bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of High-Resolution Downhole Tubular Inspection Tools by Full-Scale Field Testing
Authors: Tao Gang , Doan Quy , Islam Abrar , Abdulhameed Diana , Scoging Allen , Cardiff Steve 
Published: December 2024

Abstract
Downhole tubular corrosion poses a significant threat to underground gas storage (UGS) well integrity. Therefore, integrity management of UGS wells requires periodic inspection of tubular conditions using various inspection tools to properly identify and size corrosion anomalies. The corrosion inspection data are then used to estimate corrosion growth rates and the remaining strength of the tubulars through various methods. However, the calculated remaining life and remaining strength can have a significant uncertainty due to the variations of the input parameters, including the corrosion growth rate, accuracy of reported corrosion feature sizes from the inspection tools, tubular material property variations, uncertain in-situ load conditions, and prediction model uncertainties.
In order to improve the tubular corrosion management for UGS wells, this study focused on a quantitative performance evaluation of a few selected state-of-the-art downhole tubular corrosion inspection tools based on a full-scale field test program. This paper presents the process and methodology of the field test and performance evaluation of four high-resolution tools based on principles of ultrasonic testing and magnetic flux leakage, which can provide relatively accurate sizes (including depth, length and width) of corrosion features. Statistical approaches were employed to determine the quantitative tool performance metrics, including the probability of detection, probability of false call and sizing accuracy. Moreover, the statistical performance results not only allow the determination of the feature sizing tolerances that can be used in deterministic integrity assessment methods but also provide valuable inputs for further development of a probability-based tubular integrity assessment workflow.
Technical ILI System – Verification Versus Validation Based on Sound Engineering Practice Solely on Industry Recognized and Standardized Methodology
Authors: Hoening Patrick , Stubbe Thomas 
Published: December 2024

Abstract
For the qualification of technical In-Line Inspection (ILI) systems for pipeline inspections, API 1163 standard allows two different approaches to demonstrate the system’s performance; verification or validation, based on tests or simulations and validation using historical data, i.e. verified field measurements from excavations.
Verification ensures evidence of the entire performance specification in terms of Probability of Detection (POD), Probability of Identification (POI) and sizing capability, while validation defends the performance specification on a sample basis respectively derives individual aspects of the as-run performance. Successful verification of the ILI system should be a prerequisite for carrying out the validation.
Usually, verification takes place on test fields or in laboratories under controlled conditions in order to test the essential variables and thus to prove every aspect of the performance specification in regards to POD, POI and sizing capability.
API 1163 provides statistical methods for the practical implementation of measurement performance qualification, but these methods are described solely for the validation approach. This paper closes the gap by adapting industry recognized and standardized statistical methodologies to the problem of verifying technical ILI systems in terms of detection and sizing and comparing these methods to the ones, described in API 1163, proposed for the system’s validation.
Specifically, these methods for verifying ILI performance are the 29/29 method with Clopper-Pearson for POD and the Expanded Measurement Uncertainty method for sizing in accordance with GUM.
Efficacy of a Multicomponent Physical Activity Intervention for Teachers With or At Risk of Type 2 Diabetes: The Support, Motivation, and Physical Activity Research for Teachers Health Randomized Controlled Trial
Authors: Plotnikoff Ronald C. , Murphy Maria , Wilczynska Magdalena , Courneya Kerry S. , Brown Wendy J. , Sigal Ronald J. , Lubans David R. 
Published: December 2024

