bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for sternal wound infection after open‐heart operations: A systematic review and meta‐analysis
Authors: Chen Dongsheng , Zhang Jianghe , Wang Yuting , Jiang Weiqian , Xu Yujian , Xiong Chenlu , Feng Zekun , Han Yan , Chen Youbai 
Published: November 2023

AbstractWe aimed to quantitatively and systematically elucidate the rationality of the examined variables as independent risk factors for sternal wound infection. We searched databases to screen studies, ascertained the variables to be analysed, extracted the data and applied meta‐analysis to each qualified variable. Odds ratios and mean differences were considered to be the effect sizes for binary and continuous variables, respectively. A random‐effects model was used for these procedures. The source of heterogeneity was evaluated using a meta‐regression. Publication bias was tested by funnel plot and Egger's test, the significant results of which were then calculated using trim and fill analysis. We used a sensitivity analysis and bubble chart to describe their robustness. After screening all variables in the eligible literature, we excluded 55 because only one or no research found them significant after multivariate analysis, leaving 33 variables for synthesis. Two binary variables (age over 65 years, NYHA class >2) and a continuous variable (preoperative stay) were not significant after the meta‐analysis. The most robust independent risk factors in our study were diabetes mellitus, obesity, use of bilateral internal thoracic arteries, chronic obstructive pulmonary disease, prolonged surgery time, prolonged ventilation and critical preoperative state, followed by congestive heart failure, atrial fibrillation, renal insufficiency, stroke, peripheral vascular disease and use of an intra‐aortic balloon pump. Relatively low‐risk factors were emergent/urgent surgery, smoking, myocardial infarction, combined surgery and coronary artery bypass grafting. Sternal wound infection after open‐heart surgery is a multifactorial disease. The detected risk factors significantly affected the wound healing process, but some were different in strength. Anything that affects wound healing and antibacterial ability, such as lack of oxygen, local haemodynamic disorders, malnutrition condition and compromised immune system will increase the risk, and this reminds us of comprehensive treatment during the perioperative period.
Experimental and thermodynamic modeling study of phase equilibria in the PbO–NiO–SiO2 system
Authors: Abdeyazdan Hamed , Shevchenko Maksym , Jak Evgueni 
Published: November 2023

AbstractAn integrated experimental and thermodynamic modeling investigation of the phase equilibria in the PbO–NiO–SiO2 system in air and also in equilibrium with liquid metal has been undertaken to better characterize the chemical reactions taking place in the Ni‐containing Pb processing slags. New experimental phase equilibria data at 720°C–1740°C were obtained for this system using high‐temperature equilibration of synthetic mixtures with predetermined compositions in sealed silica ampoules or in Au/Pt–Ir foils, a rapid quenching technique, and electron probe x‐ray microanalysis of the equilibrated phase compositions. Phase equilibria and liquidus isotherms in the quartz/tridymite/cristobalite (SiO2), olivine (Ni2SiO4), monoxide (NiO), Ni‐barysilite (Pb8NiSi6O21), massicot (PbO), and di‐lead silicate (Pb2SiO4) primary phase fields were revealed and the extent of the high‐SiO2 two‐liquid immiscibility gap in equilibrium with cristobalite was determined. New experimental data were used in the development of a thermodynamic database describing this ternary system. Also, modeling revision of the NiO–SiO2 binary system was conducted, resulting in a smaller miscibility gap in ternary systems that was closer to the experimental results.
The origin of calcite in calc‐silicate rocks from the Kokchetav ultrahigh‐pressure metamorphic complex
Authors: Mikhno Anastasia O. , Shatskiy Anton F. , Korsakov Andrey V. , Vinogradova Yulia G. , Berndt Jasper , Klemme Stephan , Rashchenko Sergey V. 
Published: November 2023

