bluuebunny/crossref_metadata_2025 huggingface dataset:
Mesothelioma in the pleura, pericardium and peritoneum: Recommendations from the International Collaboration on Cancer Reporting (ICCR)
Authors: Klebe Sonja , Judge Meagan , Brcic Luka , Dacic Sanja , Galateau‐Salle Francoise , Nicholson Andrew G , Roggli Victor , Nowak Anna K , Cooper Wendy A
Published: December 2023

Aims

Mesothelioma is a rare malignancy of the serosal membranes that is commonly related to exposure to asbestos. Despite extensive research and clinical trials, prognosis to date remains poor. Consistent, comprehensive and reproducible pathology reporting form the basis of all future interventions for an individual patient, but also ensures that meaningful data are collected to identify predictive and prognostic markers.

Methods and results

This article details the International Collaboration on Cancer Reporting (ICCR) process and the development of the international consensus mesothelioma reporting data set. It describes the ‘core’ and ‘non‐core’ elements to be included in pathology reports for mesothelioma of all sites, inclusive of clinical, macroscopic, microscopic and ancillary testing considerations. An international expert panel consisting of pathologists and a medical oncologist produced a set of data items for biopsy and resection specimens based on a critical review and discussion of current evidence, and in light of the changes in the 2021 WHO Classification of Tumours. The commentary focuses particularly upon new entities such as mesothelioma in situ and provides background on relevant and essential ancillary testing as well as implementation of the new requirement for tumour grading.

Conclusion

We recommend widespread and consistent implementation of this data set, which will facilitate accurate reporting and enhance the consistency of data collection, improve the comparison of epidemiological data, support retrospective research and ultimately help to improve clinical outcomes. To this end, all data sets are freely available worldwide on the ICCR website (www.iccr‐cancer.org/data‐sets).
Predicted factors of surgical site infection in glioblastoma patients: A meta‐analysis
Authors: Gu Zhaowen , Wang Qiangwei , Chen Jiarui , Zhu Yongjian
Published: December 2023

Surgical site infection (SSI) is one of the common postoperative complications after craniotomy for glioblastoma patients. Previous studies have investigated the risk factors for SSI in patients with glioblastoma. Whereas big differences in research results exist, and the correlation coefficients of different research results are quite different. A meta‐analysis was conducted to examine the risk factors related to surgical site infection in patients with glioblastoma. We searched English databases to collect case–control studies or cohort studies published before 15 October 2023 including PubMed, Web of Science, Embase. The risk of bias of the included studies was assessed via Newcastle‐Ottawa Scale. The analysis was performed using RevMan 5.4.1 tool. A total of 4 articles (n = 2222) were selected in this meta‐analysis. The following risk factors were presented to be correlated with SSI in glioblastoma: irradiation (OR = 1.88, 95% CI [0.46, 7.60]), more than 3 surgeries (OR = 2.99, 95% CI [1.47, 6.08]). Occurrence of SSI is influenced by a variety of factors. Thus, we should pay close attention to high‐risk subjects and take crucial targeted interventions to lower the SSI risk following craniotomy. Owing to the limited quality and quantity of the included studies, more rigorous studies with adequate sample sizes are needed to verify the conclusion.
Adaptive interviewing for the inclusion of people with intellectual disability in qualitative research
Authors: McFarland Bridget , Bryant Lia , Wark Stuart , Morales‐Boyce Tyson
Published: December 2023

Background

Historically the voices of people with intellectual disability have been occluded by barriers imposed by research practice. More recently, adaptive research approaches have been proposed to enhance the inclusion of people with intellectual disability in qualitative research.

Method

This article presents an adaptive interviewing approach employed with five people ageing with intellectual disabilities in rural South Australia. The interviews were conducted within a broader participatory action research project in which tools and resources were co‐designed for post‐parental care planning.

Results

We describe our adaptive interviewing approach incorporating multiple methods: (i) responsive communication techniques; (ii) the inclusion and support of family carers; (iii) visual tools; (iv) walking interviews.

Conclusion

Findings contribute knowledge about how an adaptive interview approach supports the participation of people with an intellectual disability in qualitative research.
Patient‐reported quality of life and acceptance of the extravascular implantable cardioverter‐defibrillator: Results from pivotal study
Authors: Sears Samuel F. , Harrell Rebecca , Crozier Ian , Murgatroyd Francis , Boersma Lucas V. A. , Manlucu Jaimie , Knight Bradley P. , Leclercq Christophe , Birgersdotter‐Green Ulrika Maria , Wiggenhorn Christopher , Hilleren Gregory , Friedman Paul
Published: December 2023

Introduction

The pivotal study of the extravascular implantable cardioverter‐defibrillator (EV ICD) recently demonstrated primary efficacy and safety endpoints comparable to previous ICD systems. Patient experience with this novel device has not been reported. The current study examined the standardized patient‐reported outcome (PRO) metrics of quality of life (QOL) and patient acceptance of the device.

Methods

The EV ICD Pivotal Study was a prospective, single‐arm, nonrandomized, global, premarket approval trial. Patients completed the 12‐Item Short Form Survey (SF‐12) QOL surveys at baseline and at 6 months following implant. Additionally, patients completed the Florida Patient Acceptance Survey (FPAS) QOL survey at 6 months.

