Miracle-dz/UniFAR-FTUs huggingface dataset:
Succession of soil microbial community in a developing mid-channel bar: The role of environmental disturbance and plant community

Succession of microbial and plant communities is crucial for the development and the stability of soil ecological functions. The relative role of plant communities and environmental disturbance in shaping the microbial community in a newly established habitat remains unclear. In this study, a mid-channel bar (MCB) exposed to an environmental disturbance gradient in the Yangtze River was studied to explore the effects of such disturbance and plant community traits on the succession of the soil microbial community. Bulk and rhizospheric soils were collected from the MCB and classified according to their level of exposure to environmental disturbance: head, central and tail. These subsequently underwent high-throughput sequencing and interdomain ecological network (IDEN) analysis to identify and characterize the predominant microbial groups present in the soils at each disturbance level. Furthermore, at each site, the presence and distribution of the plant community was also noted. The present study demonstrated that both bulk soil nutrients and plant community exhibited significant spatial distribution dependent on the level of disturbance and this influenced the composition of the microbial community. In less eroded parts of the MCB, i.e., the central, nutrients accumulated, promoting growths of plants. This in turn encouraged a more diverse microbial community, dominated by the bacterial genus Pseudarthrobacter. Plant showed a stronger association with bulk soil microbial communities compared to rhizosphere soil microbial communities. Particularly, Triarrhena sacchariflora and Hemarthria altissima, present in sites of low disturbance, exhibiting a more extensive plant-microbe association. They thus played a key role in shaping the soil microbial community. In general, however, plant species did not directly determine the composition of the bacterial community, but instead altered the nutritive state of the soil to promote microbial growth. Such findings are of significant value for conservation practices of newly formed ecosystems, which requires an integrated understanding of the role of environmental disturbance and plants on soil microbial community assemblage.
RNA-seq analysis reveals genes related to photosynthetic carbon partitioning and lipid production in Phaeodactylum tricornutum under alkaline conditions

Alkaline pH can induce triacylglyceride accumulation in microalgae, however its molecular mechanism remains elusive. Here, we investigated the effect of 2-[N-cyclohexylamino]-ethane-sulfonic acid (CHES) -induced intracellular alkalization on the lipid production in Phaeodactylum tricornutum. Intracellular pH was increased upon CHES treatment, displaying a high BCECF fluorescence ratio. CHES treatment significantly induced lipid accumulation but had no change in cell density and biomass. The expression of genes involved in photoreaction, carbon fixation, glycolysis, pentose phosphate pathway, amino acid catabolism, GS/GOGAT cycle, TCA cycle, triacylglyceride assembly, de novo fatty acid synthesis were up-regulated, while that in amino acid biosynthesis were down-regulated under CHES conditions. Correspondingly, the activity of phosphoribulokinase, carbonic anhydrase, pyruvate dehydrogenase and acetaldehyde dehydrogenase were enhanced by CHES treatment. Chloroplast-specific biological processes were activated by CHES treatment in P. tricornutum, which redirects the flux of carbon into lipid biosynthesis, meanwhile stimulates de novo fatty acid biosynthesis, leading to lipid accumulation under CHES conditions. These indicate an enhancement of intermediate metabolism, resulting in lipid accumulation by CHES.
Tropheryma whipplei detection by metagenomic next-generation sequencing in bronchoalveolar lavage fluid: A cross-sectional study

