Miracle-dz/UniFAR-FTUs huggingface dataset:
Lactobacillus reuteri ATG-F4 Alleviates Chronic Stress-induced Anhedonia by Modulating the Prefrontal Serotonergic System

Mental health is influenced by the gut-brain axis; for example, gut dysbiosis has been observed in patients with major depressive disorder (MDD). Gut microbial changes by fecal microbiota transplantation or probiotics treatment reportedly modulates depressive symptoms. However, it remains unclear how gut dysbiosis contributes to mental dysfunction, and how correction of the gut microbiota alleviates neuropsychiatric disorders. Our previous study showed that chronic consumption of Lactobacillus reuteri ATG-F4 (F4) induced neurometabolic alterations in healthy mice. Here, we investigated whether F4 exerted therapeutic effects on depressive-like behavior by influencing the central nervous system. Using chronic unpredictable stress (CUS) to induce anhedonia, a key symptom of MDD, we found that chronic F4 consumption alleviated CUS-induced anhedonic behaviors, accompanied by biochemical changes in the gut, serum, and brain. Serum and brain metabolite concentrations involved in tryptophan metabolism were regulated by CUS and F4. F4 consumption reduced the elevated levels of serotonin (5-HT) in the brain observed in the CUS group. Additionally, the increased expression of Htr1a, a subtype of the 5-HT receptor, in the medial prefrontal cortex (mPFC) of stressed mice was restored to levels observed in stress-naïve mice following F4 supplementation. We further demonstrated the role of Htr1a using AAV-shRNA to downregulate Htr1a in the mPFC of CUS mice, effectively reversing CUS-induced anhedonic behavior. Together, our findings suggest F4 as a potential therapeutic approach for relieving some depressive symptoms and highlight the involvement of the tryptophan metabolism in mitigating CUS-induced depressive-like behaviors through the action of this bacterium.
Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies

Abstract The human microbiome plays a crucial role in maintaining health, with advances in high‐throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next‐Generation Sequencing (mNGS), and Targeted Next‐Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high‐throughput microbial single‐cell genome sequencing technology and 2bRAD‐M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
Treating amblyopia using altered reality enhances the fine‐scale functional correlations in early visual areas

Amblyopia is a developmental visual disorder that causes substantial visual deficits. Studies using resting‐state functional magnetic resonance imaging have disclosed abnormal brain functional connectivity (FC) both across long‐range cortical sites and within the visual cortex in amblyopes, which is considered to be related to impaired visual functions. However, little work has examined whether restoring the vision of amblyopes accompanies with an improvement of FC. Here in adult amblyopes and healthy participants, we compared their brain FC before and after an altered‐reality adaptation training. Before the training, the voxel‐wise FCs of amblyopia patients were substantially weaker than those of healthy control participants both within and across the early visual areas. After the training, visual acuities improved in amblyopes but not in the control participants. The effect kept strengthening in the subsequent month without further adaptation. Importantly, we observed enhanced voxel‐wise FC both within and across the early visual areas of amblyopes. Moreover, the enhancement continued for at least 1 month. These results suggest that the effective treatment can improve both the amblyopes' vision and functional connections in the visual cortex.
RNA virus diversity in three parasitoid wasps of tephritid flies: insights from novel and known species

