bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomarkers for early complications post hematopoietic cell transplantation: Insights and challenges
Authors: Balakrishnan Balaji , Kulkarni Uday Prakash , Pai Aswin Anand , Illangeswaran Raveen Stephen Stallon , Mohanan Ezhilpavai , Mathews Vikram , George Biju , Balasubramanian Poonkuzhali
Published: February 2023

Hematopoietic cell transplantation is an established curative treatment option for various hematological malignant, and non-malignant diseases. However, the success of HCT is still limited by life-threatening early complications post-HCT, such as Graft Versus Host Disease (GVHD), Sinusoidal Obstruction Syndrome (SOS), and transplant-associated microangiopathy, to name a few. A decade of research in the discovery and validation of novel blood-based biomarkers aims to manage these early complications by using them for diagnosis or prognosis. Advances in this field have also led to predictive biomarkers to identify patients’ likelihood of response to therapy. Although biomarkers have been extensively evaluated for different complications, these are yet to be used in routine clinical practice. This review provides a detailed summary of various biomarkers for individual early complications post-HCT, their discovery, validation, ongoing clinical trials, and their limitations. Furthermore, this review also provides insights into the biology of biomarkers and the challenge of obtaining a universal cut-off value for biomarkers.
IgE+ plasmablasts predict the onset of clinical allergy
Authors: Simonin Elisabeth M. , Babasyan Susanna , Tarsillo Justine , Wagner Bettina
Published: February 2023

Introduction

IgE+ plasmablasts develop following allergen exposure and B cell activation. They secrete IgE and therefore are directly linked to maintain the mechanisms of IgE-mediated allergies. Here, we show that the presence of IgE+ plasmablasts in peripheral blood not only coincides with clinical allergy, but also predicts the upcoming development of clinical disease.

Methods

Using an equine model of naturally occurring allergy, we compared the timing of allergen exposure, arrival of IgE+ plasmablasts in peripheral blood, and onset of clinical disease.

Results

We found that IgE+ plasmablasts predict the development of clinical allergy by at least 3 weeks and can be measured directly by flow cytometry or by IgE secretion following in vitro culture. We also compared the IgE secretion by IgE+ plasmablasts with total plasma IgE concentrations and found that while IgE secretion consistently correlates with clinical allergy, total plasma IgE does not.

Discussion

Together, we describe IgE+ plasmablasts as a reliable and sensitive predictive biomarker of allergic disease development.
Approaches to demonstrating the effectiveness of filovirus vaccines: Lessons from Ebola and COVID-19
Authors: Gruber Marion F. , Rubin Steven , Krause Philip R.
Published: February 2023

Zaire ebolavirus (EBOV), Sudan ebolavirus (SUDV) and Marburg virus (MARV), are members of the Filoviridae family that can cause severe disease and death in humans and animals. The reemergence of Ebola, Sudan and Marburg virus disease highlight the need for continued availability of safe and effectives vaccines as well as development of new vaccines. While randomized controlled trials using disease endpoints provide the most robust assessment of vaccine effectiveness, challenges to this approach include the unpredictable size, location, occurrence and duration of filovirus disease outbreaks. Thus, other approaches to demonstrating vaccine effectiveness have been considered. These approaches are discussed using examples of preventive vaccines against other infectious diseases. In addition, this article proposes a clinical immunobridging strategy using licensed EBOV vaccines as comparators for demonstrating the effectiveness of filovirus vaccine candidates that are based on the same licensed vaccine platform technology.
Severely ill and high-risk COVID-19 patients exhibit increased peripheral circulation of CD62L+ and perforin+ T cells
Authors: Lesteberg Kelsey E. , Araya Paula , Waugh Katherine A. , Chauhan Lakshmi , Espinosa Joaquin M. , Beckham J. David
Published: February 2023

Introduction

The emergence of SARS-CoV-2, which causes COVID-19, has led to over 400 million reported cases worldwide. COVID-19 disease ranges from asymptomatic infection to severe disease and may be impacted by individual immune differences.

Methods

We used multiparameter flow cytometry to compare CD4+ and CD8+ T cell responses in severe (ICU admitted) and non-severe (admitted to observational unit) hospitalized COVID-19 patients.

Results

We found that patients with severe COVID- 19 had greater frequencies of CD4+ T cells expressing CD62L compared to non-severe patients and greater frequencies of perforin+ CD8+ T cells compared to recovered patients. Furthermore, greater frequencies of CD62L+ CD4+ and CD8+ T cells were seen in severely ill diabetic patients compared to non-severe and non-diabetic patients, and increased CD62L+ CD4+ T cells were also seen in severely ill patients with hypertension.

Discussion

This is the first report to show that CD62L+ T cells and perforin+ T cells are associated with severe COVID-19 illness and are significantly increased in patients with high-risk pre-existing conditions including older age and diabetes. These data provide a potential biological marker for severe COVID-19.
Investigating how river flow regimes impact on river delta salinization through idealized modeling
Authors: Matsoukis Constantinos , Amoudry Laurent O. , Bricheno Lucy , Leonardi Nicoletta
Published: February 2023

Introduction

Excessive salinity can harm ecosystems and compromise the various anthropogenic activities that take place in river deltas. The issue of salinization is expected to exacerbate due to natural and/or anthropogenic climate change. Water regulations are required to secure a sufficient water supply in conditions of limited water volume availability. Research is ongoing in seek of the optimum flow distribution establishing longer lasting and fresher conditions in deltas.