Background: Type 2 diabetes is a major cause of illness and disability and physical activity reduces these risks. The SMART Health study aim was to compare the efficacy of a multicomponent intervention to promote aerobic physical activity and resistance training in schoolteachers at risk of or diagnosed with type 2 diabetes, with and without a technology-based behavior change package. Methods: We randomized participants (N = 104) into 3 groups: “wait-list” control group, 5 face-to-face visits with a psychologist and exercise specialist (SH group), or 5 face-to-face visits over a 3-month period with a psychologist and exercise specialist, plus a technology-based behavior change package for an additional 6 months (SH+ group). Physical activity was the primary outcome (daily steps measured by pedometers). Systolic and diastolic blood pressure, waist circumference, body mass index, fasting blood glucose, glycosylated hemoglobin, plasma lipids, self-reported resistance training, anxiety and depression were also assessed at 3 and 9 months (primary time point). Linear mixed models were used to assess the intervention efficacy of SH and SH+ compared with wait-list control. Results: There were no significant group-by-time effects for steps in the SH or SH+ groups compared to the wait-list control group. Self-reported participation in monthly minutes of resistance training significantly increased at 3-month postbaseline in both groups (SH: 136 min, P < .01, d = 0.33 and SH+: 145 min P < .001, d = 0.4) versus the control group. The improvements were maintained for the SH group at 9 months. There was also a meaningful effect (P < .06, d = −0.23) for reducing anxiety for SH group at 9 months. Conclusions: SMART Health was a feasible, multicomponent intervention, which increased self-reported resistance training but no other secondary outcomes.
Outer membrane lipoproteins: late to the party, but the center of attention
Authors: May Kerrie L. , Grabowicz Marcin 
Published: December 2024

ABSTRACT

An outer membrane (OM) is the hallmark feature that is often used to distinguish “Gram-negative” bacteria. Our understanding of how the OM is built rests largely on studies of
Escherichia coli
. In that organism—and seemingly in all species of the Proteobacterial phyla—the essential pathways that assemble the OM each rely on one or more lipoproteins that have been trafficked to the OM. Hence, the lipoprotein trafficking pathway appeared to be foundational for the ability of these bacteria to build their OM. However, such a notion now appears to be misguided. New phylogenetic analyses now show us that lipoprotein trafficking was likely the very last of the essential OM assembly systems to have evolved. The emergence of lipoprotein trafficking must have been a powerful innovation for the ancestors of Proteobacteria, given how it assumed such a central place in OM biogenesis. In this minireview, we broadly discuss the biosynthesis and trafficking of lipoproteins and ponder why the newest OM assembly system (lipoprotein trafficking) has become so key to building the Proteobacterial OM. We examine the diversity among lipoprotein trafficking systems, noting uniting commonalities and highlighting key differences. Current novel antibiotic development is targeted against a small subset of Proteobacterial species that cause severe human diseases; several inhibitors of lipoprotein biosynthesis and OM trafficking have been recently reported that may become new antibiotics. Understanding the diversity in lipoprotein trafficking may yield selective new antibiotics that preferentially kill important human pathogens while sparing species of normal healthy flora.
Transcriptomic analysis of coxsackievirus B3 infection in induced pluripotent stem cell-derived brain-like endothelial cells
Authors: Hathcock Sarah F. , Mamana Julia , Keyzer Taryn E. , Vollmuth Nadine , Shokri Mohammad-Reza , Mauser Henry D. , Correll Robert N. , Lam Daryl W. , Kim Brandon J. , Sin Jon 
Published: December 2024

ABSTRACT

Viral aseptic meningitis is a neuroinflammatory condition that occurs when viruses gain access to the central nervous system (CNS) and induce inflammation. The blood–brain barrier (BBB) is comprised of brain endothelial cells (BECs) that stringently regulate the passage of molecules, toxins, and pathogens from the circulation into the CNS. Through their unique properties, such as complex tight junctions, reduced rates of endocytosis, expression of efflux transporters, and restricted expression of leukocyte adhesion molecules, the BBB is often able to limit pathogen entry into the brain; however, certain neurotropic pathogens, such as coxsackievirus B3 (CVB3) are able to infect the CNS. We have previously demonstrated that CVB3 can infect and disrupt induced pluripotent stem cell-derived brain-like endothelial cells (iBECs), but the host response to this infection remains unknown. Here, we investigate global host transcriptional changes during CVB3 infection of iBECs using RNA sequencing. We validated our data set by exploring pathways altered by CVB3 using quantitative real-time PCR (qPCR) and enzyme-linked immunosorbent assay of upregulated cytokines and interferon signaling molecules.

