Miracle-dz/UniFAR-FTUs huggingface dataset:
Gut microbiota and inflammation patterns for specialized athletes: a multi-cohort study across different types of sports

ABSTRACT Regular high-intensity exercise can cause changes in athletes’ gut microbiota, and the extent and nature of these changes may be affected by the athletes’ exercise patterns. However, it is still unclear to what extent different types of athletes have distinct gut microbiome profiles and whether we can effectively monitor an athlete’s inflammatory risk based on their microbiota. To address these questions, we conducted a multi-cohort study of 543 fecal samples from athletes in three different sports: aerobics (n = 316), wrestling (n = 53), and rowing (n = 174). We sought to investigate how athletes’ gut microbiota was specialized for different types of sports, and its associations with inflammation, diet, anthropometrics, and anaerobic measurements. We established a microbiota catalog of multi-cohort athletes and found that athletes have specialized gut microbiota specific to the type of sport they engaged in. Using latent Dirichlet allocation, we identified 10 microbial subgroups of athletes’ gut microbiota, each of which had specific correlations with inflammation, diet, and anaerobic performance in different types of athletes. Notably, most inflammation indicators were associated with Prevotella-driven subgroup 7. Finally, we found that the effects of sport types and exercise intensity on the gut microbiota were sex-dependent. These findings shed light on the complex associations between physical factors, gut microbiota, and inflammation in athletes of different sports types and could have significant implications for monitoring potential inflammation risk and developing personalized exercise programs. IMPORTANCE This study is the first multi-cohort investigation of athletes across a range of sports, including aerobics, wrestling, and rowing, with the goal of establishing a multi-sport microbiota catalog. Our findings highlight that athletes’ gut microbiota is sport-specific, indicating that exercise patterns may play a significant role in shaping the microbiome. Additionally, we observed distinct associations between gut microbiota and markers of inflammation, diet, and anaerobic performance in athletes of different sports. Moreover, we expanded our analysis to include a non-athlete cohort and found that exercise intensity had varying effects on the gut microbiota of participants, depending on sex. This study is the first multi-cohort investigation of athletes across a range of sports, including aerobics, wrestling, and rowing, with the goal of establishing a multi-sport microbiota catalog. Our findings highlight that athletes’ gut microbiota is sport-specific, indicating that exercise patterns may play a significant role in shaping the microbiome. Additionally, we observed distinct associations between gut microbiota and markers of inflammation, diet, and anaerobic performance in athletes of different sports. Moreover, we expanded our analysis to include a non-athlete cohort and found that exercise intensity had varying effects on the gut microbiota of participants, depending on sex.
PAN–Precursor Relationship and Process Analysis of PAN Variations in the Pearl River Delta Region

Peroxy acetyl nitrate (PAN) is an important photochemical product formed from the reactions between volatile organic compounds (VOCs) and nitrogen oxides (NOx) under sunlight. In this study, a field measurement was conducted at a rural site (the backgarden site, or BGS) of the Pearl River Delta (PRD) region in 2006, with the 10 min maximum PAN mixing ratios of 3.9 ppbv observed. The factors influencing the abundance of PAN at the BGS site was evaluated by the process analysis through the Weather Research and Forecasting-Community Multiscale Air Quality (WRF-CMAQ) model. The results suggested that the increase of PAN abundance at the BGS site was mainly controlled by the gas-phase chemistry, followed by vertical transport, while its loss was modulated mainly by dry deposition and horizontal transport. As the dominant important role of gas-phase chemistry, to provide detailed information on the photochemical formation of PAN, a photochemical box model with near-explicit chemical mechanism (i.e., the master chemical mechanism, MCM) was used to explore the relationship of photochemical PAN formation with its precursors based on the measured data at the BGS site. It was found that PAN formation was VOC-limited at the BGS site, with the oxidation of acetaldehyde the most important pathway for photochemical PAN production, followed by the oxidation and photolysis of methylglyoxal (MGLY). Among all the primary VOC precursors, isoprene and xylenes were the main contributors to PAN formation. Overall, our study provides new insights into the PAN photochemical formation and its controlling factors, and highlighted the importance of gas chemistry on the PAN abundance in the PRD region.
Preoperative resting‐state microstate as a marker for chronic pain after breast cancer surgery

Chronic postoperative pain poses challenges, emphasizing the importance of accurately predicting pain in advance. Generally, pain perception is associated with the temporal dynamics of the brain, which can be represented by microstates. Specifically, microstates are transient and patterned brain topographies formed by temporally overlapping and spatially synchronized oscillatory activities. Consequently, by characterizing brain activity, microstates offer valuable insights into pain perception.
On the excessive use of coefficient of variation as a metric of quantitation quality in proteomics