Methods

In this study a three–dimensional (3D) numerical model built for an idealized delta configuration was utilized to investigate how different river discharge annual distributions affect saltwater in deltas. Five simulations were carried out by implementing annual distributions of equal water volume but different shape.

Results

The results showed that peak flow magnitude, time of occurrence and the length of a hydrograph’s tails can be important parameters affecting stratification, freshwater residence, and renewal times. Hydrographs of small flow range and light tails were the most successful in keeping the delta and its trunk channel fresher for longer periods. Salinity distributions showed a slower response to decreasing rather than increasing river discharges. An increase in the flow rate can result in salinity standards demanded for certain activities (e.g., farming, irrigation etc.) in much shorter times. On the other hand, hydrographs with heavy tails can push the salt intrusion limit further away and be more efficient in mixing the water column. However, they present low freshwater residence and high-water renewal times.

Discussion

These results provide strong indications that it is possible to improve the freshwater conditions in deltas without seeking for additional water resources but by modifying the water distribution. The main outcomes of this work may be able to support and assist coastal scientists and stakeholders dealing with the management of freshwater resources in river deltas across the world.
Developing machine learning methods for automatic recognition of fishing vessel behaviour in the Scomber japonicus fisheries
Authors: Wang Shuxian , Zhang Shengmao , Tang Fenghua , Shi Yongchuang , Sui Yanming , Fan Xiumei , Chen Junlin
Published: February 2023

Introduction

With a higher degree of automation, fishing vessels have gradually begun adopting a fishing monitoring method that combines human and electronic observers. However, the objective data of electronic monitoring systems (EMS) has not yet been fully applied in various fishing boat scenarios such as ship behavior recognition.

Methods

In order to make full use of EMS data and improve the accuracy of behaviors recognition of fishing vessels, the present study proposes applying popular deep learning technologies such as convolutional neural network, long short-term memory, and attention mechanism to Chub mackerel (Scomber japonicus) fishing vessel behaviors recognition. The operation process of Chub mackerel fishing vessels was divided into nine kinds of behaviors, such as “pulling nets”, “putting nets”, “fish pick”, “reprint”, etc. According to the characteristics of their fishing work, four networks with different convolutional layers were designed in the pre-experiment. And the feasibility of each network in behavior recognition of the fishing vessels was observed. The pre-experiment is optimized from the perspective of the data set and the network. From the standpoint of the data set, the size of the optimized data set is significantly reduced, and the original data characteristics are preserved as much as possible. From the perspective of the network, different combinations of pooling, long short-term memory(LSTM) network, and attention(including CBAM and SE) are added to the network, and their effects on training time and recognition effect are compared.

Results

The experimental results reveal that the deep learning methods have outstanding performance in behaviors recognition of fishing vessels. The LSTM and SE module combination produced the most apparent optimization effect on the network, and the optimized model can achieve an F1 score of 97.12% in the test set, surpassing the classic ResNet, VGGNet, and AlexNet.

Discussion

This research is of great significance to the management of intelligent fishery vessels and can promote the development of electronic monitoring systems for ships.
Energy-efficient clustering protocol for underwater wireless sensor networks using optimized glowworm swarm optimization
Authors: Bharany Salil , Sharma Sandeep , Alsharabi Naif , Tag Eldin Elsayed , Ghamry Nivin A.
Published: February 2023

In the past few decades, cutting-edge information and communication technology has been used in several ways to keep an eye on the marine environment. Underwater wireless sensor networks (UWSNs) can measure the amount of water and soil conditions, such as soil salinity, moisture, and movements, to predict landslides. UWSNs are made up of many wireless underwater sensor nodes (WSNs) that are spread out across the thalassic environment. These networks have several uses, including data collection, navigation, resource analysis, surveillance, disaster prediction, etc. Nowadays, energy efficiency becomes a complex issue to handle in the design of the UWSN due to the limited battery capacity and the challenges associated with changing or charging the integrated batteries. According to previous research, clustering and routing have already been effective methods of improving energy efficiency in the UWSN, as unreplaceable batteries and long-distance communication delays are particularly vulnerable. As a result, one of the UWSN’s critical issues is determining how to extend the network’s lifespan while balancing its energy consumption and shortening transmission distances. In UWSN clustering, the most important considerations are acquiring a suitable count of clusters, constituting the clusters, and picking the most satisfactory cluster head (CH) for each cluster. Based on several factors, such as residuary energy, total energy consumption, and other considerations, our proposed approach picks CHs and arranges them into clusters. Also, the proposed SS-GSO method constructs a fitness function by including various sources of information, like total energy, residual energy, and luciferin value. Several simulation runs were executed to test how much better the SS-GSO approach worked. The comparison results showed that while evaluating clustering time, our proposed SS-GSO technique performs 22.91%, 50.03%, 42.42%, 58.06% better, in case of Total energy consumption 27.02%,14%,33.76%,41.97% more energy efficient, in Cluster lifetime 9.2%,19.88%,35.91%,40.54% less and in Packet delivery rate 8.29%,14.05%,17.67%,23.97% better as compared with other heuristic techniques, such as ACO, GWO, MFO and LEACH.
The impact of COVID-19 disease on the natural course of cirrhosis: Before and after starting vaccination
Authors: Keskin Onur , Oral Hakan , Sahin Tevhide , Kav Taylan , Parlak Erkan
Published: February 2023

