
Background
Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.

Results
We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (108–103 cells, 0.4–80% contamination) with even or staggered taxon compositions and a skin microbiome dataset. Results depended strongly on user-selected algorithm parameters. Overall, sample-based algorithms separated mock and contaminant sequences best in the even mock, whereas control-based algorithms performed better in the two staggered mocks, particularly in low-biomass samples (≤ 106 cells). We show that a correct decontamination benchmarking requires realistic staggered mock communities and unbiased evaluation measures such as Youden’s index. In the skin dataset, the Decontam prevalence filter and MicrobIEM’s ratio filter effectively reduced common contaminants while keeping skin-associated genera.

Conclusions
MicrobIEM’s ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
RIPK1 polymorphisms and expression levels: impact on genetic susceptibility and clinical outcome of epithelial ovarian cancer
Authors: Wang Xuedong , Deng Kui , Tao Jing , Zou Juan , Du Yiting , Dai Li 
Published: November 2023

Abstract
Background
The aim of this study was to explore the associations of RIPK1 polymorphisms, plasma levels and mRNA expression with susceptibility to epithelial ovarian cancer (EOC) and clinical outcome.

Methods
Three hundred and nineteen EOC patients included in a 60-month follow-up program and 376 controls were enrolled. Two tag SNPs (rs6907943 and rs9392453) of RIPK1 were genotyped using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) method. Plasma levels of RIPK1 and RIPK1 mRNA expression in white blood cells were determined by ELISA and qPCR, respectively.

Results
For rs9392453, significantly increased EOC risk was found to be associated with C allele (P = 0.002, OR = 1.49, 95%CI  1.15–1.92), and with CT/CC genotypes in the dominant genetic model (P = 0.006, OR = 1.54, 95%CI  1.12–2.08). CC haplotype (rs6907943-rs9392453) was associated with increased EOC susceptibility. CC genotype of rs6907943 and CT/CC genotypes of rs9392453 were associated with early onset (age ≤ 50 years) of EOC (OR = 2.5, 95%CI  1.03–5.88, and OR = 1.64, 95%CI  1.04–2.63, respectively). AC genotype of rs6907943 was associated with better overall survival of EOC patients in the over-dominant genetic model (P = 0.035, HR = 0.41, 95%CI  0.18–0.94). Multivariate survival analysis identified the AC genotype of rs6907943 as an independent protective factor for survival of early onset patients (P = 0.044, HR = 0.12, 95%CI  0.02–0.95). Compared to controls, significantly increased plasma levels of RIPK1 and reduced RIPK1 mRNA expression were observed in patients.

Conclusions
Our results suggest that tag SNPs of RIPK1, increased plasma levels of RIPK1 protein and reduced RIPK1 mRNA expression in white blood cells, may influence the susceptibility to EOC. SNP rs6907943 may be a useful marker to distinguish EOC patients with high risk of death.
Plasmodium vivax merozoite-specific thrombospondin-related anonymous protein (PvMTRAP) interacts with human CD36, suggesting a novel ligand–receptor interaction for reticulocyte invasion
Authors: Nguyen Thau Sy , Park Ji-Hoon , Nguyen Tuyet-Kha , Nguyen Truong Van , Lee Seong-Kyun , Na Sung-Hun , Han Jin-Hee , Park Won-Sun , Chun Wanjoo , Lu Feng , Han Eun-Taek 
Published: November 2023

Abstract
Background
The Plasmodium vivax merozoite restrictively invades immature erythrocytes, suggesting that its ligand(s) might interact with corresponding receptor(s) that are selectively abundant on reticulocytes to complete the invasion. Finding the ligand‒receptor interaction involved in P. vivax invasion is critical to vivax malaria management; nevertheless, it remains to be unraveled.

Methods
A library of reticulocyte receptors and P. vivax ligands were expressed by a HEK293E mammalian cell expression system and were then used to screen the interaction using enzyme-linked immunosorbent assay (ELISA). A flow cytometry-based erythrocyte binding assay and bio-layer interferometry experiment were further utilized to cellularly and quantitatively identify the ligand‒receptor interaction, respectively.

Results
Plasmodium vivax merozoite-specific thrombospondin-related anonymous protein (PvMTRAP) was found to interact with human CD36 using systematic screening. This interaction was specific at a molecular level from in vitro analysis and comparable to that of P. vivax Duffy binding protein (PvDBP) and Duffy antigen receptor for chemokines (DARC) (KD: 37.0 ± 1.4 nM and 7.7 ± 0.5 nM, respectively). Flow cytometry indicated that PvMTRAP preferentially binds to reticulocytes, on which CD36 is selectively present.