The coefficient of variation (CV) is often used in proteomics as a proxy to characterize the performance of a quantitation method and/or the related software. In this note, we question the excessive reliance on this metric in quantitative proteomics that may result in erroneous conclusions. We support this note using a ground‐truth Human‐Yeast‐E. coli dataset demonstrating in a number of cases that erroneous data processing methods may lead to a low CV which has nothing to do with these methods’ performances in quantitation.
Multi-phase ionization dynamics of carbon thin film irradiated by high power short pulse laser

The ionization dynamics of a carbon thin film irradiated by a high power short pulse laser in the range of 1019−20 W/cm2 are studied using the extended particle-based integrated code (EPIC), which includes atomic and collisional processes. Two types of ionization dynamics exhibiting different spatio-temporal structures are found to predominantly regulate the process, and arise depending on the laser amplitude. The first is a fast convective propagation for charge states up to C4+, which keeps a steep ionization front. The velocity of the front is of the order of the speed of light. The front formation results from the localized longitudinal electrostatic field and associated field ionization, which in turn propagates inside the film. This convective propagation is triggered when the laser field becomes high enough that electron bunches accelerated by the laser ponderomotive force reach relativistic energies and penetrate inside the film across the surface. The second dynamics is a fast non-diffusive propa.
Physicochemical processes in the indirect interaction between surface air plasma and deionized water

One of the most central scientific questions for plasma applications in healthcare and environmental remediation is the chemical identity and the dose profile of plasma-induced reactive oxygen and nitrogen species (ROS/RNS) that can act on an object inside a liquid. A logical focus is on aqueous physicochemical processes near a sample with a direct link to their upstream gaseous processes in the plasma region and a separation gap from the liquid bulk. Here, a system-level modeling framework is developed for indirect interactions of surface air plasma and a deionized water bulk and its predictions are found to be in good agreement with the measurement of gas-phase ozone and aqueous long-living ROS/RNS concentrations. The plasma region is described with a global model, whereas the air gap and the liquid region are simulated with a 1D fluid model. All three regions are treated as one integrated entity and computed simultaneously. With experimental validation, the system-level modeling shows that the dominant aqueous ROS/RNS are long-living species (e.g. H2O2aq, O3aq, nitrite/nitrate, H+aq). While most short-living gaseous species could hardly survive their passage to the liquid, aqueous short-living ROS/RNS are generated in situ through reactions among long-living plasma species and with water molecules. This plasma-mediated remote production of aqueous ROS/RNS is important for the abundance of aqueous HO2aq, HO3aq, OHaq and O2− ? >aq as well as NO2aq and NO3aq. Aqueous plasma chemistry offers a novel and significant pathway to activate a given biological outcome, as exemplified here for bacterial deactivation in plasma-activated water. Additional factors that may synergistically broaden the usefulness of aqueous plasma chemistry include an electric field by aqueous ions and liquid acidification. The system-modeling framework will be useful in assisting designs and analyses of future investigations of plasma-liquid and plasma–cell interactions.
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics

Abstract Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that are used. Unfortunately, Bayesian methods are computationally expensive, and typical applications involve at most a few hundred sequences. This is problematic in the age of rapidly expanding genomic data and increasing scope of evolutionary analyses, forcing researchers to resort to less accurate but faster methods, such as maximum parsimony and maximum likelihood. Does this spell doom for Bayesian methods? Not necessarily. Here, we discuss some recently proposed approaches that could help scale up Bayesian analyses of evolutionary problems considerably. We focus on two particular aspects: online phylogenetics, where new data sequences are added to existing analyses, and alternatives to Markov chain Monte Carlo (MCMC) for scalable Bayesian inference. We identify 5 specific challenges and discuss how they might be overcome. We believe that online phylogenetic approaches and Sequential Monte Carlo hold great promise and could potentially speed up tree inference by orders of magnitude. We call for collaborative efforts to speed up the development of methods for real-time tree expansion through online phylogenetics.
Parallel Direct Method of DNS for Two-Dimensional Turbulent Rayleigh-Bénard Convection

A highly efficient parallelization scheme of direct numerical simulation (DNS) for two-dimensional Rayleigh-Benard convection is presented. By introducing the parallel diagonal dominant (PDD) algorithm to solve the pressure Poisson equation and adjusting the domain decomposition accordingly, all-to-all communication as the usual obstacle to parallel computing can be eliminated. Excellent strong scaling and weak scaling for the parallel efficiency are achieved. Numerical results show that very complex structures in flow exist at very high Ra numbers. The required high resolution both in space and in time can be obtained by the present method at low parallel overhead.
Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance?