Tropheryma whipplei is the bacterium associated with Whipple’s disease (WD), a chronic systemic infectious disease primarily involving the gastrointestinal tract. T. whipplei can also be detected in different body site of healthy individuals, including saliva and feces. Traditionally, Tropheryma whipplei has a higher prevalence in bronchoalveolar lavage fluid (BALF) of immunocompromised individuals. Few studies have explored the significance of the detection of T. whipplei in BALF. Herein, we retrospectively reviewed 1725 BALF samples which detected for metagenomic next-generation sequencing (mNGS) from March 2019 to April 2022 in Zhuhai, China. Seventy BALs (70/1725, 4.0%) from 70 patients were positive for T. whipplei. Forty-four patients were male with an average age of 50 years. The main symptoms included cough (23/70), expectoration (13/70), weight loss (9/70), and/or dyspnea (8/70), but gastrointestinal symptoms were rare. Chronic liver diseases were the most common comorbidity (n=15, 21.4%), followed by diabetes mellitus (n=13, 18.6%). Only nine patients (12.9%) were immunocompromised. Twenty-four patients (34.3%) were finally diagnosed with reactivation tuberculosis and 15 patients (21.4%) were diagnosed with lung tumors, including 13 primary lung adenocarcinoma and two lung metastases. Fifteen patients (21.4%) had pneumonia. Among the 20 samples, T. whipplei was the sole agent, and Mycobacterium tuberculosis complex was the most common detected other pathogens. Among the non-tuberculosis patients, 31 (31/46, 67.4%) had ground glass nodules or solid nodules on chest CT. Our study indicates that T. whipplei should be considered as a potential contributing factor in some lung diseases. For non-immunocompromised patients, the detection of T. whipplei also needs attention. The mNGS technology improves the detection and attention of rare pathogens. In the future, the infection, colonization, and prognosis of T. whipplei in lung still need to be studied.
Gut microbiota and short-chain fatty acids may be new biomarkers for predicting neonatal necrotizing enterocolitis: A pilot study

Background Dysbacteriosis is thought to play an important role in the pathogenesis of necrotizing enterocolitis (NEC). We aimed to identify new biomarkers among gut microbiota and short-chain fatty acids (SCFAs) for the early prediction of NEC. Materials and methods Thirty-four preterm infants with gestational ages of ≤ 34 weeks who developed gastrointestinal symptoms were divided into the NEC group (n = 17) and non-NEC group (n = 17). In the NEC group, the gut microbiota and SCFAs in feces were assessed when the infants were enrolled (Group P) and when they were diagnosed with NEC (Group N). In the non-NEC group, samples were assessed when the infants were enrolled (Group C). Results The Ace and Chao1 indices were higher in Group P than in Group C (P < 0.05), and there was no difference between Groups C and N or between Groups P and N (P > 0.05). There was no significant difference in the Simpson and Shannon indices among Groups C, P and N (P > 0.05). The four main phyla showed no differences (P > 0.05) in composition, while at the genus level, compared with Group C, in Group P, Clostridioides, Blautia and Clostridium_sensu_stricto_1 were increased, while Lactobacillus and Bifidobacterium were decreased (P < 0.05). At the species level, Streptococcus salivarius and Rothia mucilaginosa increased, while Bifidobacterium animals subsp. lactis decreased (P < 0.05). In Group N, at the genus level, Stenotrophomonas, Streptococcus and Prevotella increased (P < 0.05). Compared with those in Group C, the levels of acetic acid, propanoic acid and butyric acid decreased significantly in Groups P and N (P < 0.05), and the areas under the curves (AUCs) of these three SCFAs between groups C and P were 0.73, 0.70, and 0.68, respectively. Conclusion The increase in Streptococcus salivarius and Rothia mucilaginosa and decrease in Bifidobacterium_animals_subsp. _lactis, as well as the decrease in acetic, propionic and butyric acids, may help in the early prediction of NEC.
Treatment, pathological characteristics, and prognosis of pulmonary inflammatory myofibroblastic tumor–a retrospective study of 8 cases