Background

Cirrhosis has been reported as an important risk factor for death in coronavirus disease 2019 (COVID-19) disease. In this study, we aimed to investigate the effects of COVID-19 on the natural course of cirrhosis before and after starting vaccination.

Methods

The cirrhosis patients in our cohort (n: 140; median age:56; 71 female) were included in this study. The median MELD (Model For End-stage Liver Disease) score was 11 (6–25) and CCI (Charlson Comorbidity Index) score was 4 (1–11). In total, 85 had CTP (Child-Turcotte-Pugh)-A, 44 had CTP-B and 11 had CTP-C cirrhosis. The course of COVID-19 in this patient group was evaluated before and after COVID-19 vaccination.

Results

Between March 2020 and January 2021, 36 of the 140 cirrhosis patients had developed COVID-19. Cirrhosis (+)/COVID-19 (+) and Cirrhosis (+)/COVID-19 (–) groups did not differ in terms of age, CCI and MELD-Na scores, or gender. There were six deaths in the Cirrhosis (+)/COVID-19 (+) group and five in the Cirrhosis (+)/COVID-19 (–) group [6/36 (16.6%) vs. 5/104 (4.8%); p: 0.03]. Patients who died were older, had higher CCI and MELD-Na scores, and lower albumin levels. Having had COVID-19 [6.45 (1.43–29.4); p: 0.015], higher MELD-Na score [1.35 (1.18–1.60); p: 0.001] and higher CCI score [1.65 (1.14–2.39); p: 0.008] were found to be independent predictors of mortality. After effective vaccination started in Turkey, only 11 of the remaining 129 patients developed COVID-19, and only one patient died, who was unvaccinated.

Discussion

In our cirrhotic cohort, COVID-19 disease was associated with 16% mortality in the pre-vaccination period. COVID-19 vaccination prevents serious illness and death due to COVID-19 in cirrhotic patients.
Survival status and predictors of mortality among patients admitted to surgical intensive care units of Addis Ababa governmental hospitals, Ethiopia: A multicenter retrospective cohort study
Authors: Endeshaw Amanuel Sisay , Fekede Mulualem Sitot , Gesso Ashenafi Seifu , Aligaz Esubalew Muluneh , Aweke Senait
Published: February 2023

Introduction

Critical care is a serious global healthcare burden. Although a high number of surgical patients are being admitted to the surgical intensive care unit (SICU), the mortality remained high, particularly in low and middle-income countries. However, there is limited data in Ethiopia. Therefore, this study aimed to investigate the survival status and predictors of mortality in surgical patients admitted to the SICUs of Addis Ababa governmental hospitals, Ethiopia.

Methods

A multicenter retrospective cohort study was conducted on 410 surgical patients admitted to the SICUs of three government hospitals in Addis Ababa selected using a simple random sampling from February 2017 to February 2020. The data were entered into Epidata version 4.6 and imported to STATA/MP version 16 for further analysis. Bi-variable and multivariable Cox regression models were fitted in the analysis to determine the predictor variables. A hazard ratio (HR) with a 95% confidence interval (CI) was computed, and variables with a p-value <0.05 were considered statistically significant.

Results

From a sample of 410 patients, 378 were included for final analysis and followed for a median follow-up of 5 days. The overall mortality among surgical patients in the SICU was 44.97% with an incidence rate of 5.9 cases per 100 person-day observation. Trauma (AHR = 1.83, 95% CI: 1.19–2.08), Glasgow coma score (GCS) <9 (AHR = 2.06, 95% CI: 1.28–3.31), readmission to the SICU (AHR = 3.52, 95% CI: 2.18–5.68), mechanical ventilation (AHR = 2.52, 95% CI: 1.23–5.15), and creatinine level (AHR = 1.09, 95% CI: 1.01–1.18) were found to be significantly associated with mortality in the SICU.