ABSTRACT Parasitoid wasps are a diverse group of parasitoid insects that play a crucial role in biological control and integrated pest management programs due to their wide range of host species and complex behaviors. Previous studies have reported that select RNA viruses in parasitoid wasps can affect either the host-parasitoid wasp or the pest host parasitized by the wasps. Therefore, a study of the dynamics of RNA viruses in parasitoid wasps is essential for artificial breeding programs and improving their parasitic capabilities. In this study, we detected the presence of nine novel and three known RNA viruses with complete genomes in three parasitoid wasp species: Diachasmimorpha longicaudata, Fopius arisanus, and Spalangia endius. These wasps are parasitoids that can parasitel tephritid flies, one of the most important pest groups of fruits and vegetables. In D. longicaudata, the small RNAs derived from the viruses exhibited distinct peaks at 22 nt and were symmetrically distributed across the viral genome. These findings indicate that these viruses can activate the host’s RNAi immune response. PCR detection further revealed that DlNaLV efficiently infects female individuals of D. longicaudata with 100% efficiency, and ZcNLV is capable of infecting both D. longicaudata and its host, Zeugodacus cucurbitae. Our findings contribute to a better understanding of RNA viruses in parasitoid wasps and lay the foundation for future research on the triple-level trophic relationships between tephritid flies, parasitoid wasps, and RNA viruses. IMPORTANCE Parasitoid wasp populations have developed persistent beneficial symbiotic relationships with several viruses through repeated evolution. However, there have been limited reports on RNA viruses in parasitoid wasps of tephritid flies, a significant pest group affecting fruits and vegetables. This study explores the diversity of RNA viruses in three parasitoid wasps of tephritid flies and highlights the potential biological significance of specific viruses in Diachasmimorpha longicaudata. These findings have important implications for the development of sustainable pest management strategies and the enhancement of artificial rearing techniques for parasitoid wasps. Parasitoid wasp populations have developed persistent beneficial symbiotic relationships with several viruses through repeated evolution. However, there have been limited reports on RNA viruses in parasitoid wasps of tephritid flies, a significant pest group affecting fruits and vegetables. This study explores the diversity of RNA viruses in three parasitoid wasps of tephritid flies and highlights the potential biological significance of specific viruses in Diachasmimorpha longicaudata. These findings have important implications for the development of sustainable pest management strategies and the enhancement of artificial rearing techniques for parasitoid wasps.
Emergence and Growth of Mjärdevi Science Park in Linköping, Sweden1

Abstract The development of science parks constitutes an interesting example of policy to enhance the technology-based development of a region. These parks, it is argued, contribute to fostering technological innovation and transfer and stimulating the growth of high-level economic activities. This article examines the role that science parks play in the promotion of regional development with particular reference to one of Sweden's most successful science parks, the Mjärdevi Science Park. During the 1990s, Mjärdevi was recognized as one of Northern Europe's most rapidly growing science parks, and it has an enviable record with respect to the launching of local, new technology-based firms. This article traces the historical events related to the creation of Mjärdevi Science Park that have influenced its technological and industrial development. It then outlines the park's path of development and subsequently addresses key factors affecting the growth dynamics of the park.
Analysis of seagrass reflectivity by using a water column correction algorithm

Seagrass in optically shallow water can generate optical signals that can be tracked remotely. Unfortunately the signals from the bottom are relatively weak and can be affected by the water column when concentrations of suspended particles, chlorophyll and coloured dissolved organic matter are high. An optical model simulating the propagation of light for retrieving the bottom reflectance was developed. Implementation of the method was found to be effective for improving the accuracy of coastal habitat maps, and essential for deriving empirical relationships between remotely sensed data and interesting features in the marine environment. The appropriate wavebands for seagrass mapping, which generally lay between 500 and 630 nm and 680 and 710 nm, were obtained by means of full visual inspection and analysis of the correct spectra. Additionally, a strong relationship between the reflectance value at 715 nm and Leaf Area Index was found, with a correlation coefficient of 0.99.
Salt decay of Morley limestone

Salt weathering is one of the main causes of decay of natural stone, and by consequence a major problem to the conservation of cultural heritage. In the present case, the performance of Morley limestone from the Departement Meuse, France, as a replacement stone under saltloaded conditions is evaluated. Morley limestone was used in the Netherlands as a replacement stone for sandy Eocene Belgian limestones (Gobertange, Lede).
Spy - See - Advanced vision system for phenotyping in greenhouses