Abstract Purpose Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. Conclusions The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
Management of diabetic neuropathy with memantine: A randomized clinical trial

Background Diabetes patients frequently experience diabetic neuropathy (DN), a microvascular complication that significantly reduces patients’ quality of life. Memantine has demonstrated potential benefits for neuropathic pains in preclinical studies. This study aimed to assess the efficacy of memantine in the management of peripheral neuropathy in patients with type 2 diabetes mellitus (T2DM). Method This randomized clinical trial includes 143 diabetic patients (aged between 18 and 75 years) with a confirmed diagnosis of diabetic neuropathy. Patients were randomly assigned to receive memantine 5 mg twice daily for 1 week, followed by 10 mg twice daily plus gabapentin 300 mg daily (n = 72) or just gabapentin 300 mg daily (n = 71) for 8 weeks. The DN4 questionnaire, monofilament, tuning fork, and Tip-therm tests were used to measure neuropathy at baseline and after the 8-week intervention. Results The mean score of the DN4 questionnaire in the memantine group was significantly lower than the control group (p. value: .001). The number of patients with diabetic neuropathy remarkably decreased in the memantine group at the end of the study based on the performed tests (p. value: .001). Conclusion Memantine functions as a beneficial agent in the management of diabetic neuropathy, which would significantly improve the quality of life in diabetic patients.
Three‐dimensional quantitative muscle ultrasound in patients with facioscapulohumeral dystrophy and myotonic dystrophy

Ultrasound imaging of muscle tissue conventionally results in two‐dimensional sampling of tissue. For heterogeneously affected muscles, a sampling error using two‐dimensional (2D) ultrasound can therefore be expected. In this study, we aimed to quantify and extend ultrasound imaging findings in neuromuscular disorders by using three‐dimensional quantitative muscle ultrasound (3D QMUS).
Basic Image Analysis and Manipulation in ImageJ/Fiji

Microscopy‐generated images contain quantitative information that can be extracted using a variety of analysis methods and automated pipelines. In this protocol, basic aspects of image analysis are outlined, including software installation, data import, image processing functions, and analytical tools that can be used to extract information from microscopy data using the open‐source software ImageJ/Fiji. Step‐by‐step protocols for analyzing objects (i.e., nuclei) in a fluorescence image are included, focusing on segmentation routines. © 2023 Wiley Periodicals LLC.
In-depth review of delivery carriers associated with vaccine adjuvants: current status and future perspectives

ABSTRACT Introduction Vaccines are powerful tools for controlling microbial infections and preventing epidemics. To enhance the immune response to antigens, effective subunit vaccines or mRNA vaccines often require the combination of adjuvants or delivery carriers. In recent years, with the rapid development of immune mechanism research and nanotechnology, various studies based on the optimization of traditional adjuvants or various novel carriers have been intensified, and the construction of vaccine adjuvant delivery systems (VADS) with both adjuvant activity and antigen delivery has become more and more important in vaccine research. Areas covered This paper reviews the common types of vaccine adjuvant delivery carriers, classifies the VADS according to their basic carrier types, introduces the current research status and future development trend, and emphasizes the important role of VADS in novel vaccine research. Expert opinion As the number of vaccine types increases, conventional aluminum adjuvants show limitations in effectively stimulating cellular immune responses, limiting their use in therapeutic vaccines for intracellular infections or tumors. In contrast, the use of conventional adjuvants as VADS to carry immunostimulatory molecules or deliver antigens can greatly enhance the immune boosting effect of classical adjuvants. A comprehensive understanding of the various delivery vehicles will further facilitate the development of vaccine adjuvant research.
Dissecting morphogenetic apoptosis through a genetic screen in Drosophila

This genetic screen identifies elements of the “morphogenetic apoptosis pathway” potentially involved in the regulation, the orchestration or the impact of the apoptotic process on morphogenesis. Apoptosis is an essential cellular process both in normal development and pathological contexts. Screens performed to date have focused on the cell autonomous aspect of the process, deciphering the apoptotic cascade leading to cell destruction through the activation of caspases. However, the nonautonomous aspect of the apoptotic pathway, including signals regulating the apoptotic pattern or those sent by the apoptotic cell to its surroundings, is still poorly understood. Here, we describe an unbiased RNAi-based genetic screen whose goal is to identify elements of the “morphogenetic apoptosis pathway” in an integrated model system, the Drosophila leg. We screened about 1,400 candidates, using adult joint morphology, morphogenetic fold formation, and apoptotic pattern as readouts for the identification of potential apoptosis-related genes. We identified 41 genes potentially involved in specific aspects of morphogenetic apoptosis: (1) regulation of the apoptotic process; (2) formation, extrusion, and elimination of apoptotic bodies; and (3) contribution to morphogenesis downstream of apoptosis. Graphical Abstract
Post-traumatic stress in war veterans and secondary traumatic stress among parents of war veterans five years after the 2014 Israel-Gaza military conflict