Conclusion

The mortality of surgical patients in the SICU was high. Trauma, GCS <9 upon admission, readmission to the SICU, mechanical ventilation, and increased in the creatinine level on admission to the SICU were the identified predictors of mortality in the SICU.
Recent findings on the impact of ErbB receptors status on prognosis and therapy of head and neck squamous cell carcinoma
Authors: Palumbo Camilla , Benvenuto Monica , Focaccetti Chiara , Albonici Loredana , Cifaldi Loredana , Rufini Alessandra , Nardozi Daniela , Angiolini Valentina , Bei Arianna , Masuelli Laura , Bei Roberto
Published: February 2023

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer type, has often an aggressive course and is poorly responsive to current therapeutic approaches, so that 5-year survival rates for patients diagnosed with advanced disease is lower than 50%. The Epidermal Growth Factor Receptor (EGFR) has emerged as an established oncogene in HNSCC. Indeed, although HNSCCs are a heterogeneous group of cancers which differ for histological, molecular and clinical features, EGFR is overexpressed or mutated in a percentage of cases up to about 90%. Moreover, aberrant expression of the other members of the ErbB receptor family, ErbB2, ErbB3 and ErbB4, has also been reported in variable proportions of HNSCCs. Therefore, an increased expression/activity of one or multiple ErbB receptors is found in the vast majority of patients with HNSCC. While aberrant ErbB signaling has long been known to play a critical role in tumor growth, angiogenesis, invasion, metastatization and resistance to therapy, more recent evidence has revealed its impact on other features of cancer cells’ biology, such as the ability to evade antitumor immunity. In this paper we will review recent findings on how ErbB receptors expression and activity, including that associated with non-canonical signaling mechanisms, impacts on prognosis and therapy of HNSCC.
Impact of reduced antibiotic treatment duration on antimicrobial resistance in critically ill patients in the randomized controlled SAPS-trial
Authors: Shajiei Arezoo , Berends Matthijs S. , Luz Christian F. , van Oers Jos A. , Harmsen Hermie J. M. , Vos Piet , Klont Rob , Loef Bert G. , Reidinga Auke C. , Bormans-Russell Laura , Linsen Kitty , Dormans Tom , Otten Martine , van der Bij Akke , Beishuizen Albertus , de Lange Dylan W. , de Jong Evelien , Nijsten Maarten W.
Published: February 2023

Background

In the previously reported SAPS trial (https://clinicaltrials.gov/ct2/show/NCT01139489), procalcitonin-guidance safely reduced the duration of antibiotic treatment in critically ill patients. We assessed the impact of shorter antibiotic treatment on antimicrobial resistance development in SAPS patients.

Materials and methods

Cultures were assessed for the presence of multi-drug resistant (MDR) or highly resistant organisms (HRMO) and compared between PCT-guided and control patients. Baseline isolates from 30 days before to 5 days after randomization were compared with those from 5 to 30 days post-randomization. The primary endpoint was the incidence of new MDR/HRMO positive patients.

Results

In total, 8,113 cultures with 96,515 antibiotic test results were evaluated for 439 and 482 patients randomized to the PCT and control groups, respectively. Disease severity at admission was similar for both groups. Median (IQR) durations of the first course of antibiotics were 6 days (4–10) and 7 days (5–11), respectively (p = 0.0001). Antibiotic-free days were 7 days (IQR 0–14) and 6 days (0–13; p = 0.05). Of all isolates assessed, 13% were MDR/HRMO positive and at baseline 186 (20%) patients were MDR/HMRO-positive. The incidence of new MDR/HRMO was 39 (8.9%) and 45 (9.3%) in PCT and control patients, respectively (p = 0.82). The time courses for MDR/HRMO development were also similar for both groups (p = 0.33).

Conclusions

In the 921 randomized patients studied, the small but statistically significant reduction in antibiotic treatment in the PCT-group did not translate into a detectable change in antimicrobial resistance. Studies with larger differences in antibiotic treatment duration, larger study populations or populations with higher MDR/HRMO incidences might detect such differences.
Predictors of pulmonary sequelae after COVID-19 pneumonia: A 12-month follow-up study
Authors: Bernardinello Nicol , Cocconcelli Elisabetta , Giraudo Chiara , Daverio Matteo , Castelli Gioele , Petrarulo Simone , Bovo Matteo , Fichera Giulia , Cavinato Silvia , Cattelan Anna Maria , Saetta Marina , Spagnolo Paolo , Balestro Elisabetta
Published: February 2023

Background

Since the beginning of the SARS-CoV-2 pandemic, over 550 million people have been infected worldwide. Despite these large numbers, the long-term pulmonary consequences of COVID-19 remain unclear.

Aims

The aim of this single-center observational cohort study was to identify and characterize pulmonary sequelae of COVID-19 at 12 months from hospitalization and to reveal possible predictors for the persistence of long-term lung consequences.

Methods

Based on the persistence or absence of radiological changes after 12 months from hospitalization, the whole population was categorized into NOT-RECOVERED (NOT-REC) and RECOVERED (REC) groups, respectively. Clinical and pulmonary function data tests and clinical data were also collected and compared in the two groups. In the NOT-REC group, high resolution computed tomography (HRCT) images were semiquantitatively scored analyzing ground-glass opacities (GGO), interstitial thickening (IT), consolidations (CO), linear and curvilinear band opacities, and bronchiectasis for each lung lobe. Logistic regression analyses served to detect the factors associated with 12-month radiological consequences.