AbstractUnderstanding calcite genesis in ultrahigh‐pressure crustal rocks is a key to the reconstruction of the evolution of ultrahigh‐pressure metacarbonate rocks. Here, we present new data and a new model on the genesis and the P–T conditions of the formation of calcite found in the ultrahigh‐pressure calc‐silicate rocks from the Kokchetav massif. In the studied sample aragonite inclusions coexist with Type A calcite inclusions (previously interpreted as mineral inclusions) and the inclusions of Type B calcite (previously interpreted as derived from the crystallization of carbonatitic melt) in cores of garnet porphyroblasts. The most Mg‐rich calcite from Type A inclusions coexisting with aragonite inclusions in one garnet growth zone shows XCa = 0.935 implying their crystallization during a retrograde metamorphic stage at P ~ 2.3 GPa and T ~ 870°C along the P–T path. Type A calcite and aragonite inclusions were also found coexisting in one growth zone with K‐bearing clinopyroxene inclusion (ω[K2O] = 0.5 wt.%). Such a high K2O‐content in clinopyroxene testify that the pressure of inclusion capture exceeded 3.5 GPa, which contradicts the P–T conditions estimated by XCa in magnesian calcite. Thus, Type A calcite inclusions were initially captured as an aggregate of aragonite+ magnesian calcite at ultrahigh pressure metamorphic stage (P ≥ 3.5 GPa, T = 900–1,000°C) and then re‐equilibrated at lower conditions (P ≤ 2.3 GPa and T ≤ 870°C). The trace element composition of aragonite and Type A and Type B calcite from inclusions was also studied to clarify calcite genesis in these inclusions. Aragonite shows high LREE (5–57 ppm) and Sr‐content (600–800 ppm). Calcite from Type A inclusions shows low LREE (2.9–19.8 ppm) and Sr‐content (490–670 ppm). Calcite from Type B inclusions forms two groups according to the LREE and Sr content distribution (Type B1 and Type B2). Trace element distribution in Type B1 calcite is identical to that of Type A calcite, while Type B2 calcite shows high LREE (6.8–64.9 ppm) concentrations along with low Sr‐content (180–340 ppm). Type A and Type B1 calcite is interpreted to have been re‐equilibrated. Type B2 calcite inclusions crystallized from the hydrous carbonatitic melt.
Sonography of the pituitary gland in pet rats
Authors: Pelligra Tina , Petrini Daniele , Puccinelli Caterina , Unti Serena , Citi Simonetta 
Published: November 2023

AbstractPituitary gland (PG) tumors are common in rats over the age of 2. CT and MRI can be difficult to apply in this species, whereas ultrasound is more feasible and useful. To our knowledge, there are no studies on PG ultrasound in rats. The aim of this prospective, analytical study was to evaluate the reliability of ultrasound in identifying PG, to define the ultrasound dimension of the gland in a group of rats with no evidence of pituitary diseases, and to examine its correlations with age, sex, and weight. After localizing the PG with an MRI study on one rat, the gland was identified in 21 rats by ultrasound by two sonographers using a ventral neck approach and a transversal scan with a linear probe. The gland appears as a hypoechoic oval structure with a thin hyperechoic margin. The rats (15 male and 6 female) ranged from 4 to 18 months in age (median 6 months) and from 270 to 640 g in weight (median 370 g). The median pituitary width was 3.96 mm (interquartile range 25–75%: 6–4.5 mm), and the median height was 1.48 mm (interquartile range 25–75%: 1.3–1.67 mm). There was no statistically significant correlation between PG size and rat weight, gender, or age. We believe that these ultrasound measurements could be useful for the diagnosis of pituitary disease, irrespective of whether neurological symptoms are present. We report a clinical case of a rat with a pituitary mass detected by ultrasound and CT.
Multi-Modal Machine Learning in Engineering Design: A Review and Future Directions
Authors: Song Binyang , Zhou Rui , Ahmed Faez 
Published: November 2023