ABSTRACT Secondary traumatic stress (STS) has been studied in therapists, spouses, and mainly in children of traumatised individuals. To date, the relationship between children’s posttraumatic stress disorder (PTSD) symptoms and their parents’ mental health outcomes have been understudied, and specifically, long term STS symptoms of parents of war veterans were not investigated. The current study examined PTSD symptoms among veterans of the 2014 Israel-Gaza war and STS among their parents, five years after the war. The control group consisted of veterans from combat military units who were on active duty at the time of the war but did not actively participate in the war (stand-by units) – providing a natural experiment condition. We found that PTSD symptoms were almost twice as high in the directly active war veterans (DAV, N = 32) group compared to the indirectly active war veterans (IAV, N = 26) group. Results showed that mothers had higher STS symptoms in general, and DAV PTSD symptoms correlated with their fathers STS symptoms. The current study provides novel evidence for: (a) subclinical PTSD symptoms in war veterans 5 years after the war, and (b) transmission of trauma from war veterans to their parents. The overall negative effect of sending a child to war on the parents are also discussed. HIGHLIGHTS The current study examined post-traumatic stress symptoms among undiagnosed war veterans of the 2014–2014 Israel-Gaza Military Conflict compared to matched control who were on active military duty at the same time but did not actively participate in the war. We found higher post-traumatic stress symptoms in the veterans who actively participated in the war, roughly five years after the war. Parents of veterans who actively participated in the war exhibited higher secondary traumatic stress compared to parents of veterans who did not actively participate in the war. This is especially interesting given that parents of all veterans were not aware of their whereabouts during the war. Overall, mothers exhibited higher secondary traumatic stress compared to fathers. However, fathers were more ‘in-sync’ with their sons’ traumatic experience as evident by a significant correlation between the war veterans’ post-traumatic stress and the fathers’ secondary traumatic stress symptoms.
Yellow oleander (Thevetia peruviana) toxicosis in 4 goats

Four alpine goats developed diarrhea soon after the owner placed plant clippings believed to be yellow oleander (Thevetia peruviana) into their pen on a suburban property near Palm Desert, CA, USA. A 1-y-old female goat died suddenly ~1 h after eating the plant clippings and was submitted to the San Bernardino Branch of the California Animal Health and Food Safety Laboratory System for postmortem examination. The main autopsy and histopathologic findings were myocardial hemorrhage and necrosis, consistent with cardiac glycoside intoxication. Rumen contents were analyzed by LC-MS/MS; peruvoside, a cardiac glycoside, was detected, but oleandrin, the cardiac glycoside of common oleander (Nerium oleander), was not. An LC–high-resolution MS (LC-HRMS) analysis revealed the presence of peruvoside and neriifolin in the rumen contents and in a tested plant fragment, indicating that the plant was a member of the Thevetia genus. A clipping from the plant fed to the goats and submitted by the owner was identified as yellow oleander, Thevetia peruviana (also known as Cascabela thevetia).
The relationships between passions, intentions, habit and exercise frequency

ABSTRACT There were three purposes to this research. First, we sought to test the differential role of harmonious and obsessive passion in predicting intention and habit for exercise. The second goal of this research was to test the associations between intention, habit and exercise frequency. Last, the third goal was to assess the mediation role of intention and habit in the relationship between both forms of passion and exercise frequency. The sample consisted of 284 participants (140 males, 144 females) aged 18–60 years old (M age = 29.81, SD = 9.16). Regression paths of the structural model indicated significant associations: a) harmonious passion was significantly associated with intentions and habit; b) obsessive passion was significantly associated with habit; c) intentions and habit were significantly associated with exercise frequency. The mediation model variance explained was 17% (p < .001). The total effect via harmonious and obsessive passion was β = . 57 (IC95% = .42, .73) and the total indirect effect was β = . 11 (IC95% = .02, .24). Having harmonious passion for a fitness activity appears to have the potential to increase regular physical activity among exercisers. Individuals who recognize the significance of physical exercise and participate in activities they enjoy the most can affirm the positive effects on their health from being active.
Genomic signatures of barley breeding for environmental adaptation to the new continents

Genomic signatures of barley breeding for environmental adaptation to the new continents Haifei Hu , Penghao Wang, Tefera Tolera Angessa, Xiao-Qi Zhang, Kenneth J. Chalmers, Gaofeng Zhou, Camilla Beate Hill, Yong Jia , Craig Simpson, John Fuller, Alka Saxena, Hadi Al Shamaileh, Munir Iqbal , Brett Chapman, Parwinder Kaur , Olga Dudchenko, Erez Lieberman Aiden, Gabriel Keeble-Gagnere, Sharon Westcott, David Leah, Josquin F. Tibbits, Robbie Waugh, Peter Langridge, Rajeev Varshney , Tianhua He* and Chengdao Li*