Objective Inflammatory myofibroblastic tumor (IMT) is a rare disease. We reviewed data from eight patients diagnosed with pulmonary IMT (PIMT) at our hospital with the aim of summarizing and analyzing the characteristics of PIMT to improve our understanding of the disease. Methods From January 2012 to December 2019, eight patients underwent surgical intervention for PIMT at The First Affiliated Hospital of Bengbu Medical College. Resected tumors were subjected to pathological and immunohistochemical analyses. The follow-up duration for all patients ranged from 2 years and 3 months to 9 years and 9 months (median: 6 years and 9 months). Results The male:female ratio was 5:3, and the mean age was 48.50 years (21–74 years). Two patients (25%) with lung disease discovered via chest computed tomography during physical examinations had not experienced any symptoms. Six patients (75%) presented at the hospital because of cough, expectoration, blood in sputum, and chest tightness. Lesions from all eight patients were surgically removed, and PIMT was confirmed based on pathological examinations and immunohistochemical results. No patient received additional treatment after discharge. All cases have been followed up to the time of writing, without any tumor recurrence or distant metastasis. Conclusion The age of onset of PIMT is usually over 40 years, and its clinical symptoms are easily confused with those of lung cancer. PIMT can only be diagnosed by histopathology and immunohistochemistry. Complete surgical resection is the preferred treatment, as patients undergoing surgery require no additional treatment, such as chemotherapy, and the survival rate is good.
General Pavlovian-to-instrumental transfer in humans: Evidence from Bayesian inference

When repeatedly paired with rewarding outcomes (i.e., Pavlovian conditioning), environmental cues may acquire predictive and motivational significance and later enhance instrumental responding for the same (i.e., outcome-specific transfer) or motivationally similar (i.e., general transfer) outcomes. Although outcome-specific and general Pavlovian-to-Instrumental Transfer (PIT) are characterized by different neural substrates and behavioral mechanisms, general transfer has never been studied in isolation from outcome-specific transfer in humans. The first aim of the present study was to test whether the general transfer effect could emerge in isolation and independently of outcome-specific transfer. Our results showed that general transfer can be elicited without the concurrent presence of outcome-specific transfer, supporting the idea that outcome-specific and general transfer can be studied independently of each other. The second aim of the present study was to clarify whether the affordance-like properties of the outcomes can affect the general transfer. In fact, a critical difference in current studies on general transfer concerns the use of cues associated with outcomes for which an action was previously learned (or not) during the instrumental training. This apparently minor difference affects the affordance-like properties of the outcome and may also be transferred to the cue, in turn impacting general transfer. Results revealed a general transfer of the same magnitude regardless of whether cues were associated with reward earned or not during instrumental conditioning. These findings increase the current knowledge on the incentive motivational mechanism behind general transfer, indicating that it is independent of the motor features of the outcome.
A nomogram predicting 30-day mortality in patients undergoing percutaneous coronary intervention

Background and aims Early detection of mortality after percutaneous coronary intervention (PCI) is crucial, whereas most risk prediction models are based on outdated cohorts before the year 2000. This study aimed to establish a nomogram predicting 30-day mortality after PCI. Materials and methods In total, 10,444 patients undergoing PCI in National Center for Cardiovascular Diseases in China were enrolled to establish a nomogram to predict 30-day mortality after PCI. The nomogram was generated by incorporating parameters selected by logistic regression with the stepwise backward method. Results Five features were selected to build the nomogram, including age, male sex, cardiac dysfunction, STEMI, and TIMI 0–2 after PCI. The performance of the nomogram was evaluated, and the area under the curves (AUC) was 0.881 (95% CI: 0.8–0.961). Our nomogram exhibited better performance than a previous risk model (AUC = 0.7, 95% CI: 0.586–0.813) established by Brener et al. The survival curve successfully stratified the patients above and below the median score of 4. Conclusion A novel nomogram for predicting 30-day mortality was established in unselected patients undergoing PCI, which may help risk stratification in clinical practice.
Physical active lifestyle promotes static and dynamic balance performance in young and older adults