Abstract
In the rapidly advancing field of multi-modal machine learning (MMML), the convergence of multiple data modalities has the potential to reshape various applications. This paper presents a comprehensive overview of the current state, advancements, and challenges of MMML within the sphere of engineering design. The review begins with a deep dive into five fundamental concepts of MMML: multi-modal information representation, fusion, alignment, translation, and co-learning. Following this, we explore the cutting-edge applications of MMML, placing a particular emphasis on tasks pertinent to engineering design, such as cross-modal synthesis, multi-modal prediction, and cross-modal information retrieval. Through this comprehensive overview, we highlight the inherent challenges in adopting MMML in engineering design, and proffer potential directions for future research. To spur on the continued evolution of MMML in engineering design, we advocate for concentrated efforts to construct extensive multi-modal design datasets, develop effective data-driven MMML techniques tailored to design applications, and enhance the scalability and interpretability of MMML models. MMML models, as the next generation of intelligent design tools, hold a promising future to impact how products are designed.
Retroviral hijacking of host transport pathways for genome nuclear export
Authors: Behrens Ryan T. , Sherer Nathan M. 
Published: November 2023

ABSTRACT
Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
The nonstructural protein 1 of respiratory syncytial virus hijacks host mitophagy as a novel mitophagy receptor to evade the type I IFN response in HEp-2 cells
Authors: Cheng Jing , Wang Yutong , Yin Lizheng , Liang Wenzhang , Zhang Jing , Ma Cuiqing , Zhang Yu , Liu Bo , Wang Jiachao , Zhao Weiting , Li Miao , Wei Lin 
Published: November 2023

ABSTRACT
Mitochondria are good targets for viruses to manipulate their hosts. However, it remains obscure whether respiratory syncytial virus (RSV) target mitochondria to suppress the type I interferon (IFN) responses. Here, we show that nonstructural protein 1 (NS1) protein of RSV interacts with Tu translation elongation factor mitochondrial (TUFM), which can lead to its localization in mitochondria and finally induce TUFM-dependent mitophagy and inhibition of IFNβ. Mechanically, NS1-mediated TUFM-dependent mitophagy does not depend on the PINK1-PARKIN pathway and classic mitophagy receptors. Importantly, NS1 may act as a new receptor protein to bridge mitochondria and autophagosomes by interacting with TUFM and LC3B. The LIR motif of NS1 protein is essential for its interaction with LC3B and is of great importance for its mitophagy induction and IFNβ suppression. Finally, NS1-induced TUFM-dependent mitophagy was essential for its attenuated IFNβ response using autophagy-deficient cells and mice. Our study provides a novel mitophagy receptor molecular and a new antiviral option by suppressing antiviral innate immune via targeting TUFM-dependent mitophagy.

IMPORTANCE

It is a worthy concern for us to understand virus-host interactions which affect progression and prognosis of disease. We demonstrated that the non-structural protein 1 of respiratory syncytial virus (RSV NS1) may act as a novel mitophagy receptor to induce mitophagy by binding LC3B and mitochondrial protein TUFM, and finally dampen interferon (IFN) responses induced by RIG1 and RSV infection. TUFM is beneficial for RSV replication
in vivo
and
vitro
. It is new and interesting that RSV NS1 may function as a mitophagy receptor to interact with LC3B. The LIR motif of NS1 protein is essential for its interaction with LC3B. We further confirm that RSV NS1 inhibited IFNβ response and promoted RSV replication in autophagy-dependent mechanisms
in vivo
and
vitro
. Our study contributes to understanding virus-host interaction, enriching our insights into RSV pathogenic mechanism and exploiting new antiviral treatments targeting TUFM.
Aedes aegypti
D7 long salivary proteins modulate blood feeding and parasite infection
Authors: Martin-Martin Ines , Kojin Bianca Burini , Aryan Azadeh , Williams Adeline E. , Molina-Cruz Alvaro , Valenzuela-Leon Paola Carolina , Shrivastava Gaurav , Botello Karina , Minai Mahnaz , Adelman Zach N. , Calvo Eric 
Published: November 2023