Results

From baseline to 6 months, patients within the EV ICD Pivotal Study (n = 247) reported statistically significant SF‐12 improvements in physical QOL (45.4 ± 9.4 vs. 46.8 ± 9.1 respectively, p = .020) and no changes in mental QOL (49.3 ± 10.4 vs. 50.5 ± 9.7, p = .061). No differences were noted by sex, atrial fibrillation, or the experience of ICD shock. EV ICD patients reported better total FPAS patient acceptance of their ICD than TV‐ICD or S‐ICD patients using historical norms comparisons (80.4 ± 15.7 vs. 70.2 ± 17.8, p < .0001 for S‐ICD and 73.0 ± 17.4, p = .004 for TV‐ICD).

Conclusion

The initial PROs for EV ICD patients indicated that patients had improvements in physical QOL from baseline to 6‐month follow‐up and markedly better overall acceptance of their ICD compared to a previous study with S‐ICD and TV‐ICD data. These initial results suggest that the EV ICD is evaluated positively by patients.
Board talk: How members of executive hospital boards influence the positioning of nursing in crisis through talk
Authors: Verhoeven Arjan , Marres Henri , van de Loo Erik , Lalleman Pieterbas
Published: December 2023

Talk by members of executive hospital boards influences the organizational positioning of nurses. Talk is a relational leadership practice. Using a qualitative‐interpretive design we organized focus group meetings wherein members of executive hospital boards (7), nurses (14), physicians (7), and managers (6), from 15 Dutch hospitals, discussed the organizational positioning of nursing during COVID crisis. We found that members of executive hospital boards consider the positioning of nursing in crisis a task of nurses themselves and not as a collective, interdependent, and/or specific board responsibility. Furthermore, members of executive hospital boards talk about the nursing profession as (1) more practical than strategic, (2) ambiguous in positioning, and (3) distinctive from the medical profession. Such talk seemingly contrasts with the notion of interdependence that highlights how actors depend on each other in interaction. Interdependence is central to collaboration in hospital crises. In this paper, therefore, we depart from the members of executive hospital boards as leader and “positioner,” and focus on talk—as a discursive leadership practice—to illuminate leadership and governance in hospitals in crisis, as social, interdependent processes.
The regeneration conferring transcription factor complex ERF115‐PAT1 coordinates a wound‐induced response in root‐knot nematode induced galls
Authors: Ribeiro Cleberson , de Melo Bruno Paes , Lourenço‐Tessutti Isabela Tristan , Ballesteros Helkin Forero , Ribeiro Karla Veloso Gonçalves , Menuet Killian , Heyman Jefri , Hemerly Adriana , de Sá Maria Fatima Grossi , De Veylder Lieven , de Almeida Engler Janice
Published: December 2023

The establishment of root‐knot nematode (RKN; Meloidogyne spp.) induced galls in the plant host roots likely involves a wound‐induced regeneration response. Confocal imaging demonstrates physical stress or injury caused by RKN infection during parasitism in the model host Arabidopsis thaliana.

The ERF115‐PAT1 heterodimeric transcription factor complex plays a recognized role in wound‐induced regeneration. ERF115 and PAT1 expression flanks injured gall cells likely driving mechanisms of wound healing, implying a local reactivation of cell division which is also hypothetically involved in gall genesis.

Herein, functional investigation revealed that ectopic ERF115 expression resulted in premature induction of galls, and callus formation adjacent to the expanding female RKN was seen upon PAT1 upregulation. Smaller galls and less reproduction were observed in ERF115 and PAT1 knockouts. Investigation of components in the ERF115 network upon overexpression and knockdown by qRT‐PCR suggests it contributes to steer gall wound‐sensing and subsequent competence for tissue regeneration. High expression of CYCD6;1 was detected in galls, and WIND1 overexpression resulted in similar ERF115OE gall phenotypes, also showing faster gall induction.

Along these lines, we show that the ERF115‐PAT1 complex likely coordinates stress signalling with tissue healing, keeping the gall functional until maturation and nematode reproduction.
Comparison of the anticancer effects of various statins on canine oral melanoma cells
Authors: Ishikawa Takuro , Irie Nanami , Tashiro Jiro , Osaki Tomohiro , Warita Tomoko , Warita Katsuhiko , Naito Munekazu
Published: December 2023

Canine oral melanoma is a highly malignant cancer with a poor prognosis. Statins, commonly used drugs for treating dyslipidemia, exhibit pleiotropic anticancer effects and marked anti‐proliferative effects against melanoma cells. The anticancer effects among statins vary; in human cancers, lipophilic statins have shown stronger anticancer effects compared with hydrophilic statins. However, data on the differences in the effects of various statins on canine cancer cells are lacking, hence the optimal statins for treating canine melanoma remain unknown. Therefore, this study aimed to clarify the most effective statin by comparing the anticancer effects of hydrophilic rosuvastatin and lipophilic atorvastatin, simvastatin, fluvastatin and pitavastatin on three canine oral melanoma cell lines. Time‐dependent measurement of cell confluence showed that lipophilic statins had a stronger anti‐proliferative effect on all cell lines than hydrophilic rosuvastatin. Quantification of lactate dehydrogenase release, an indicator of cytotoxicity, showed that lipophilic statins more effectively induced cell death than hydrophilic rosuvastatin. Lipophilic statins affected both inhibition of cell proliferation and induction of cell death. The anticancer effects of statins on canine oral melanoma cells differed in the following ascending order of IC50 values: pitavastatin < fluvastatin = simvastatin < atorvastatin < rosuvastatin. The required concentration of pitavastatin was approximately 1/20th that of rosuvastatin. Among the statins used in this study, pitavastatin had the highest anticancer effect. Our results suggest lipophilic pitavastatin as the optimal statin for treating canine oral melanoma.
Efficacy of therapeutic plasma exchange in a case of severe, generalised canine pemphigus foliaceus
Authors: Edmonds Kaitlyn Bello , Her Jiwoong , Langston Catherine , Jennings Ryan , Diaz Sandra
Published: December 2023