Conclusions
Human CD36 is selectively abundant on reticulocytes and is able to interact specifically with PvMTRAP, suggesting that it may function as a ligand and receptor during the invasion of reticulocytes by P. vivax.

Graphical Abstract
Final-year medical students’ perspective: a survey on the use of computed tomography in sepsis
Authors: Pohlan Julian , Hernando Maria Isabel Opper , Waschinsky Roderic , Biavati Federico , Peters Harm , Knauss Samuel , Steinhagen Peter Richard , Rubarth Kerstin , Witham Denis , Dewey Marc 
Published: November 2023

Abstract
Objectives
To determine the perspective of final-year medical students on the use of computed tomography (CT) in patients with sepsis.

Methods
A total of 207 questionnaires were distributed to final-year medical students at a large university medical center, and 113 returned questionnaires met the criteria for inclusion in the analysis. Questions referred to sepsis guidelines, CT indications, and the use of contrast agents. Control variables included a level of practical experience as a final-year student (trimester of student’s practical year) and previous radiological experience. Statistical hypothesis tests such as the Mann-Whitney U test and chi-square test were performed.

Results
The majority of participating students, 85% (n = 91/107), considered a Systemic Organ Failure Assessment (SOFA) score ≥ 2 as a diagnostic criterion for sepsis. The presence of ≥ 2 positive systemic inflammatory response syndrome (SIRS) criteria was considered relevant for diagnosing sepsis by 34% (n = 34/100). Ninety-nine percent (n = 64/65) of the participants who fully agreed with a SOFA score ≥ 2 being relevant for diagnosing sepsis would also use it as an indication for a CT scan. Seventy-six percent (n = 78/103) of the students rated a known severe allergic reaction to contrast agents as an absolute contraindication for its administration. Ninety-five percent (n = 78/82) considered radiation exposure as problematic in CT examinations, especially in repeat CTs.

Conclusion
Most final-year medical students were familiar with the sepsis criteria. Still, some referred to outdated diagnostic criteria. Participants saw the ability to plan further patient management based on CT as a major benefit. Most participants were aware of radiation as a risk of CT.

Critical relevance statement
More detailed knowledge of CT in septic patients should be implemented in the medical curriculum. Retraining of medical students could help increase student confidence potentially improving patient care.

Key points
1. Whereas the majority of final-year medical students were familiar with sepsis criteria, some referred to outdated diagnostic criteria.
2. Participants saw the ability to plan further patient management based on CT as a major benefit.
3. Most participants were aware of radiation as a risk of CT.

Graphical Abstract
Lactate: an alternative pathway for the immunosuppressive properties of mesenchymal stem/stromal cells
Authors: Pradenas Carolina , Luque-Campos Noymar , Oyarce Karina , Contreras-Lopez Rafael , Bustamante-Barrientos Felipe A. , Bustos Andrés , Galvez-Jiron Felipe , Araya María Jesús , Asencio Catalina , Lagos Raúl , Herrera-Luna Yeimi , Abba Moussa Daouda , Hill Charlotte Nicole , Lara-Barba Eliana , Altamirano Claudia , Ortloff Alexander , Hidalgo-Fadic Yessia , Vega-Letter Ana María , García-Robles María de los Ángeles , Djouad Farida , Luz-Crawford Patricia , Elizondo-Vega Roberto 
Published: November 2023

Abstract
Background
The metabolic reprogramming of mesenchymal stem/stromal cells (MSC) favoring glycolysis has recently emerged as a new approach to improve their immunotherapeutic abilities. This strategy is associated with greater lactate release, and interestingly, recent studies have proposed lactate as a functional suppressive molecule, changing the old paradigm of lactate as a waste product. Therefore, we evaluated the role of lactate as an alternative mediator of MSC immunosuppressive properties and its contribution to the enhanced immunoregulatory activity of glycolytic MSCs.

Materials and methods
Murine CD4+ T cells from C57BL/6 male mice were differentiated into proinflammatory Th1 or Th17 cells and cultured with either L-lactate, MSCs pretreated or not with the glycolytic inductor, oligomycin, and MSCs pretreated or not with a chemical inhibitor of lactate dehydrogenase A (LDHA), galloflavin or LDH siRNA to prevent lactate production. Additionally, we validated our results using human umbilical cord-derived MSCs (UC-MSCs) in a murine model of delayed type 1 hypersensitivity (DTH).