G. Polder 1 , G.W. A.M. Van Der Heijden 1 , C.A. Glasbey 2 , Y. Song 2 and J.A. Dieleman 3 . 1 Wageningen UR, Biometris, P.O. Box 100, 6700 AC, Wageningen, Netherlands, 2 Biomathematics & Statistics Scotland, JCMB, The Kings buildings, Edinburgh EH9 3JZ, Scotland, United Kingdom, 3 Wageningen UR, Plant Research International, P.O. Box 16, 6700 AA, Wageningen, Netherlands. Email main author: gerrit.polder@wur.nl
Breast adipose tissue‐derived extracellular vesicles from obese women alter tumor cell metabolism

Breast adipose tissue is an important contributor to the obesity–breast cancer link. Extracellular vesicles (EVs) are nanosized particles containing selective cargo, such as miRNAs, that act locally or circulate to distant sites to modulate target cell functions. Here, we find that long‐term education of breast cancer cells with EVs obtained from breast adipose tissue of women who are overweight or obese (O‐EVs) results in increased proliferation. RNA‐seq analysis of O‐EV‐educated cells demonstrates increased expression of genes involved in oxidative phosphorylation, such as ATP synthase and NADH: ubiquinone oxidoreductase. O‐EVs increase respiratory complex protein expression, mitochondrial density, and mitochondrial respiration in tumor cells. The mitochondrial complex I inhibitor metformin reverses O‐EV‐induced cell proliferation. Several miRNAs—miR‐155‐5p, miR‐10a‐3p, and miR‐30a‐3p—which promote mitochondrial respiration and proliferation, are enriched in O‐EVs relative to EVs from lean women. O‐EV‐induced proliferation and mitochondrial activity are associated with stimulation of the Akt/mTOR/P70S6K pathway, and are reversed upon silencing of P70S6K. This study reveals a new facet of the obesity‐breast cancer link with human breast adipose tissue‐derived EVs causing metabolic reprogramming of breast cancer cells.
Markers of cardiac injury in patients with liver cirrhosis

Liver cirrhosis is an increasing public health problem and a major cause of morbidity and mortality. Accordingly, cirrhotic cardiomyopathy, a frequently underdiagnosed condition, is becoming a growing health problem. In the last 20 years, cardioselective biomarkers have been investigated for their diagnostic and prognostic properties for numerous conditions. The aim of this article is to review the literature on the relationship between the most commonly used cardioselective biomarkers (cardiac troponins I and T, N-terminal pro-B-type natriuretic peptide, brain natriuretic peptide, and heart-type fatty-acid binding protein) and the presence, functional stage, and clinical outcomes of liver cirrhosis. Elevated plasma levels of these biomarkers have been reported in patients with liver cirrhosis, and there is mounting evidence on their predictive value for clinical outcomes in this disease. In addition, elevated plasma levels of these biomarkers have been reported in patients before, during, and after liver transplantation, but in fewer studies. Due to their predictive value for clinical outcomes, we advocate the use of these markers in patients with liver cirrhosis and cirrhotic cardiomyopathy, as well as in candidates for liver transplant.
3D Laplace-domain Modeling, Including Configuration of the Sea Bottom Using the Gaussian Quadrature Method of Integration

3D Laplace-domain waveform inversion can recover a large velocity model for successive waveform inversion in the frequency domain. However, the grid interval in 3D Laplace-domain modeling and inversion cannot be sufficiently small because of the heavy computational cost. Therefore, we cannot assess whether or not the modeled wavefield is reliable if our model has an abruptly undulated sea bottom surface. The irregular finite element method can provide a solution; however, it increases the number of bands of the impedance matrix. Instead, we applied the Gaussian quadrature integration method in order to reflect two properties on one element at the irregular sea bottom. In order to verify this modeling algorithm, we compared our modeled wavefield with the analytic solutions for an unbounded homogeneous model, an unbounded two-layer model and an obliquely-inclined two-layer model. The results of the verification tests show that our modeling algorithm better describes a wavefield with an irregular sea bottom in the 3D Laplace domain than the conventional modeling algorithm.
Evolution of moisture transport to the western U.S. during the last deglaciation