Successful treatment of pemphigus foliaceus (PF) often requires a multimodal therapeutic approach. The dog described herein underwent four therapeutic plasma exchange treatments for severe, refractory PF, resulting in a 50% reduction of lesional body surface area. This treatment option should be considered for the management of canine PF.
What is the Effect of a Magnetic Field on Dye Adsorption onto Graphite Carbon?
Authors: Attan Nursyafreena , Ramadhani Desmilia Putri , Munadhiroh Asmi , Nur Hadi
Published: December 2023

This research explores the impact of magnetic fields on dye adsorption onto graphite carbon, utilizing electric currents to generate varying magnetic field strengths, as determined by the Biot-Savart law. The study demonstrates that even with small current magnitudes typically used in physics laboratories, the generated magnetic fields significantly influence dye adsorption. Through experiments with currents ranging from 1.5 A to 7.5 A, resulting in magnetic fields from 1.54 µT to 4.63 µT, we observed enhanced adsorption for congo red, methylene blue, and methyl orange. In contrast, phenol red exhibited a unique desorption pattern due to electrostatic repulsion. Temperature variations were noted but were considered to have a negligible effect on the adsorption behavior. The findings highlight the crucial role of magnetic energy density and the charge of dye molecules in the adsorption process, leading to the conclusion that magnetic fields, indeed, play a significant role in influencing dye adsorption onto graphite carbon, with potential applications in environmental conservation and industrial waste management.
Subsets of without L-shaped configurations
Authors: Peluse Sarah
Published: December 2023

Fix a prime $p\geq 11$. We show that there exists a positive integer $m$ such that any subset of $\mathbb {F}_p^n\times \mathbb {F}_p^n$ containing no nontrivial configurations of the form $(x,y)$, $(x,y+z)$, $(x,y+2z)$, $(x+z,y)$ must have density $\ll 1/\log _{m}{n}$, where $\log _{m}$ denotes the $m$-fold iterated logarithm. This gives the first reasonable bound in the multidimensional Szemerédi theorem for a two-dimensional four-point configuration in any setting.
Endurance exercise training changes the limitation on muscle V̇O2max${\dot{V}}_{{{\mathrm{O}}}_{\mathrm{2}}{\mathrm{max}}}$ in normoxia from the capacity to utilize O2 to the capacity to transport O2
Authors: Broxterman Ryan M. , Wagner Peter D. , Richardson Russell S.
Published: December 2023

Maximal oxygen (O2) uptake () is an important parameter with utility in health and disease. However, the relative importance of O2 transport and utilization capacities in limiting muscle before and after endurance exercise training is not well understood. Therefore, the present study aimed to identify the mechanisms determining muscle pre‐ and post‐endurance exercise training in initially sedentary participants. In five initially sedentary young males, radial arterial and femoral venous (blood samples), leg blood flow (thermodilution), and myoglobin (Mb) desaturation (1H nuclear magnetic resonance spectroscopy) were measured during maximal single‐leg knee‐extensor exercise (KE) breathing either 12%, 21% or 100% O2 both pre and post 8 weeks of KE training (1 h, 3 times per week). Mb desaturation was converted to intracellular using an O2 half‐saturation pressure of 3.2 mmHg. Pre‐training muscle was not significantly different across inspired O2 conditions (12%: 0.47 ± 0.10; 21%: 0.52 ± 0.13; 100%: 0.54 ± 0.01 L min–1, all q > 0.174), despite significantly greater muscle mean capillary–intracellular gradients in normoxia (34 ± 3 mmHg) and hyperoxia (40 ± 7 mmHg) than hypoxia (29 ± 5 mmHg, both q < 0.024). Post‐training muscle was significantly different across all inspired O2 conditions (12%: 0.59 ± 0.11; 21%: 0.68 ± 0.11; 100%: 0.76 ± 0.09 mmHg, all q < 0.035), as were the muscle mean capillary–intracellular gradients (12%: 32 ± 2; 21%: 37 ± 2; 100%: 45 ± 7 mmHg, all q < 0.029). In these initially sedentary participants, endurance exercise training changed the basis of limitation on muscle in normoxia from the mitochondrial capacity to utilize O2 to the capacity to transport O2 to the mitochondria.

image

Key points

Maximal O2 uptake is an important parameter with utility in health and disease.

The relative importance of O2 transport and utilization capacities in limiting muscle maximal O2 uptake before and after endurance exercise training is not well understood.

We combined the direct measurement of active muscle maximal O2 uptake with the measurement of muscle intracellular before and after 8 weeks of endurance exercise training.

We show that increasing O2 availability did not increase muscle maximal O2 uptake before training, whereas increasing O2 availability did increase muscle maximal O2 uptake after training.