Although regular physical activity exposure leads to positive postural balance control (PBC) adaptations, few studies investigated its effects, or the one of inactivity, on PBC in populations of different age groups. Thus, this study investigated the impact of a physically active lifestyle on static and dynamic PBC in young and older adults. Thirty-five young physically active subjects (YA), 20 young sedentary subjects (YS), 16 physically active older adults (OA), and 15 sedentary older adults (OS) underwent a static and a dynamic PBC assessment. A force platform and an instrumented proprioceptive board were employed to measure the center of pressure (COP) trajectory and the anteroposterior oscillations, respectively. In static conditions, no significant differences were detected among groups considering the overall postural balance performance represented by the area of confidence ellipse values. Conversely, the YA highlighted a higher efficiency (i.e., lower sway path mean velocity) in PBC maintenance compared to the other groups (YA vs OA: p = 0.0057, Cohen’s d = 0.94; YA vs OS p = 0.043, d = 1.07; YA vs YS p = 0.08, d = 0.67). OS exhibited an overall worse performance in dynamic conditions than YA and YS. Surprisingly, no differences were found between YS and OA for all the static and dynamic parameters considered. In conclusion, our results suggest that a physically active lifestyle may promote static and dynamic balance performance in young and older adults, thus with potentially positive effects on the age-related decline of postural balance performance. Dynamic PBC assessment seems more sensitive in detecting differences between groups than the static evaluation.
A comparative analysis of extraction protocol performance on degraded mammalian museum specimens

The extraction of nucleic acids is one of the most routine procedures used in molecular biology laboratories, yet kit performance may influence the downstream processing of samples, particularly for samples which are degraded, and in low concentrations. Here we tested several commercial kits for specific use on commonly sampled mammalian museum specimens to evaluate the yield, size distribution, and endogenous content. Samples were weighed and had approximately equal input material for each extraction. These sample types are typical of natural history repositories ranged from 53 to 130 years old. The tested protocols spanned spin-column based extractions, magnetic bead purification, phenol/chloroform isolation, and specific modifications for ancient DNA. Diverse types of mammalian specimens were tested including adherent osteological material, bone and teeth, skin, and baleen. The concentration of DNA was quantified via fluorometry, and the size distributions of extracts visualized on an Agilent TapeStation. Overall, when DNA isolation was successful, all methods had quantifiable concentrations, albeit with variation across extracts. The length distributions varied based on the extraction protocol used. Shotgun sequencing was performed to evaluate if the extraction methods influenced the amount of endogenous versus exogenous content. The DNA content was similar across extraction methods indicating no obvious biases for DNA derived from different sources. Qiagen kits and phenol/chloroform isolation outperformed the Zymo magnetic bead isolations in these types of samples. Statistical analyses revealed that extraction method only explained 5% of the observed variation, and that specimen age explained variation (29%) more effectively.
Empowering roots—Some current aspects of root bioenergetics

Roots of higher plants provide the shoot with nutrients and water. In exchange, they receive photosynthates, which serve both as energy source and building blocks for maintenance and growth. While studies in plant bioenergetics used to focus on photosynthesis, several more recent findings also aroused or renewed interest in energy conversion and allocation in roots. Root building costs were identified as a long-undervalued trait, which turned out to be highly relevant for stress tolerance and nutrient use efficiency. Reduced building costs per root length (e.g., by aerenchyma formation or by increasing the cell size) are beneficial for exploring the soil for nutrient-rich patches, especially in low-input agrosystems. Also, an apparent mismatch was frequently found between the root energy budget in the form of the ATP pool on the one side and the apparent costs on the other side, particularly the costs of membrane transport under stress conditions, e.g., the Na+ detoxification costs resulting from Na+ sequestration at the plasma membrane. Ion transport across the plasma membrane (and also endomembranes) is coupled to the proton motive force usually believed to be exclusively generated by H+ ATPases. Recently, an alternative mechanism, the biochemical pH clamp, was identified which relies on H+ formation and binding in the apoplast and the cytosol, respectively, driven by metabolism (so-called active buffering). On this background, several aspects of root bioenergetics are discussed. These are (1) root respiration in soil, with a critical view on calorimetric vs. gas exchange measurements; (2) processes of energy conversion in mitochondria with a special focus on the role of the alternative oxidases, which allow adjusting carbon flow through metabolic pathways to membrane transport processes; and (3) energy allocation, in particular to transport across the plasma membrane forming the interface to soil solution. A concluding remark is dedicated to modeling root bioenergetics for optimizing further breeding strategies. Apparent “energy spoilers” may bestow the plant with a yet unidentified advantage only unfolding their beneficial effect under certain environmental conditions.
A randomized, double-blinded, placebo-controlled, single dose analgesic study of preoperative intravenous ibuprofen for tonsillectomy in children