We investigate climate dynamics and teleconnections governing moisture transport to the western U.S. during past warm and cool intervals of the last deglaciation using paleoclimate simulations of the Bølling warm (~14 ka) and Younger Dryas cool (~12 ka) events. Results suggest that the waning continental ice sheet weakened atmospheric pressure centers in the region leading to a progression from a more sinuous to more zonal Pacific winter storm track throughout the deglaciation. Furthermore, variations in meltwater flux to the Atlantic influenced the meridional temperature gradient over the Pacific and thereby modulated storm track intensity. Changing sinuosity of the storm track may be reflected in broad increases in modeled δ18Oprecip and observed δ18Ospeleothem values from the western U.S. over the last deglaciation, whereas abrupt δ18Ospeleothem shifts are dynamically consistent with the response of storm track intensity to variations in meltwater flux to the Atlantic.
Significant increase in the prevalence of Panton–Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus, particularly the USA300 variant ΨUSA300, in the Japanese community

ABSTRACT USA300, a major Panton–Valentine leukocidin (PVL)-producing methicillin-resistant Staphylococcus aureus (MRSA) clone associated with skin and soft tissue infections (SSTIs), carries a type IV staphylococcal cassette chromosome mec (SCCmec) element. Recently, a USA300 variant, ΨUSA300, with a 12-bp deletion of ccrB2 in the SCCmec element, was identified in Japan by Takadama et al. (15). To understand the current status of PVL-positive MRSA in the community, a nationwide surveillance of MRSA isolated from outpatients at dermatology departments was conducted. This study included 1,619 outpatients who visited dermatology departments at 22 healthcare facilities in 11 prefectures in Japan between 2018 and 2021; S. aureus were isolated from these outpatients. Molecular epidemiological analysis was performed using PCR, SCCmec and spa typing, pulsed-field gel electrophoresis, multilocus sequence typing, and antimicrobial susceptibility testing. A total of 980 S. aureus were isolated, 293 of which were identified as MRSA. Among MRSA isolates, PVL genes were detected in 18 of 63 (28.6%) in 2018, 34 of 85 (40.0%) in 2019, 29 of 65 (44.6%) in 2020, and 40 in 80 (50.0%) in 2021. Among the PVL-positive MRSA, 16 of 121 (13.2%) and 94 of 121 (77.7%) isolates were identified as USA300 and ΨUSA300, respectively. ΨUSA300 strains were collected from six prefectures in Japan: Kagawa, Osaka, Tokyo, Kanagawa, Fukushima, and Saitama. ΨUSA300 was isolated more frequently than USA300 from patients with deep-seated SSTIs (P < 0.05). Our findings showed that PVL-positive MRSA isolates were significantly increased in the Japanese community. Furthermore, the USA300 variant ΨUSA300 has emerged as the predominant PVL-positive MRSA clone across the Kanto, Kinki, and Shikoku regions of Japan, and this variant may possess a greater propensity to cause deep-seated SSTIs than in USA300. IMPORTANCE USA300 is an MRSA clone producing PVL, a toxin associated with SSTIs. ΨUSA300 is a USA300 variant recently identified in Japan by Takadama et al. (15). Here, we found that the prevalence rate of PVL-positive MRSA in S. aureus was elevated in the Japanese community, and ΨUSA300 accounted for most of them. ΨUSA300 strains have been isolated from several areas in Japan and were associated with deep-seated SSTIs. This study highlighted the emerging threat posed by ΨUSA300 in Japan. USA300 is an MRSA clone producing PVL, a toxin associated with SSTIs. ΨUSA300 is a USA300 variant recently identified in Japan by Takadama et al. (15). Here, we found that the prevalence rate of PVL-positive MRSA in S. aureus was elevated in the Japanese community, and ΨUSA300 accounted for most of them. ΨUSA300 strains have been isolated from several areas in Japan and were associated with deep-seated SSTIs. This study highlighted the emerging threat posed by ΨUSA300 in Japan.
Characteristics of Month-by-Month Blood Pressure Variability in Patients on Hemodialysis