The results suggest that, in these initially sedentary participants, endurance exercise training changed the basis of limitation on muscle maximal O2 uptake in normoxia from the mitochondrial capacity to utilize O2 to the capacity to transport O2 to the mitochondria.
Hydrodynamic Performance of an Array of Stratified Pile Rock Breakwaters Placed on Elevated Seabed
Authors: Dhanunjaya E. , Sanjeeva Rayudu E. , Venkateswarlu V.
Published: December 2023

The present study outlines the hydrodynamic performance of stratified pile-rock breakwaters (SPRBs) in series using the analytical calculation under the framework of linearized potential flow theory. The rubble mounds are separated into two porous layers (surface and bottom layers) and tightly packed within the space available between the seaside and leeside vertical piles. The SPRB is installed on the elevated bed, and it is considered as a bottom rigid layer. The newly proposed breakwater is titled as stratified pile-rock breakwater and vertical piles are suggested to minimize the unwanted displacements of rubble mounds from frequent failures due to the incident wave stroke. The analytical model is developed based on the method of matched eigenfunction expansions (MMEEs) along with suitable boundary conditions to assess the hydrodynamic performance of the SPRB. The study results are compared with the literature based on experimental and analytical methods for specific conditions. The wave reflection, transmission, and energy damping by a series of SPRBs are reported for changes in incident wave properties and breakwater physical properties. The effect of layer porosity, angle of contact, free spacing, and number of breakwaters on the hydrodynamic coefficients is reported. The study suggested that a pair of SPRBs having 80% and 40% porosities for surface and bottom layers, with clear spacing, varied within 1 ≤ w/h1 ≤ 2, and the angle of contact varied within 30 deg ≤ θ ≤ 45 deg to achieve a 90% wave-damping when the relative wavenumber is k10h1 = 1.
Resistance Exercise Training, a Simple Intervention to Preserve Muscle Mass and Strength in Prostate Cancer Patients on Androgen Deprivation Therapy
Authors: Houben Lisanne H.P. , Beelen Milou , van Loon Luc J.C. , Beijer Sandra
Published: December 2023

Androgen deprivation therapy (ADT) forms the cornerstone in the treatment of advanced prostate cancer. However, by suppressing testosterone ADT results in a decrease of skeletal muscle mass. In this narrative review, we explore the magnitude and mechanisms of ADT-induced muscle mass loss and the consequences for muscle strength and physical performance. Subsequently, we elucidate the effectiveness of supervised resistance exercise training as a means to mitigate these adverse effects. Literature shows that resistance exercise training can effectively counteract ADT-induced loss of appendicular lean body mass and decline in muscle strength, while the effect on physical performances is inconclusive. As resistance exercise training is feasible and can be safely implemented during ADT (with special attention for patients with bone metastases), it should be incorporated in standard clinical care for prostate cancer patients (starting) with ADT.
Developing Self-Awareness and Emotional Intelligence in Adolescent Soccer: A Community Outreach Pilot Program
Authors: Gomez Souffront Sabrina , Everett Enzo R.N. , Kostrna Jason
Published: December 2023

Sport provides opportunities for adolescents to develop psychological skills. To realize this potential, sport facilitators must actively create a culture that develops adolescent athletes. Psychological skills training and biofeedback training have been effective at developing psychological skills in adult athletes. However, little research has focused on the effects of psychological skills training and biofeedback training in adolescent athletes. This study tests the efficacy of a pilot community outreach program to promote psychological skills development in adolescent soccer players from a travel soccer team (n = 21). During the 2-week intervention, researchers taught participants psychophysiological content related to self-awareness, emotional intelligence, and decision making. The psychological skills training sessions included active learning activities, group discussions, and reflection. Throughout the sessions, researchers used biofeedback to demonstrate and train participants in psychophysiological concepts. The 2-week intervention gave participants opportunities each day to monitor and reflect on their psychological performance state. Program evaluation data showed descriptive improvements in the ability to focus, control arousal, reduce stress, and control emotions. Wilcoxon signed-rank tests revealed significant positive changes occurred for decision-making self-efficacy. The intervention and efficacy of this study support applied practitioners’ integration of biofeedback and psychological skills training to improve adolescents’ self-awareness, emotional intelligence, and decision making.
A novel Shiga toxin 2a neutralizing antibody therapeutic with low immunogenicity and high efficacy
Authors: Kirkland Marina E. , Patfield Stephanie , Hughes Anna C. , Hernlem Bradley , He Xiaohua
Published: December 2023

Shiga toxin-producing
Escherichia coli
infections are difficult to treat due to the risk of antibiotic-induced stress upregulating the production of toxins, medical treatment is consequently limited to supportive care to prevent the development of hemolytic uremic syndrome (HUS). Here, we introduce a potentially therapeutic humanized mouse monoclonal antibody (Hu-mAb 2-5) targeting Stx2a, the most common Shiga toxin subtype identified from outbreaks. We demonstrate that Hu-mAb 2-5 has low immunogenicity in healthy adults
ex vivo
and high neutralizing efficacy
in vivo
, protecting mice from mortality and HUS-related tissue damage.
Pharmacokinetic and pharmacodynamic evaluation of the atypical tetracyclines chelocardin and amidochelocardin in murine infection models
Authors: Rox Katharina , Jansen Rolf , Lukežič Tadeja , Greweling-Pils Marina , Herrmann Jennifer , Miethke Marcus , Hüttel Stephan , Hennessen Fabienne , Abou Fayad Antoine , Holzhausen Cornelia , Lundberg Carina Vingsbo , Teague Joanne , Sudarman Enge , Bülter Lisa , Hesterkamp Thomas , Stadler Marc , Brönstrup Mark , Müller Rolf
Published: December 2023