Results
Our results showed that 50 mM of exogenous L-lactate inhibited the proliferation rate and phenotype of CD4+ T cell-derived Th1 or Th17 by 40% and 60%, respectively. Moreover, the suppressive activity of both glycolytic and basal MSCs was impaired when LDH activity was reduced. Likewise, in the DTH inflammation model, lactate production was required for MSC anti-inflammatory activity. This lactate dependent-immunosuppressive mechanism was confirmed in UC-MSCs through the inhibition of LDH, which significantly decreased their capacity to control proliferation of activated CD4+ and CD8+ human T cells by 30%.

Conclusion
These findings identify a new MSC immunosuppressive pathway that is independent of the classical suppressive mechanism and demonstrated that the enhanced suppressive and therapeutic abilities of glycolytic MSCs depend at least in part on lactate production.
The distortion in the EU feed market due to import constraints on genetically modified soy
Authors: Basnet Shyam Kumar , Ghosh Ranjan Kumar , Eriksson Mattias , Lagerkvist Carl-Johan 
Published: November 2023

AbstractFeed importers in some EU member states face constraints on imports of genetically modified (GM) soy, a practice that may compromise the interests of EU livestock farmers. Using the cases of Sweden and Austria, we analyzed price transmission in the soy supply chain originating from Brazil, applying an asymmetric non-linear auto-regressive distributed lag (ARDL) model to identify short-run and long-run asymmetries. The results revealed significant asymmetric effects in how positive and negative price changes are absorbed within the feed industry. Notably, increases in the cost of Brazilian soy swiftly affect the prices for EU farmers, while cost reductions fail to trigger corresponding price decreases. Consequently, stronger constraints on GM soy imports are likely to exacerbate the competitiveness challenges faced by livestock farmers, primarily due to their reliance on non-GM soy. This implies that the restrictions on GM imports need to be relaxed or that low-cost local protein alternatives need to be developed.
Exosome derived from tumor-associated macrophages: biogenesis, functions, and therapeutic implications in human cancers
Authors: Zhou Manli , He Xiaoyun , Mei Cheng , Ou Chunlin 
Published: November 2023

AbstractTumor-associated macrophages (TAMs), one of the most abundant immune cell types in the tumor microenvironment (TME), account for approximately 50% of the local hematopoietic cells. TAMs play an important role in tumorigenesis and tumor development through crosstalk between various immune cells and cytokines in the TME. Exosomes are small extracellular vesicles with a diameter of 50–150 nm, that can transfer biological information (e.g., proteins, nucleic acids, and lipids) from secretory cells to recipient cells through the circulatory system, thereby influencing the progression of various human diseases, including cancer. Recent studies have suggested that TAMs-derived exosomes play crucial roles in malignant cell proliferation, invasion, metastasis, angiogenesis, immune responses, drug resistance, and tumor metabolic reprogramming. TAMs-derived exosomes have the potential to be targeted for tumor therapy. In addition, the abnormal expression of non-coding RNAs and proteins in TAMs-derived exosomes is closely related to the clinicopathological features of patients with cancer, and these exosomes are expected to become new liquid biopsy markers for the early diagnosis, prognosis, and monitoring of tumors. In this review, we explored the role of TAMs-derived exosomes in tumorigenesis to provide new diagnostic biomarkers and therapeutic targets for cancer prevention.
Neuronal SNCA transcription during Lewy body formation
Authors: Kon Tomoya , Forrest Shelley L. , Lee Seojin , Martinez‑Valbuena Ivan , Li Jun , Nassir Nasna , Uddin Mohammed J. , Lang Anthony E. , Kovacs Gabor G. 
Published: November 2023

AbstractMisfolded α-synuclein (α-syn) is believed to contribute to neurodegeneration in Lewy body disease (LBD) based on considerable evidence including a gene-dosage effect observed in relation to point mutations and multiplication of SNCA in familial Parkinson’s disease. A contradictory concept proposes early loss of the physiological α-syn as the major driver of neurodegeneration. There is a paucity of data on SNCA transcripts in various α-syn immunoreactive cytopathologies. Here, the total cell body, nuclear, and cytoplasmic area density of SNCA transcripts in neurons without and with various α-syn immunoreactive cytopathologies in the substantia nigra and amygdala in autopsy cases of LBD (n = 5) were evaluated using RNAscope combined with immunofluorescence for disease-associated α-syn. Single-nucleus RNA sequencing was performed to elucidate cell-type specific SNCA expression in non-diseased frontal cortex (n = 3). SNCA transcripts were observed in the neuronal nucleus and cytoplasm in neurons without α-syn, those containing punctate α-syn immunoreactivity, irregular-shaped compact inclusion, and brainstem-type and cortical-type LBs. However, SNCA transcripts were only rarely found in the α-syn immunoreactive LB areas. The total cell body SNCA transcript area densities in neurons with punctate α-syn immunoreactivity were preserved but were significantly reduced in neurons with compact α-syn inclusions both in the substantia nigra and amygdala. This reduction was also observed in the cytoplasm but not in the nucleus. Only single SNCA transcripts were detected in astrocytes with or without disease-associated α-syn immunoreactivity in the amygdala. Single-nucleus RNA sequencing revealed that excitatory and inhibitory neurons, oligodendrocyte progenitor cells, oligodendrocytes, and homeostatic microglia expressed SNCA transcripts, while expression was largely absent in astrocytes and microglia. The preserved cellular SNCA expression in the more abundant non-Lewy body type α-syn cytopathologies might provide a pool for local protein production that can aggregate and serve as a seed for misfolded α-syn. Successful segregation of disease-associated α-syn is associated with the exhaustion of SNCA production in the terminal cytopathology, the Lewy body. Our observations inform therapy development focusing on targeting SNCA transcription in LBD.
An injectable, in situ forming and NIR-responsive hydrogel persistently reshaping tumor microenvironment for efficient melanoma therapy
Authors: Zhang Han , Hu Liangshan , Xiao Wei , Su Yanqiong , Cao Donglin 
Published: November 2023