ABSTRACT

Mosquito saliva facilitates blood meal acquisition through pharmacologically active compounds that prevent host hemostasis and immune responses. Here, we generated two knockout (KO) mosquito lines by CRISPR/Cas9 to functionally characterize D7L1 and D7L2, two abundantly expressed salivary proteins from the yellow fever mosquito vector
Aedes aegypti
. The D7s bind and scavenge biogenic amines and eicosanoids involved in hemostasis at the bite site. The absence of D7 proteins in the salivary glands of KO mosquitoes was confirmed by mass spectrometry, enzyme-linked immunosorbent assay, and fluorescence microscopy of the salivary glands with specific antibodies. D7-KO mosquitoes had longer probing times than parental wildtypes. The differences in probing time were abolished when mutant mice resistant to inflammatory insults were used. These results confirmed the role of D7 proteins as leukotriene scavengers
in vivo
. We also investigated the role of D7 salivary proteins in
Plasmodium gallinaceum
infection and transmission. Both KO lines had significantly fewer oocysts per midgut. We hypothesize that the absence of D7 proteins in the midgut of KO mosquitoes might be responsible for creating a harsh environment for the parasite. The information generated by this work highlights the biological functionality of salivary gene products in blood feeding and pathogen infection.

IMPORTANCE

During blood feeding, mosquitoes inject saliva into the host skin, preventing hemostasis and inflammatory responses. D7 proteins are among the most abundant components of the saliva of blood-feeding arthropods.
Aedes aegypti
, the vector of yellow fever and dengue, expresses two D7 long-form salivary proteins: D7L1 and D7L2. These proteins bind and counteract hemostatic agonists such as biogenic amines and leukotrienes. D7L1 and D7L2 knockout mosquitoes showed prolonged probing times and carried significantly less
Plasmodium gallinaceum
oocysts per midgut than wild-type mosquitoes. We hypothesize that reingested D7s play a vital role in the midgut microenvironment with important consequences for pathogen infection and transmission.
Genome-sequenced bacterial collection from sorghum epicuticular wax
Authors: Mechan-Llontop Marco E. , Mullet John , Shade Ashley 
Published: November 2023

ABSTRACT
A collection of 44 isolates isolated from the epicuticular wax of stems of energy sorghum is available at the Great Lakes Bioenergy Researcher Center, Michigan State University, MI, USA. We enriched bacteria with putative plant-beneficial phenotypes and include information on their phenotypic diversity, taxonomy, and whole-genome sequences.
Single-cell quantitative bioimaging of
P. berghei
liver stage translation
Authors: McLellan James L. , Sausman William , Reers Ashley B. , Bunnik Evelien M. , Hanson Kirsten K. 
Published: November 2023

ABSTRACT

Plasmodium
parasite resistance to existing antimalarial drugs poses a devastating threat to the lives of many who depend on their efficacy. New antimalarial drugs and novel drug targets are in critical need, along with novel assays to accelerate their identification. Given the essentiality of protein synthesis throughout the complex parasite lifecycle, translation inhibitors are a promising drug class, capable of targeting the disease-causing blood stage of infection, as well as the asymptomatic liver stage, a crucial target for prophylaxis. To identify compounds capable of inhibiting liver stage parasite translation, we developed an assay to visualize and quantify translation in the
Plasmodium berghei-
HepG2 infection model. After labeling infected monolayers with o-propargyl puromycin (OPP), a functionalized analog of puromycin permitting subsequent bioorthogonal addition of a fluorophore to each OPP-terminated nascent polypeptide, we use automated confocal feedback microscopy followed by batch image segmentation and feature extraction to visualize and quantify the nascent proteome in individual
P. berghei
liver stage parasites and host cells simultaneously. After validation, we demonstrate specific, concentration-dependent liver stage translation inhibition by both parasite-selective and pan-eukaryotic active compounds and further show that acute pre-treatment and competition modes of the OPP assay can distinguish between known direct translation inhibitors and other compounds which we identify as indirect translation inhibitors. Using this framework, we identify a Malaria Box compound, MMV019266, as a direct translation inhibitor in
P. berghei
liver stages and confirm this potential mode of action in
Plasmodium falciparum
asexual blood stages.