The quest for novel anti-infectives against drug-resistant pathogens of the so-called ESKAPE panel is accompanied by intensive research aiming to find treatment options for the future. In this study, we evaluated the pharmacokinetics and pharmacodynamics of the two atypical tetracyclines: chelocardin (CHD) and amidochelocardin (CDCHD). Although CHD was in phase II clinical trials in the 1970s against urinary tract infections (UTI), CDCHD is a novel derivative obtained by biosynthetic engineering. A pharmacokinetic evaluation in uninfected, non-neutropenic CD-1 outbred mice using intravenous, peroral, and subcutaneous routes showed that CHD had higher plasma exposure than CDCHD but underwent an epimerization that was not observed for CDCHD. CDCHD showed persistently high exposure levels in urine lasting for more than 24 hours, whereas CHD urine concentrations decreased faster over time. Pharmacodynamic characterization in the neutropenic thigh infection model with
K. pneumoniae
and
E. coli
as challenge pathogens in CD-1 outbred mice proved that CHD was more effective in reducing bacterial burden in the thigh, in particular against
E. coli
, whereas CDCHD effectively reduced bacterial burden in kidneys affected by hematogenous seeding from the primary inoculation site, that is, thigh. Assessment of both atypical tetracyclines in an ascending UTI model with bladder as the primary inoculation site against gentamicin as positive control revealed high effectiveness of CDCHD. In summary, CDCHD warrants further preclinical exploration for the indication of UTI.

IMPORTANCE

There is a strong need to find novel treatment options against urinary tract infections associated with antimicrobial resistance. This study evaluates two atypical tetracyclines, namely chelocardin (CHD) and amidochelocardin (CDCHD), with respect to their pharmacokinetics and pharmacodynamics. We show CHD and CDCHD are cleared at high concentrations in mouse urine. Especially, CDCHD is highly effective in an ascending urinary tract infection model, suggesting further preclinical evaluation.
Oxygen-driven divergence of marine group II archaea reflected by transitions of superoxide dismutases
Authors: Qu Liping , Li Meng , Gong Fahui , He Lei , Li Minchun , Zhang Chuanlun , Yin Kedong , Xie Wei
Published: December 2023

The superoxide anion radical (O
2•−
), the primary reactive oxygen species (ROS), is detrimental to cellular functions. Marine group II (MGII) archaea predominantly inhabit surface ocean environments that are rich in ROS; however, their defense mechanisms against ROS damage remain unknown. In this study, we integrated the analyses of archaeal 16S rRNA gene amplicons and metagenome-assemblage genomes of MGII archaea from the northern South China Sea and 250 other previously published MGII genomes to investigate their antioxidant mechanisms. The results show that the proportion of oxygen-promoted MGII operational taxonomic units in the iron/manganese superoxide dismutase (Fe/MnSOD) gene-containing group was significantly higher than that in the nickel SOD (NiSOD) group, suggesting that MGII members with Fe/MnSOD may have superior antioxidant capacity relative to members possessing NiSOD. Molecular clock analysis of MGII genomes revealed frequent species divergence correlating to the differentiation of Fe/MnSOD or NiSOD genes. The acquisition/loss of these genes in the MGII genomes was synchronized with the historical changes in atmospheric oxygen and oceanic metal element concentrations over the last 2.4 billion years, suggesting that variations in the antioxidant capacity of MGII archaea in response to changing oxygen levels may have driven their divergences over time.

IMPORTANCE

Reactive oxygen species (ROS), including superoxide anion, is a series of substances that cause oxidative stress for all organisms. Marine group II (MGII) archaea are mainly live in the surface seawater and exposed to considerable ROS. Therefore, it is important to understand the antioxidant capacity of MGII. Our research found that Fe/Mn- superoxide dismutase (Fe/MnSOD) may be more suitable for MGII to resist oxidative damage, and the changes in oxygen concentrations and SOD metallic cofactors play an important role in the selection of SOD by the 17 clades of MGII, which in turn affects the species differentiation of MGII. Overall, this study provides insight into the co-evolutionary history of these uncultivated marine archaea with the earth system.
Systemic and cerebrospinal fluid biomarkers for tuberculous meningitis identification and treatment monitoring
Authors: Yao Xiang-Ping , Hong Jian-Chen , Jiang Zai-Jie , Pan Yu-Ying , Liu Xiao-Feng , Wang Jun-Mei , Fan Rui-Jie , Yang Bi-Hui , Zhang Wei-Qing , Fan Qi-Chao , Li Li-Xiu , Lin Bi-Wei , Zhao Miao
Published: December 2023

Tuberculous meningitis (TBM) is a severe infectious disease affecting the central nervous system, causing high mortality and disability. However, current diagnostic methods for TBM using cerebrospinal fluid (CSF) lack sensitivity and predictive biomarkers for prognosis. We conducted a study on cytokine profiles in CSF and serum samples from TBM patients to identify disease-specific biomarkers. Patients were categorized into three groups: TBM (
n
= 17), cryptococcal meningitis (
n
= 10), and non-infection (
n
= 6), and cytokine levels were quantified using a 48-plex panel. After treatment, we observed a significant reduction in the levels of 12 cytokines, indicating their potential use as biomarkers for treatment monitoring. Among them, monokine induced by interferon-γ (MIG) and interleukin-18 showed significant differences in serum or CSF cytokine levels compared to the control groups. CSF levels of MIG in TBM patients were negatively correlated with the CSF/blood glucose ratio (
r
= −0.4728,
P
= 0.0475). Positive correlations were found between CSF leukocyte counts and several cytokines, including fibroblast growth factor-basic, granulocyte colony-stimulating factor (G-CSF), monocyte chemotactic protein-3, macrophage inflammatory protein 1 alpha (MIP-1α), and tumor necrosis factor alpha. G-CSF and MIP-1α were also positively correlated with CSF protein levels. Receiver operating characteristic curve analysis revealed that MIG exhibited the highest area under the curve of 0.92 [95% confidence interval (CI) 0.82–1.00] with a sensitivity of 0.85 (95% CI 0.58–0.97) and a specificity of 0.87 (95% CI 0.62–0.98), making it a promising diagnostic biomarker for TBM. Our study provides valuable insights into TBM’s pathogenesis and identifies potential biomarkers for diagnosis and evaluating treatment monitoring.