IMPORTANCE
Coxsackievirus B3 (CVB3) is a leading cause of viral aseptic meningitis that can produce severe disease in susceptible individuals. To gain access to the central nervous system, CVB3 must cross central nervous system barriers, such as the blood–brain barrier. Previously, we have shown that CVB3 infects a human stem cell-derived brain-like endothelial cell model. Here, we report the global transcriptome of stem cell-derived brain-like endothelial cells to CVB3 infection and provide proof-of-concept validation of the dataset using molecular biology techniques. These data could inform novel mechanisms of CVB3-mediated blood–brain barrier dysfunction.
Gcn2 rescues reprogramming in the absence of Hog1/p38 signaling in
C. neoformans
during thermal stress
Authors: Goich David , Bloom Amanda L. M. , Duffy Sean R. , Ventura Maritza N. , Panepinto John C. 
Published: December 2024

ABSTRACT

The fungus
Cryptococcus neoformans
is an opportunistic pathogen of humans that reprograms its translatome to facilitate adaptation and virulence within the host. We studied the role of Hog1/p38 in reprogramming translation during thermal stress adaptation and found that this pathway acts on translation
via
crosstalk with the Gcn2 pathway, a well-studied regulator of general translation control. Using a combination of molecular assays and phenotypic analysis, we show that increased output from the Gcn2 pathway in a Hog1 deletion mutant is associated with rescue of thermal stress adaptation at both molecular and phenotypic scales. We characterize known outputs of the Hog1 pathway during thermal stress as either Gcn2-dependent or Gcn2-independent and demonstrate that Hog1 activation regulates the Gcn2 pathway even in the absence of thermal stress. Finally, we implicate this phenomenon in another Hog1-regulated process, morphogenesis, and recapitulate Hog1–Gcn2 crosstalk in the distantly related fungal pathogen,
Candida albicans
. Our results point to an important link between the stress response machinery and translation control and clarify the etiology of phenotypes associated with Hog1 deletion. More broadly, this study highlights complex interplay between core conserved signal transduction pathways and the utility of molecular assays to better understand how these pathways are connected.

IMPORTANCE

Cryptococcus neoformans
is an opportunistic pathogen of humans that causes deadly cryptococcal meningitis, which is is responsible for an estimated 19% of AIDS-related mortality. When left untreated, cryptococcal meningitis is uniformly fatal, and in patients receiving the most effective antifungal regimens, mortality remains high. Thus, there is a critical need to identify additional targets that play a role in the adaptation to the human host and virulence. This study explores the role of the stress response kinases Hog1 and Gcn2 in thermoadaptation, which is a pre-requisite for virulence. Our results show that compensatory signaling occurs
via
the Gcn2 pathway when Hog1 is deleted, and that disruption of both pathways increases sensitivity to thermal stress. Importantly, our study highlights the insufficiency of using single-gene deletion mutants to study gene function, since many phenotypes associated with Hog1 deletion were driven by Gcn2 signaling in this background, rather than loss of direct Hog1 activity.
Development of an sRNA-mediated conditional knockdown system for
Chlamydia trachomatis
Authors: Ehses Janina , Wang Kevin , Densi Asha , Ramirez Cuper , Tan Ming , Sütterlin Christine 
Published: December 2024