Results

Out of the 421 patients followed after hospitalization for SARS-CoV-2 pneumonia, 347 met inclusion and exclusion criteria and were enrolled in the study. The NOT-REC patients (n = 24; 6.9%) were significantly older [67 (62–76) years vs. 63 (53–71) years; p = 0.02], more frequently current smokers [4 (17%) vs. 12 (4%); p = 0.02], and with more severe respiratory failure at the time of hospitalization [PaO2/FiO2 at admission: 201 (101–314) vs. 295 (223–343); p = 0.01] compared to REC group (n = 323; 93.1%). On multivariable analysis, being a current smoker resulted in an independent predictor for lung sequelae after 12 months from hospitalization [5.6 OR; 95% CI (1.41–22.12); p = 0.01].

Conclusion

After 12 months from hospital admission, a limited number of patients displayed persistent pulmonary sequelae with minimal extension. Being a current smoker at the time of SARS-CoV-2 infection is an independent predictive factor to lung consequences, regardless of the disease severity.
White blood cell count affects fetal fraction and test failure rates in noninvasive prenatal screening
Authors: Qiao Longwei , Cao XiaoJu , Tang Haoyu , Yu Zheng , Shi Jingye , Xue Ying , Wang Ting , Liang Yuting , Huang Chao , Wang Jiucun
Published: February 2023

Objective

To investigate the effects of white blood cell (WBC) count on fetal fraction (FF), which is an essential quality control for obtaining reliable results, and on the rate of screen failures in noninvasive prenatal screening (NIPS).

Methods

Noninvasive prenatal screening, serum lipid and liver enzyme level measurements, and WBC count were performed for 4,281 pregnancies with male fetuses. After adjusting for confounders, including the maternal characteristics and alanine aminotransferase (ALT) levels, the effect of WBC count on FF and test failure rate was measured by linear and logistic regression analyses.

Results

Fetal fraction was negatively associated with BMI, ALT, IVF conceptions, and WBC count and positively correlated with gestational age in the multivariate linear regression model. Moreover, WBC count was the most important factor affecting FF after BMI according to the standardization coefficient analysis. In the 4,281 pregnancy samples with male fetuses, FF decreased with WBC count from 11.45% at ≤8 to 9.02% at >12, and FF markedly decreased to 7.40% in pregnancies with a higher WBC count (>12) and higher BMI (≥25 kg/m2). Meanwhile, the test failure rates were significantly higher in the WBC count > 12 group (4.29%) than in the WBC count ≤ 8 group (0.89%). Notably, when the BMI of pregnancies with a WBC count of >12 was >25, the rate reached 7.53%. Subsequently, multivariate logistic regression analysis further confirmed that an increased BMI and WBC count were independently and significantly associated with the test failure rates.

Conclusion

An increased WBC count was associated with lower FF and higher test failure rates, suggesting that these important factors should be carefully considered during genetic counseling in pregnant women who decide to undergo blood collection or resampling.
Rheumatoid arthritis and the risk of end-stage renal disease: A nationwide, population-based study
Authors: Suh Sang Heon , Jung Jin Hyung , Oh Tae Ryom , Yang Eun Mi , Choi Hong Sang , Kim Chang Seong , Bae Eun Hui , Ma Seong Kwon , Han Kyung-Do , Kim Soo Wan
Published: February 2023

Introduction

Despite the risk of incident chronic kidney disease among the patients with rheumatoid arthritis (RA), the association of RA and the risk of end-stage renal disease (ESRD) has not been clearly elucidated. We aimed to investigate the association of RA and the risk of ESRD.

Materials and methods

A total of 929,982 subjects with (n = 154,997) or without (n = 774,985) RA from the National Health Insurance Service (NHIS) database in Koreas (corresponding to the period between 2009 and 2017) were retrospectively analyzed. RA was defined by the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM), codes plus any dispensing of disease-modifying anti-rheumatic drugs. The primary outcome was incident ESRD, identified by a combination of the ICD-10-CM codes and a special code assigned to patients receiving maintenance dialysis for ≥ 3 months or those with a transplant kidney.

Results

Compared to the subjects without RA, the subjects with RA resulted in an increased incidence of ESRD (incidence rates of 0.374 versus 0.810 cases per 1,000 person-years). Accordingly, compared to the subjects without RA, the risk of ESRD was significantly increased among the subjects with RA (adjusted hazard ratio 2.095, 95% confidence interval 1.902–2.308). Subgroup analyses revealed that the risk of ESRD imposed by RA is relatively higher in relatively young and healthy individuals.

Conclusion

Rheumatoid arthritis (RA) increase the risk of ESRD. As the risk of ESRD imposed by RA is relatively higher in relatively young and healthy individuals, kidney-protective treatment, such as biologic agents, should be preferentially considered among these patients with RA.
Effects of the addition of leucine on flavor and quality of sausage fermented by Lactobacillus fermentum YZU-06 and Staphylococcus saprophyticus CGMCC 3475
Authors: Liu Rui , Ma Yong , Chen Lei , Lu Chenyan , Ge Qingfeng , Wu Mangang , Xi Jun , Yu Hai
Published: February 2023