IMPORTANCE

Tuberculous meningitis is a life-threatening infection with high mortality and disability rates. Current diagnostic methods using cerebrospinal fluid (CSF) samples have limited sensitivity and lack predictive biomarkers for evaluating prognosis. This study’s findings reveal excessive activation of the immune response during tuberculous meningitis (TBM) infection. Notably, a strong negative correlation was observed between CSF levels of monokine induced by interferon-γ (MIG) and the CSF/blood glucose ratio in TBM patients. MIG also exhibited the highest area under the curve with high sensitivity and specificity. This study suggests that MIG may serve as a novel biomarker for differentiating TBM infection in CSF or serum, potentially leading to improved diagnostic accuracy and better patient outcomes.
Environmental surveillance of fungi and susceptibility to antifungal agents in tertiary care hospitals
Authors: Badiee Parisa , Ghadimi-Moghadam Abdolkarim , Bayatmanesh Habibeh , Soltani Jafar , Salimi-Khorashad Ali Reza , Ghasemi Fatemeh , Amin Shahidi Maneli , Jafarian Hadis
Published: December 2023

This study aimed to evaluate the epidemiology of fungi in environment of tertiary care hospitals and their susceptibility patterns to seven antifungal agents for controlling and preventing fungal infections in patients. Environmental samplings on the surfaces of different parts of hospitals were collected from four university-affiliated teaching hospitals in Iran. Routine and molecular procedures identified isolated fungi, and antifungal susceptibility tests were performed
in vitro
. Of the 400 samples, 152 presented positive culture results, and 193 fungal species were isolated. Mold fungi accounted for 59.1% (115 species) of isolates. Most isolated fungal species in descending order were 22
Aspergillus flavus
(11.4%), 21
Candida albicans
(10.9%), 17
Mucor
species (8.8%), 16
Penicillium
species (8.3%), 16
Candida famata
(8.3%), 15
Alternaria
species (7.8%), 13
Fusarium
species (6.7%), 11
Candida parapsilosis
(5.7%), and 10
Aspergillus niger sensu stricto
(5.2%). The isolated
Aspergillus
species revealed relatively low susceptibility to itraconazole and posaconazole with MIC90 values of 8 µg/mL. The MIC90 values of amphotericin and luliconazole in
Candida
species were 0.5 and 0.064 µg/mL, respectively. In this study, different species of filamentous and yeast fungi with varying susceptibility to antifungal agents were reported from the environment of the studied hospitals.

IMPORTANCE

Saprophytic fungi can cause nosocomial infections in high-risk patients. These infections are related to high mortality and cost. In the current study, different species of filamentous fungi and yeast were isolated from the environment of the studied hospitals. Some species were resistant to antifungal drugs. We suggest that the future work concentrates on the relationship between the level/quantification of saprophytic contamination in the environment of hospitals and fungal infections in patients.
Immunogenicity and protective efficacy of recombinant adenovirus expressing a novel genotype G2b PEDV spike protein in protecting newborn piglets against PEDV
Authors: Song Xin , Zhou Qun , Zhang Jiaqi , Chen Taoyun , Deng Gunan , Yue Hua , Tang Cheng , Wu Xuejing , Yu Jifeng , Zhang Bin
Published: December 2023

Porcine epidemic diarrhea virus (PEDV) causes porcine epidemic diarrhea (PED). The emergence of the novel G2b strains of PEDV has increased the need for new vaccines. We generated a recombinant adenovirus expressing the spike (S) protein of G2b PEDV based on human adenovirus serotype 5 (Ad5), named rAd5-PEDV-S. Immunization with rAd5-PEDV-S elicited a significant PEDV-specific humoral immune response in sows, including IgA and IgG in colostrum and serum and circulating neutralizing antibodies. The efficacy of rAd5-PEDV-S was superior to that of the commercial inactivated vaccine, and the intramuscular (IM) route was more effective than the intranasal route. Interestingly, there was no significant difference in immunization effect between the twice and once-immunized IM groups (administered 5 weeks before farrowing). Five-day-old piglets born to sows immunized with the rAd5-PEDV-S through the IM route had less diarrhea and weight loss when challenged with PEDV. Fecal PEDV RNA expression in the PEDV-challenged rAd5-PEDV-S IM group piglets was considerably lower than that in the other groups; all five piglets from the rAd5-PEDV-S IM group survived the infection period. Histopathological examination of small intestinal sections revealed evident shedding of ileum intestinal mucosal epithelial cells in the phosphate-buffered saline (PBS) group. These findings suggest that vaccinating pregnant sows with rAd5-PEDV-S induces immune responses in the pregnant sows and passively protects piglets. Our findings highlight the potential of rAd5-PEDV-S as a candidate vaccine for PED.