Abstract

Background
Melanoma is a highly aggressive form of skin cancer with increasing incidence and mortality rates. Chemotherapy, the primary treatment for melanoma, is limited by hypoxia-induced drug resistance and suppressed immune response at the tumor site. Modulating the tumor microenvironment (TME) to alleviate hypoxia and enhance immune response has shown promise in improving chemotherapy outcomes.

Methods

In this study, a novel injectable and in situ forming hydrogel named MD@SA was developed using manganese dioxide (MnO
2
) nanosheets pre-loaded with the chemotherapy drug doxorubicin (DOX) and mixed with sodium alginate (SA). The sustainable drug delivery, oxygen generation ability, and photothermal property of MD@SA hydrogel were characterized. The therapeutic efficacy of hydrogel was studied in B16F10 in vitro and B16F10 tumor-bearing mice in vivo. The immune effects on macrophages were analyzed by flow cytometry, real-time quantitative reverse transcription PCR, and immunofluorescence analyses.

Results

The MD@SA hydrogel catalyzed the tumoral hydrogen peroxide (H
2
O
2
) into oxygen, reducing the hypoxic TME, down-regulating hypoxia-inducible factor-1 alpha (HIF-1α) and drug efflux pump P-glycoprotein (P-gp). The improved TME conditions enhanced the uptake of DOX by melanoma cells, enhancing its efficacy and facilitating the release of tumor antigens. Upon NIR irradiation, the photothermal effect of the hydrogel induced tumor apoptosis to expose more tumor antigens, thus re-educating the M2 type macrophage into the M1 phenotype. Consequently, the MD@SA hydrogel proposes an ability to constantly reverse the hypoxic and immune-inhibited TME, which eventually restrains cancer proliferation.

Conclusion
The injectable and in situ forming MD@SA hydrogel represents a promising strategy for reshaping the TME in melanoma treatment. By elevating oxygen levels and activating the immune response, this hydrogel offers a synergistic approach for TME regulation nanomedicine.
Mechanisms of Ovarian Cancer-Associated Cachexia
Authors: Callaway Chandler S , Mouchantat Lila M , Bitler Benjamin G , Bonetto Andrea 
Published: November 2023

Abstract
Cancer-associated cachexia occurs in 50% to 80% of cancer patients and is responsible for 20% to 30% of cancer-related deaths. Cachexia limits survival and treatment outcomes, and is a major contributor to morbidity and mortality during cancer. Ovarian cancer is one of the leading causes of cancer-related deaths in women, and recent studies have begun to highlight the prevalence and clinical impact of cachexia in this population. Here, we review the existing understanding of cachexia pathophysiology and summarize relevant studies assessing ovarian cancer–associated cachexia in clinical and preclinical studies. In clinical studies, there is increased evidence that reduced skeletal muscle mass and quality associate with worse outcomes in subjects with ovarian cancer. Mouse models of ovarian cancer display cachexia, often characterized by muscle and fat wasting alongside inflammation, although they remain underexplored relative to other cachexia-associated cancer types. Certain soluble factors have been identified and successfully targeted in these models, providing novel therapeutic targets for mitigating cachexia during ovarian cancer. However, given the relatively low number of studies, the translational relevance of these findings is yet to be determined and requires more research. Overall, our current understanding of ovarian cancer–associated cachexia is insufficient and this review highlights the need for future research specifically aimed at exploring mechanisms of ovarian cancer–associated cachexia by using unbiased approaches and animal models representative of the clinical landscape of ovarian cancer.