ABSTRACT

We describe a new
Chlamydia trachomatis
protein depletion method that uses an engineered small RNA (sRNA) to inhibit translation of a target gene. In proof-of-principle experiments, we induced functional knockdown of IncA, a fusion-mediating inclusion membrane protein, as shown with Western blots, loss of IncA staining at the inclusion membrane, and production of multiple chlamydial inclusions within an infected cell. These effects were titratable and reversible. To test for polar effects, we separately targeted the inclusion membrane proteins IncE and IncG, which are expressed from the
incDEFG
operon. Knockdown of IncE caused loss of IncE and its interacting host protein SNX6 at the inclusion membrane, without affecting IncG protein levels. Similarly, IncG knockdown significantly reduced IncG levels and prevented recruitment of its interacting host protein 14-3-3β, without altering IncE protein levels. These data provide the first genetic evidence that IncE and IncG are necessary for the recruitment of SNX6 and 14-3-3β, respectively, demonstrating the value of this knockdown approach. We also successfully depleted the major chlamydial surface protein, major outer membrane protein (MOMP), which is encoded by a likely essential gene that has not been previously disrupted or knocked down. MOMP knockdown caused severe defects in bacterial morphology and progeny production. Thus, our sRNA-based approach has broad potential as a conditional knockdown method for studying the function of
C. trachomatis
genes, including essential genes and genes in an operon.

IMPORTANCE

We describe a new method to reduce protein levels of a selected gene in the pathogenic bacterium
Chlamydia trachomatis
. This approach utilizes an engineered small RNA (sRNA) to inhibit translation of the mRNA for a target gene and produced inducible and reversible protein knockdown. Our method successfully knocked down four proteins, including a likely essential gene and individual genes in an operon, without altering protein levels of a neighboring gene. This conditional knockdown method will be useful for studying the function of genes in
Chlamydia
. It also has the potential to be applied to other obligate intracellular bacteria, including
Rickettsia
and
Coxiella
.
Draft genome sequence of
Bremerella cremea
LHWP2 isolated from dead ark clam revealing potential nitrogen metabolism pathways
Authors: Seo Jin-Hee , Yim Kyung June , Lim Jongbin , Chun Ji-Yeon , Lee Hae-Won 
Published: December 2024

ABSTRACT

We present the draft genome sequence of
Bremerella cremea
LHWP2, a notable member of the Planctomycetes–Verrucomicrobia–Chlamydiae group, isolated from a dead ark clam. The 6,211,343-bp genome contains 5,304 coding gene sequences with a guanine–cytosine content of 56.5 %. The draft genome also reveals potential nitrogen metabolic pathways.
Near full-length genome sequence of a vesicular stomatitis New Jersey virus isolate collected from a naturally infected cow in the endemic state of Chiapas, Mexico
Authors: Valdez Federico , Velazquez-Salinas Lauro , Zhou Lawrence H. , Smoliga George R. , Fish Ian , Navarro-Lopez Roberto , Lopez-Gonzalez Irene , Hanley Kathryn A. , Mire Chad E. , Rodriguez Luis L. , Arzt Jonathan 
Published: December 2024

ABSTRACT

Here, we report the near full-length genome sequence of a
Vesiculovirus newjersey
isolate obtained from a naturally infected cow (
Bos taurus
) in the state of Chiapas, Mexico. This sequence will support future efforts to improve our understanding of the evolutionary dynamics of this pathogen in endemic regions of Mexico.
Protein kinases MpkA and SepH transduce crosstalk between CWI and SIN pathways to activate protective hyphal septation under echinocandin cell wall stress
Authors: Doan Alexander G. , Schafer Jessica E. , Douglas Casey M. , Quintanilla Matthew S. , Morse Meredith E. , Edwards Harley , Huso Walker D. , Gray Kelsey J. , Lee JungHun , Dayie Joshua K. , Harris Steven D. , Marten Mark R. 
Published: December 2024