IMPORTANCE

Porcine epidemic diarrhea (PED) is a highly infectious and economically significant gastrointestinal disorder that affects pigs of all ages. Preventing and controlling PED is achieved by immunizing sows with vaccines, enabling passive piglet immunization via colostrum. The prevalence of G2b porcine epidemic diarrhea virus (PEDV) continues in China despite the use of commercial vaccines, raising questions regarding current vaccine efficacy and the need for novel vaccine development. Adenovirus serotype 5 (Ad5) has several advantages, including high transduction efficiency, a wide range of host cells, and the ability to infect cells at various stages. In this study, we expressed the immunogenic proteins of spike (S) using an Ad5 vector and generated a PED vaccine candidate by inducing significant humoral immunity. The rAd5-PEDV-S prevented PED-induced weight loss, diarrhea, and intestinal damage in piglets. This novel vaccine candidate strain possesses the potential for use in the pig breeding industry.
Mechanical constraints to unbound expansion of
B. subtilis
on semi-solid surfaces
Authors: Krajnc Mojca , Fei Chenyi , Košmrlj Andrej , Kalin Mitjan , Stopar David
Published: December 2023

The effects of surface mechanical constraints that may promote or prevent bacterial expansion on semi-solid surfaces are largely unknown. In this work, we have manufactured agar surfaces with different viscoelasticity, topography, and roughness. To capture the essential biophysics of the bacterial expansion we have developed a continuum model that faithfully reproduces the main patterns of the short-range and long-range expansion with two critical parameters: local interfacial forces and colony viscosity. Cohesive energy of the bacterial colony that determines the extent of exploration was dependent on agar surface viscoelasticity. On soft surfaces, bacteria produce low viscoelastic colonies that allow guided population of bacteria to traverse distances that are six orders of magnitude larger than the size of the individual bacterium. Bacteria growing on stiff surfaces produce colonies with significantly increased viscoelasticity that prevent bacterial exploration of new territory and allow formation of a very steep cliff at the edge of the colony. Upon flooding of the rough surfaces, we have induced aquaplaning and spreading of bacteria. A layer of water between the bacterium and surface results in a loss of traction allowing bacteria to spread across the otherwise inhibitory rough surface. The results shed new light on the bacterial ability to rapidly colonize new territories.

IMPORTANCE

How bacterial cells colonize new territory is a problem of fundamental microbiological and biophysical interest and is key to the emergence of several phenomena of biological, ecological, and medical relevance. Here, we demonstrate how bacteria stuck in a colony of finite size can resume exploration of new territory by aquaplaning and how they fine tune biofilm viscoelasticity to surface material properties that allows them differential mobility. We show how changing local interfacial forces and colony viscosity results in a plethora of bacterial morphologies on surfaces with different physical and mechanical properties.
Targeted amplification-based whole genome sequencing of
Monkeypox virus
in clinical specimens
Authors: Isabel S. , Eshaghi A. , Duvvuri V. R. , Gubbay J. B. , Cronin K. , Li Aimin , Hasso M. , Clark S. T. , Hopkins J. P. , Patel S. N. , Braukmann T. W. A.
Published: December 2023

The 2022 mpox outbreak has led to more than 91,000 cases in 115 countries. Whole genome sequencing (WGS) has been at the forefront of surveillance and outbreak investigations for different pathogens of public health significance. Many institutions performing WGS on
Monkeypox virus
(MPXV) use a resource-intensive metagenomic approach. Here we present a targeted amplification method for WGS of MPXV from clinical specimens. We designed 43 pairs of primers (amplicons ~5 kb) with PrimalScheme to span the ~200 kb viral genome and then added 12 additional primers to optimize amplification. We extracted nucleic acid from clinical specimens and amplified the two primer pools. All libraries were sequenced on the MiniSeq platform. Resulting reads were filtered by quality and then mapped to a MPXV reference genome. Consensus sequences were generated for phylogenetic analysis. A total of 91 specimens with a real-time-PCR cycle threshold (Ct) values ≤27.9 were sequenced using our targeted amplification protocol. The sequenced MPXV genomes were of high quality with mean genome coverage of 99.56% (95% CI 99.32-99.80%), mean depth 1,395× (95% CI 1275–1515), and mean mapping quality of 52.87 (95% CI 52.1–53.6) and allowed for greater multiplexing of samples relative to metagenomics. The MPXV genomes belong to 8 of the 13 clades observed during the 2022 global mpox outbreak. Targeted amplification enrichment provides high coverage, throughput, and short turnaround times. It is an efficient low-cost method for MPXV WGS and can benefit public health surveillance and outbreak management.

IMPORTANCE

We present a protocol to efficiently sequence genomes of the MPXV-causing mpox. This enables researchers and public health agencies to acquire high-quality genomic data using a rapid and cost-effective approach. Genomic data can be used to conduct surveillance and investigate mpox outbreaks. We present 91 mpox genomes that show the diversity of the 2022 mpox outbreak in Ontario, Canada.
Overexpression of genes involved in fatty acid biosynthesis increases lipid content in the NaHCO
3
-tolerant
Chlorella
sp. JB6
Authors: Shang Hongna , Liu Songsong , Xu Chenghui , Liu Shenkui , Liu Hua
Published: December 2023

Microalgae are a potential source of biodiesel owing to their simple structure and high biomass and lipid production rates. Here, we demonstrate that fatty acid (FA) contents can be altered in
Chlorella
sp. JB6 in the presence of sodium bicarbonate (NaHCO
3
). We cloned the key genes necessary for FA
de novo
synthesis conserved in JB6, including
biotin carboxyl carrier protein
(
BCCP
),
β-carboxyltransferase
(
β-CT
),
malonyl CoA-ACP malonyl transferase
(
MCMT
),
3-ketoacyl-ACP reductase
(
KAR
),
β-ketoacyl-[acyl carrier protein] synthase I
(
KASI
), and
KASII
, and successfully transferred plasmids carrying these genes into JB6 cells. We found that overexpression of
BCCP
,
MCMT
,
KASI
,
and KASII
inhibited the growth of JB6 cells and decreased their resistance to NaHCO
3
. Notably, ectopic expression of these genes promoted very long-chain saturated FA (>20 C) accumulation. Taken together, we demonstrate that these genes are critical for JB6 growth and resistance to NaHCO
3
and can be used for metabolic engineering.