Methyl-branched aldehydes, especially 3-methylbutanal, have been reported to be perceived either as a malty or as a nutty/chocolate-like aroma and were considered an important flavor contributor in fermented meat products. Decomposition of leucine (Leu) by branched-chain amino acid transaminase (BACT) is a crucial step in the metabolism of Leu to 3-methylbutanal. This study was conducted to explore the effects of mixed-starter culture (Lactobacillus fermentum YZU-06 and Staphylococcus saprophyticus CGMCC 3475) and addition of Leu (0, 1, and 3 mM) on the flavor and quality of fermented sausages. The pH, water activity, texture profile analysis, color, counts of lactic acid bacteria (LAB) and staphylococci, peptide, and flavor compounds were detected during fermentation. The results showed that the starter culture group increased hardness, elasticity, the counts of LAB and staphylococci, peptide content, volatile flavor compounds, as well as the sensorial scores of sausage, while decreasing pH, aw, and L* and b* values compared with the non-inoculation group. The mixed starter of adding with 3 mM Leu enhanced the content of 3-methylbutanal and overall flavor of fermented sausages. It is applicable to directionally produce methyl-branched aldehydes and improve the overall quality of fermented sausage by the addition of Leu and using starter of L. fermentum YZU-06 and S. saprophyticus CGMCC 3475.
Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater
Authors: Nuppunen-Puputti Maija , Kietäväinen Riikka , Kukkonen Ilmo , Bomberg Malin
Published: February 2023

Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of ∼3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.
The power of light: Impact on the performance of biocontrol agents under minimal nutrient conditions
Authors: Karlsson Maria E. , Hellström Maria , Flöhr Adam , Bergstrand Karl-Johan , Alsanius Beatrix W.
Published: February 2023

Background

The spectral distribution of light (different wavelength) has recently been identified as an important factor in the dynamics and function of leaf-associated microbes. This study investigated the impact of different wavelength on three commercial biocontrol agents (BCA): Bacillus amyloliquefaciens (BA), Pseudomonas chlororaphis (PC), and Streptomyces griseoviridis (SG).

Methods

The impact of light exposure on sole carbon source utilization, biofilm formation, and biosurfactant production by the selected BCA was studied using phenotypic microarray (PM) including 190 sole carbon sources (OmniLog®, PM panels 1 and 2). The BCA were exposed to five monochromatic light conditions (420, 460, 530, 630, and 660 nm) and darkness during incubation, at an intensity of 50 μmol m−2 s−1.

Results

Light exposure together with specific carbon source increased respiration in all three BCA. Different wavelengths of light influenced sole carbon utilization for the different BCA, with BA and PC showing increased respiration when exposed to wavelengths within the blue spectrum (420 and 460 nm) while respiration of selected carbon sources by SG increased in the presence of red light (630 and 660 nm). Only one carbon source (capric acid) generated biosurfactant production in all three BCA. A combination of specific wavelength of light and sole carbon source increased biofilm formation in all three BCA. BA showed significantly higher biofilm formation when exposed to blue (460 nm) and green (530 nm) light and propagated in D-sucrose, D-fructose, and dulcitol. PC showed higher biofilm formation when exposed to blue light. Biofilm formation by SG increased when exposed to red light (630 nm) and propagated in citraconic acid.

Conclusion

To increase attachment and success in BCA introduced into the phyllosphere, a suitable combination of light quality and nutrient conditions could be used.
Effects of several flavonoids on human gut microbiota and its metabolism by in vitro simulated fermentation
Authors: Pan Lixia , Ye Hangyu , Pi Xionge , Liu Wei , Wang Zhao , Zhang Yinjun , Zheng Jianyong
Published: February 2023

Introduction

Flavonoids have antiviral, antitumor, anti-inflammatory, and other biological activities. They have high market value and are widely used in food and medicine fields. They also can regulate gut microbiota and promote human health. However, only a few flavonoids have been reported for their regulatory effects on human gut microbiota.

Methods

The effects of hesperidin, hesperetin-7-O-glucoside, hesperetin, naringin, prunin, naringenin, rutin, isoquercitrin, and quercetin on gut microbiota structural and metabolic differences in healthy subjects were studied by means of in vitro simulated fermentation technology.

Results

Results showed that the nine kinds of flavonoids mentioned above, especially hesperetin-7-O-glucoside, prunin, and isoquercitrin, were found to have more effect on the structure of human gut microbiota, and they could significantly enhance Bifidobacterium (p < 0.05). After 24 h of in vitro simulated fermentation, the relative abundance of intestinal probiotics (e.g., Lactobacillus) was increased by the three flavonoids and rutin. Furthermore, the relative abundance of potential pathogenic bacteria was decreased by the addition of hesperetin-7-O-glucoside, naringin, prunin, rutin, and isoquercitrin (e.g., Lachnoclostridium and Bilophila). Notably, prunin could also markedly decrease the content of H2S, NH3, and short-chain fatty acids. This performance fully demonstrated its broad-spectrum antibacterial activity.