Purpose Tonsillectomy is a recognized treatment for children with tonsil hypertrophy and results in significant postoperative oropharyngeal pain. Fentanyl and other morphine-like analgesics are widely used as perioperative analgesia but are associated with side effects such as vomiting, nausea, and respiratory depression. As the least toxic non-steroidal anti-inflammatory drug, ibuprofen may be effective and safe for pain control after tonsillectomy. We aimed to explore whether the addition of intravenous (IV) ibuprofen administered at induction can reduce the need for early postoperativeanalgesics. Study design and methods This randomized, double-blind, controlled clinical trial enrolled 95 pediatric patients who underwent tonsillectomy. Participants aged 6 months to 12 years were randomly assigned to either the experimental and control groups (1:1). The children were premedicated 15 min before surgery with IV ibuprofen 10 mg kg−1 or placebo (normal saline). Pain was scored at 15, 30, and 120 min after extubation, and IV fentanyl (0.5 mcg kg−1) was administered when the Faces, Legs, Activity, Cry, and Consolability (FLACC) Scale was ≥7 and deemed appropriate by the nursing staff in the post-anesthesia care unit (PACU). The visual analog scale was used as a supplementary evaluation for older children (≥7 years old) who were awake and could self-report pain. The primary outcome variable was the number of patients who received postoperative analgesia. Results The requirement for rescue fentanyl was reduced by 18% with the addition of IV ibuprofen (P = 0.043). There were no signficant differences in the amount of fentanyl administered postoperatively (P = 0.127). Compared with the placebo group, the number of children who needed more than one dose of rescue fentanyl decreased in the experimental group, but the differences were not significant (P = 0.056). There were no significant differences between the groups in terms of operative blood loss (P = 0.978), vomiting, or postoperative bleeding (P = 0.474). Conclusion It is safe to administer IV ibuprofen 15 min before tonsillectomy, and it can significantly reduce the need for rescue fentanyl. IV ibuprofen should be considered as an important part of the multimodal approach for postoperative analgesia in children. Clinical trial registration Chictr.org. cn, identifier: ChiCTR2100044508.
Childhood social isolation causes anxiety-like behaviors via the damage of blood-brain barrier in amygdala in female mice

Social interaction plays an essential role in species survival for socialized animals. Previous studies have shown that a lack of social interaction such as social isolation, especially in the early-life phase, increases the risk of developing mental diseases in adulthood. Chronic social stress alters blood-brain barrier (BBB) integrity and increases peripheral cytokines to infiltrate the brain, which is linked to the development of depressive-like behaviors in mice, suggesting that BBB function is crucial in environmental stimuli-driven mood disorders via increased neuroinflammation in the brain. However, the precise mechanisms of inflammation and BBB integrity underlying the behavioral profiles induced by social isolation remain poorly understood. Here we showed that chronic childhood social isolation from post-weaning for consecutive 8 weeks in female but not male C57BL/6J mice induces anxiety-like behaviors. The levels of peripheral inflammatory cytokines including interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α in the plasma of socially isolated female mice were increased. Importantly, we found decreased expression of the endothelial cell tight junction protein Claudin-5, increased BBB breakdown and microglial activation in the amygdala of isolated but not group-housed female mice. Moreover, the neuronal activity in the amygdala was increased as evidenced by c-fos positive cells, and the levels of IL-1β in the amygdala, a critical brain region for regulating social processing and interaction, were also higher in female mice exposed to social isolation. Finally, down-regulation of Claudin-5 induced anxiety-like behaviors in group-housed females and overexpression of Claudin-5 with adeno-associated virus in the amygdala to restore BBB integrity decreased subsequent anxiety-like behaviors. Together, these findings suggest that chronic childhood social isolation impaired BBB permeability and caused neuroinflammation in the amygdala by recruiting peripheral cytokines into the brain and activating microglia, consequently triggering the development of anxiety-like behaviors in female mice.