Introduction: Poor prognosis in hemodialysis (HD) patients is due to the increased prevalence of cardiovascular diseases among them. We previously reported that higher visit-by-visit blood pressure variability is associated with increased cardiovascular mortality in HD patients. This present study aimed to investigate the characteristics of month-by-month blood pressure variability (MMBPV) in these patients. Methods: A total of 324 maintenance HD patients, who could be followed up for 60 months, were recruited. We used standard deviation (SD), coefficient of variation (CV), and variation independent of the mean (VIM) in pre- and post-dialysis systolic blood pressure (pre- and post-SD, pre- and post-CV, and pre- and post-VIM) as an index of MMBPV. We investigated (1) the reproducibility of MMBPV, (2) relationship between these values and background factors, and (3) association between these values and mortality. Results: MMBPV (pre- and post-SD, pre- and post-CV, and pre- and post-VIM) showed significant reproducibility (intraclass correlation, 0.483 [p < 0.001], 0.553 [p < 0.001], 0.450 [p < 0.001], 0.518 [p < 0.001], 0.456 [p < 0.001], and 0.522 [p < 0.001], respectively). High pre-VIM was associated with high interdialytic weight gain and poor nutritional status. High post-VIM was associated with glucose intolerance, high interdialytic weight gain, and poor nutritional status and associated with high rate of cardiovascular deaths independent of other factors (hazard ratio: 1.104, 95% confidence interval: 1.011–1.207, p = 0.028). Conclusion: These data suggested that pre- and post-VIM in HD patients are reproducible and associated with various background factors, and especially post-VIM is independently correlated with cardiovascular mortality. Further studies are necessary to confirm the mechanism of increased post-VIM and clarify whether reducing post-VIM can improve the prognosis of HD patients.
Senescent tumor cells in colorectal cancer are characterized by elevated enzymatic activity of complexes 1 and 2 in oxidative phosphorylation

Background Cellular senescence is defined as an irreversible cell cycle arrest caused by various internal and external insults. While the metabolic dysfunction of senescent cells in normal tissue is relatively well-established, there is a lack of information regarding the metabolic features of senescent tumor cells. Methods Publicly available single-cell RNA-sequencing data from the GSE166555 and GSE178341 datasets were utilized to investigate the metabolic features of senescent tumor cells. To validate the single-cell RNA-sequencing data, we performed senescence-associated β-galactosidase (SA-β-Gal) staining to identify senescent tumor cells in fresh frozen colorectal cancer tissue. We also evaluated nicotinamide adenine dinucleotide dehydrogenase–tetrazolium reductase (NADH-TR) and succinate dehydrogenase (SDH) activity using enzyme histochemical methods and compared the staining with SA-β-Gal staining. MTT assay was performed to reveal the complex 1 activity of the respiratory chain in in-vitro senescence model. Results Single-cell RNA-sequencing data revealed an upregulation in the activity of complexes 1 and 2 in oxidative phosphorylation, despite overall mitochondrial dysfunction in senescent tumor cells. Both SA-β-Gal and enzyme histochemical staining using fresh frozen colorectal cancer tissues indicated a high correlation between SA-β-Gal positivity and NADH-TR/SDH staining positivity. MTT assay showed that senescent colorectal cancer cells exhibit higher absorbance in 600 nm wavelength. Conclusions Senescent tumor cells exhibit distinct metabolic features, characterized by upregulation of complexes 1 and 2 in the oxidative phosphorylation pathway. NADH-TR and SDH staining represent efficient methods for detecting senescent tumor cells in colorectal cancer.