IMPORTANCE

Fatty acid (FA) contents can be altered in Chlorella JB6 in the presence of sodium bicarbonate (NaHCO
3
). Overexpression of the FA
de novo
synthesis genes inhibited the growth of JB6 cells and decreased their resistance to NaHCO
3
, but these transgenic JB6 strains could grow in a medium containing as high as 300 mM NaHCO
3
. In JB6, ectopic expression of the FA
de novo
synthesis genes increased the synthesis of very long-chain saturated FA (> 20C).
MK-200 Plasma Gun Facility
Authors: Kostyushin V. A. , Poznyak I. M. , Toporkov D. A. , Burmistrov D. A. , Zhuravlev K. V. , Lidzhigoryaev S. D. , Usmanov R. R. , Tsybenko V. Yu. , Nemchinov V. S.
Published: December 2023

Plasma flows with high velocity, density, and energy are widely used in research on the interaction of plasma with materials, modeling of astrophysical processes, development of plasma thrusters and plasma radiation sources, and plasma injection into fusion devices. Electrodynamic plasma guns can be used to generate such flows. This paper describes the design features of a powerful pulsed plasma gun and diagnostic tools for measuring the parameters of the plasma flow generated by it.
Longitudinal Tomography of Ion Bunches in the JINR Superconducting Booster Synchrotron
Authors: Zhabitsky V. M.
Published: December 2023

Methods for processing a digital signal proportional to the longitudinal intensity of ions in bunches during their acceleration in a synchrotron are discussed. Computer tomography is employed to reconstruct the longitudinal 2D ion distribution function in a bunch using data on its longitudinal profiles that depend on the bunch length and the synchrotron motion of particles. Presented are examples of tomographic reconstruction of the longitudinal distribution function of xenon ions in the JINR superconducting booster synchrotron prior to extraction (after acceleration) and on the injection plateau also with the activated electron cooling system.
Performance and ruminal fermentation of second-trimester pregnant beef cows fed short-season high-moisture corn stover or barley greenfeed during winter in western Canada
Authors: Carey R.E. , Lardner H.A. , McAllister T.A. , Penner G.B.
Published: December 2023

This study evaluated performance and ruminal fermentation for cows fed short-season high-moisture shelled corn stover with corn dried distillers’ grains with solubles (COR) or barley greenfeed (BAR) that was either swathed (S-COR; S-BAR; Experiment 1) or baled (B-COR; B-BAR; Experiment 2) as winter-feeding systems. In Experiment 1, cows were randomly assigned to S-COR or S-BAR and fed for 52 days in the fields where crops were grown. Body weight (BW), subcutaneous rib and rump fat, and body condition score (BCS) were measured, with no differences detected between treatments ( P > 0.05). However, S-COR had a lower estimated dry matter intake (DMI) than S-BAR ( P ≤ 0.03). In Experiment 2, cows were assigned to B-COR or B-BAR for 42 days and fed in field paddocks. Cows fed B-COR had less ( P ≤ 0.01) DMI, final BW, rib fat, rump fat, and BCS than B-BAR, with no differences ( P > 0.05) for ruminal pH. Total SCFA concentration was greater ( P ≤ 0.05) on day 21 for B-BAR than B-COR, but not on day 42. Under western Canadian conditions, COR may reduce DMI and the performance of pregnant cows, suggesting that additional preservation and supplementation strategies should be investigated.
Denoised Non-Local Means with BDDU-Net Architecture for Robust Retinal Blood Vessel Segmentation
Authors: Desiani Anita , Erwin  , Suprihatin Bambang , Riana Dwiza , Arhami Muhammad , Ramayanti Indri , Utama Yadi
Published: December 2023

Retinal blood vessels can be obtained by image segmentation. This study proposes combining image enhancement and segmentation to obtain retinal blood vessels. The image enhancement stages use CLAHE and Denoised Non-Local Means to increase contrast and reduce noise on the original image, and Bottom-Hat (BTH) filtering is used to lighten dark features in the image so the features become lighter and darken the bright features in the image. Bottom Hat is applied to make the features of the blood vessels in the retinal image more visible. The segmentation architecture proposes BDDU-Net architecture which combines U-Net in the encoder part, DenseNet in the bridge part, and Bi-ConvLSTM in the decoder part. Image enhancement performance results are PSNR and SSIM. The PSNR is more than 40 dB on both the DRIVE and STARE datasets. The SSIM results are close to 1 on the DRIVE and STARE datasets. These results show that the image enhancement stages in the proposed method can enhance the quality of the original image. The segmentation performance results of BDDU-Net architecture are measured based on accuracy, sensitivity, specificity, IoU, and F1-Score. The DRIVE dataset obtained 95.578% for accuracy, 85.75% for sensitivity, 96.75% for specificity, 67.407% for IoU, and 80.53% for F1-Score. The STARE dataset obtained 97.63% for accuracy, 84.33% for sensitivity, 98.66% for specificity, 75.67% for IoU, and 86.15% for F1-Score. Based on the image enhancement and image segmentation results, these results show that the proposed method is great for enhancing image quality and excellent for blood vessel segmentation in retinal images, although IoU results on the DRIVE dataset need to be improved.