Discussion

This study demonstrates that flavonoids can regulate the imbalance of gut microbiota, and some differences in the regulatory effect are observed due to different structures. This work provides a theoretical basis for the wide application of flavonoids for food and medicine.
The role of potential probiotic strains Lactobacillus reuteri in various intestinal diseases: New roles for an old player
Authors: Yu Zihan , Chen Jihua , Liu Yaxin , Meng Qingguo , Liu Hang , Yao Qinyan , Song Wenxuan , Ren Xiangfeng , Chen Xin
Published: February 2023

Lactobacillus reuteri (L. reuteri), a type of Lactobacillus spp., is a gut symbiont that can colonize many mammals. Since it was first isolated in 1962, a multitude of research has been conducted to investigate its function and unique role in different diseases as an essential probiotic. Among these, the basic functions, beneficial effects, and underlying mechanisms of L. reuteri have been noticed and understood profoundly in intestinal diseases. The origins of L. reuteri strains are diverse, with humans, rats, and piglets being the most common. With numerous L. reuteri strains playing significant roles in different intestinal diseases, DSM 17938 is the most widely used in humans, especially in children. The mechanisms by which L. reuteri improves intestinal disorders include protecting the gut barrier, suppressing inflammation and the immune response, regulating the gut microbiota and its metabolism, and inhibiting oxidative stress. While a growing body of studies focused on L. reuteri, there are still many unknowns concerning its curative effects, clinical safety, and precise mechanisms. In this review, we initially interpreted the basic functions of L. reuteri and its related metabolites. Then, we comprehensively summarized its functions in different intestinal diseases, including inflammatory bowel disease, colorectal cancer, infection-associated bowel diseases, and pediatric intestinal disorders. We also highlighted some important molecules in relation to the underlying mechanisms. In conclusion, L. reuteri has the potential to exert a beneficial impact on intestinal diseases, which should be further explored to obtain better clinical application and therapeutic effects.
The PRMT5 inhibitor EPZ015666 is effective against HTLV-1-transformed T-cell lines in vitro and in vivo
Authors: Ernzen Kyle , Melvin Corrine , Yu Lianbo , Phelps Cameron , Niewiesk Stefan , Green Patrick L. , Panfil Amanda R.
Published: February 2023

Human T-cell leukemia virus type 1 (HTLV-1) is the infectious cause of adult T-cell leukemia/lymphoma (ATL), an extremely aggressive and fatal malignancy of CD4+ T-cells. Due to the chemotherapy-resistance of ATL and the absence of long-term therapy regimens currently available for ATL patients, there is an urgent need to characterize novel therapeutic targets against this disease. Protein arginine methyltransferase 5 (PRMT5) is a type II PRMT enzyme that is directly involved in the pathogenesis of multiple different lymphomas through the transcriptional regulation of relevant oncogenes. Recently, our group identified that PRMT5 is overexpressed in HTLV-1-transformed T-cell lines, during the HTLV-1-mediated T-cell immortalization process, and in ATL patient samples. The objective of this study was to determine the importance of PRMT5 on HTLV-1 infected cell viability, T-cell transformation, and ultimately disease induction. Inhibition of PRMT5 enzymatic activity with a commercially available small molecule inhibitor (EPZ015666) resulted in selective in vitro toxicity of actively proliferating and transformed T-cells. EPZ015666-treatment resulted in a dose-dependent increase in apoptosis in HTLV-1-transformed and ATL-derived cell lines compared to uninfected Jurkat T-cells. Using a co-culture model of infection and immortalization, we found that EPZ015666 is capable of blocking HTLV-1-mediated T-cell immortalization in vitro, indicating that PRMT5 enzymatic activity is essential for the HTLV-1 T-cell transformation process. Administration of EPZ015666 in both NSG xenograft and HTLV-1-infected humanized immune system (HIS) mice significantly improved survival outcomes. The cumulative findings of this study demonstrate that the epigenetic regulator PRMT5 is critical for the survival, transformation, and pathogenesis of HTLV-1, illustrating the value of this cellular enzyme as a potential therapeutic target for the treatment of ATL.
Structural characterization and partial properties of dextran produced by Leuconostoc mesenteroides RSG7 from pepino
Authors: Wang Binbin , Sun Xiaoling , Xu Min , Wang Fengyi , Liu Weizhong , Wu Baomei
Published: February 2023

Exopolysaccharides (EPSs) produced by lactic acid bacteria possess various bioactivities and potential attractions for scientific exploration and commercial development. An EPS-producing bacterial strain, RSG7, was previously isolated from the pepino and identified as Leuconostoc mesenteroides. Based on the analyses of high-performance size exclusion chromatography, high-performance ion chromatography, Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and methylation, the RSG7 EPS was identified as a dextran with a molecular weight of 5.47 × 106 Da and consisted of α-(1→6) glycosidic linkages as backbone and α-(1→2), α-(1→3), α-(1→4), and α-(1→6) glycosidic linkages as side chains. Scanning electron microscopy observed a honeycomb-like porous structure of RSG7 dextran, and this dextran formed aggregations with irregular hill-shaped lumps according to atomic force microscopy analysis. Physical–chemical investigations suggested that RSG7 dextran possessed excellent viscosity at high concentration, low temperature, and high pH; showed a superior emulsifying capacity of tested vegetable oils than that of hydrocarbons; and owned the maximal flocculating activity (10.74 ± 0.23) and flocculating rate (93.46 ± 0.07%) in the suspended solid of activated carbon. In addition, the dextran could coagulate sucrose-supplemented milk and implied potential probiotics in vitro. Together, these results collectively describe a valuable dextran with unique characteristics for exploitation in food applications.
Advances in the preclinical characterization of the antimicrobial peptide AS-48
Authors: Cebrián Rubén , Martínez-García Marta , Fernández Matilde , García Federico , Martínez-Bueno Manuel , Valdivia Eva , Kuipers Oscar P. , Montalbán-López Manuel , Maqueda Mercedes
Published: February 2023