ABSTRACT

This study investigates a previously unreported stress signal transduced as crosstalk between the cell wall integrity (CWI) pathway and the septation initiation network (SIN). Echinocandins, which target cell wall synthesis, are widely used to treat mycoses. Their efficacy, however, is species specific. Our findings suggest that this is due largely to CWI–SIN crosstalk and the ability of filamentous species to fortify with septa in response to echinocandin stress. To better understand this crosstalk, we used a microscopy-based assay to measure septum density, aiming to understand the septation response to cell wall stress. The echinocandin micafungin, an inhibitor of β-(1,3)-glucan synthase, was employed to induce this stress. We observed a strong positive correlation between micafungin treatment and septum density in wild-type strains. This finding suggests that CWI activates SIN under cell wall stress, increasing septum density to protect against cell wall failure. More detailed investigations, with targeted knockouts of CWI and SIN signaling proteins, enabled us to identify crosstalk occurring between the CWI kinase, MpkA, and the SIN kinase, SepH. This discovery of the previously unknown crosstalk between the CWI and SIN pathways not only reshapes our understanding of fungal stress responses, but also unveils a promising new target pathway for the development of novel antifungal strategies.

IMPORTANCE
Echinocandin-resistant species pose a major challenge in clinical mycology by rendering one of only four lines of treatment, notably one of the two that are well-tolerated, ineffective in treating systemic mycoses of these species. Previous studies have demonstrated that echinocandins fail against highly polarized fungi because they target only apical septal compartments. It is known that many filamentous species respond to cell wall stress with hyperseptation. In this work, we show that echinocandin resistance hinges on this dynamic response, rather than on innate septation alone. We also describe, for the first time, the signaling pathway used to deploy the hyperseptation response. By disabling this pathway, we were able to render mycelia susceptible to echinocandin stress. This work enhances our microbiological understanding of filamentous fungi and introduces a potential target to overcome echinocandin-resistant species.
Spatiotemporal distribution patterns and assembly mechanisms of eukaryotic plankton communities in Liujiaxia Reservoir at the northeastern edge of the Tibetan Plateau
Authors: Chen Lingyun , Cheng Jihua , Wanma Yangcuo , Zhu Shiying , Warren Alan , Ning Yingzhi 
Published: December 2024

ABSTRACT

Eukaryotic plankton are important parts of the aquatic ecosystem and their community composition and spatiotemporal distribution patterns are affected by environmental factors. The Liujiaxia Reservoir is located at the northeastern edge of the Tibetan Plateau and is a vital resource for communities and agriculture in the region. Revealing the plankton diversity and their correlation with environmental factors is essential for understanding the ecological processes and mechanisms by which plankton contribute to, and maintain the ecosystem function of, the Liujiaxia Reservoir and beyond. This study investigated the detailed spatiotemporal distribution patterns and assembly mechanisms of eukaryotic plankton communities in Liujiaxia Reservoir for three periods during 2021. Significant spatial and temporal variations of abundance and community distribution of eukaryotic plankton were demonstrated. In addition, environmental factors such as water transparency, total phosphorus, total nitrogen, ammonia nitrogen, and pH were confirmed to have the most significant impact on the distribution of these communities in the reservoir. The dominant eukaryotic plankton group was Pyrrophyta, and the species interactions were predominantly cooperative. The trophic level index indicated excellent overall water quality in the reservoir. Deterministic processes were demonstrated as the predominant factors governing the assembly of eukaryotic plankton communities. This study provides valuable insight into the eukaryotic plankton community structure in the Liujiaxia Reservoir and reveals the complex relationships between plankton communities, environmental factors, and water quality.

IMPORTANCE
Based on 18S rDNA high-throughput sequencing, the spatiotemporal distribution patterns and assembly mechanisms of eukaryotic plankton communities were investigated. This study provides valuable insight into the eukaryotic plankton community structure in the Liujiaxia Reservoir in the northeastern edge of the Tibetan Plateau, and the relationships between eukaryotic plankton communities, environmental factors, and water quality. Through the dynamic changes of these communities, the water quality of the reservoir was assessed to provide basic data for the protection of its biodiversity. The findings of the present study will help to improve knowledge and understanding of the ecological processes and mechanisms by which plankton contribute to ecosystem function in the Liujiaxia Reservoir and beyond.