IMPORTANCE

Plasmodium
parasites cause malaria in humans. New multistage active antimalarial drugs are needed, and a promising class of drugs targets the core cellular process of translation, which has many potential molecular targets. During the obligate liver stage,
Plasmodium
parasites grow in metabolically active hepatocytes, making it challenging to study core cellular processes common to both host cells and parasites, as the signal from the host typically overwhelms that of the parasite. Here, we present and validate a flexible assay to quantify
Plasmodium
liver stage translation using a technique to fluorescently label the newly synthesized proteins of both host and parasite followed by computational separation of their respective nascent proteomes in confocal image sets. We use the assay to determine whether a test set of known compounds are direct or indirect liver stage translation inhibitors and show that the assay can also predict the mode of action for novel antimalarial compounds.
Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model
Authors: Richie Tanner G. , Heeren Leah , Kamke Abigail , Monk Kourtney , Pogranichniy Sophia , Summers Trey , Wiechman Hallie , Ran Qinghong , Sarkar Soumyadev , Plattner Brandon L. , Lee Sonny T. M. 
Published: November 2023

ABSTRACT

Members of the Enterobacteriaceae and
Enterococcus
are associated with persistent gut inflammation due to rapid colonization combined with pathogenic tendencies. Here, we investigated the functions of gut microbial populations resulting in persistent gut inflammation. In this study, we utilized the IL-10 knockout mouse model and induced colitis using dextran sulfate sodium (2%) after development. Dams during gestation were provided cefoperazone to induce vertically transmitted dysbiosis in the pups that were monitored in this study. We characterized the dysbiotic gut microbial community and potential crosstalk of these microbes, and host gene expression changes to identify bacterial populations and potential functions that were involved in gut inflammation. We isolated Enterobacteriaceae populations from mice to validate the utilization of sulfur-containing amino acids. Members of Enterobacteriaceae and
Enterococcus
were highly detected in inflamed mice. Enterobacteriaceae populations containing L-cysteine dioxygenase were strongly correlated with the upregulation of host gene
CSAD
, responsible for cysteine breakdown. We observed that bacterial isolates from dysbiotic mice displayed increased growth rates when supplemented with L-cysteine, highlighting the use of sulfur metabolism. Our results show that microbial populations use alternate metabolisms and sequester host nutrients for growth, associated with inflammation in the gut.

IMPORTANCE
Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.
Ribosome profiling reveals the fine-tuned response of
Escherichia coli
to mild and severe acid stress
Authors: Schumacher Kilian , Gelhausen Rick , Kion-Crosby Willow , Barquist Lars , Backofen Rolf , Jung Kirsten 
Published: November 2023

ABSTRACT

The ability to respond to acidic environments is crucial for neutralophilic bacteria.
Escherichia coli
has a well-characterized regulatory network that triggers a multitude of defense mechanisms to counteract excess protons. Nevertheless, systemic studies of the transcriptional and translational reprogramming of
E. coli
to different degrees of acid stress have not yet been performed. Here, we used ribosome profiling and RNA sequencing to compare the response of
E. coli
(pH 7.6) to sudden mild (pH 5.8) and severe near-lethal acid stress (pH 4.4) conditions that mimic passage through the gastrointestinal tract. We uncovered new differentially regulated genes and pathways, key transcriptional regulators, and 18 novel acid-induced candidate small open reading frames. By using machine learning and leveraging large compendia of publicly available
E. coli
expression data, we were able to distinguish between the response to acid stress and general stress. These results expand the acid resistance network and provide new insights into the fine-tuned response of
E. coli
to mild and severe acid stress.

IMPORTANCE

Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract.
Escherichia coli
is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of
E. coli
K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.