Antimicrobial resistance is a natural and inevitable phenomenon that constitutes a severe threat to global public health and economy. Innovative products, active against new targets and with no cross- or co-resistance with existing antibiotic classes, novel mechanisms of action, or multiple therapeutic targets are urgently required. For these reasons, antimicrobial peptides such as bacteriocins constitute a promising class of new antimicrobial drugs under investigation for clinical development. Here, we review the potential therapeutic use of AS-48, a head-to-tail cyclized cationic bacteriocin produced by Enterococcus faecalis. In the last few years, its potential against a wide range of human pathogens, including relevant bacterial pathogens and trypanosomatids, has been reported using in vitro tests and the mechanism of action has been investigated. AS-48 can create pores in the membrane of bacterial cells without the mediation of any specific receptor. However, this mechanism of action is different when susceptible parasites are studied and involves intracellular targets. Due to these novel mechanisms of action, AS-48 remains active against the antibiotic resistant strains tested. Remarkably, the effect of AS-48 against eukaryotic cell lines and in several animal models show little effect at the doses needed to inhibit susceptible species. The characteristics of this molecule such as low toxicity, microbicide activity, blood stability and activity, high stability at a wide range of temperatures or pH, resistance to proteases, and the receptor-independent effect make AS-48 unique to fight a broad range of microbial infections, including bacteria and some important parasites.
Improved salt tolerance of Synechococcus elongatus PCC 7942 by heterologous synthesis of compatible solute ectoine
Authors: Dong Zhengxin , Sun Tao , Zhang Weiwen , Chen Lei
Published: February 2023

Salt stress is one of the essential abiotic stresses for the survival of cyanobacteria. However, the realization of large-scale cultivation of cyanobacteria is inseparable from the utilization of abundant seawater resources. Therefore, research on the regulatory mechanism, as well as the improvement of salt tolerance of cyanobacteria is fundamental. Ectoine, a compatible solute which was found in halophilic microorganisms, has potentiality to confer salt tolerance. Here in this article, the salt tolerance of Synechococcus elongatus PCC 7942 (Syn7942) was significantly improved via expressing the ectoine biosynthetic pathway, reaching an increased final OD750 by 20% under 300 mM NaCl and 80% under 400 mM NaCl than that of wild-type (WT), respectively. Encouragingly, the engineered strain could even survive under 500 mM NaCl which was lethal to WT. In addition, by introducing the ectoine synthetic pathway into the sucrose-deficient strain, the salt tolerance of the obtained strain Syn7942/Δsps-ect was restored to the level of WT under 300 mM NaCl stress, demonstrating that ectoine could substitute for sucrose to combat against salt stress in Syn7942. In order to study the difference in the regulation of mechanism on the salt adaptation process after replacing sucrose with ectoine, transcriptomic analysis was performed for Syn7942/Δsps-ect and WT. The differentially expressed gene analysis successfully identified 19 up-regulated genes and 39 down-regulated genes in Syn7942/Δsps-ect compared with WT under salt stress condition. The results also showed that the global regulation of Syn7942/Δsps-ect and WT had certain differences in the process of salt adaptation, in which Syn7942/Δsps-ect reduced the demand for the intensity of sulfur metabolism in this process. This study provides a valuable reference for further salt tolerance engineering in cyanobacteria.
Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance
Authors: Boulanger Hadrien Georges , Guo Wenbin , Monteiro Lucca de Filipe Rebocho , Calixto Cristiane Paula Gomes
Published: February 2023

To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant’s inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
Iron-tracking strategies: Chaperones capture iron in the cytosolic labile iron pool
Authors: Philpott Caroline C. , Protchenko Olga , Wang Yubo , Novoa-Aponte Lorena , Leon-Torres Andres , Grounds Samantha , Tietgens Amber J.
Published: February 2023

Cells express hundreds of iron-dependent enzymes that rely on the iron cofactors heme, iron-sulfur clusters, and mono-or di-nuclear iron centers for activity. Cells require systems for both the assembly and the distribution of iron cofactors to their cognate enzymes. Proteins involved in the binding and trafficking of iron ions in the cytosol, called cytosolic iron chaperones, have been identified and characterized in mammalian cells. The first identified iron chaperone, poly C-binding protein 1 (PCBP1), has also been studied in mice using genetic models of conditional deletion in tissues specialized for iron handling. Studies of iron trafficking in mouse tissues have necessitated the development of new approaches, which have revealed new roles for PCBP1 in the management of cytosolic iron. These approaches can be applied to investigate use of other nutrient metals in mammals.