Miracle-dz/UniFAR-FTUs huggingface dataset:
Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland.

We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2)T, isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3-15 % NaCl (w/v; optimum, 5 %), pH 7.0-9.0 (optimum, pH 7.5-8.0) and 15-35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2)T to the class Gammaproteobacteria and the genus Halomonas with highest similarity to Halomonas daqiaonensis YCSA28T (98.4 %) and Halomonas ventosae Al12T (97.9 %). Experimental and in silico DNA-DNA hybridization values were 42.7 and 35.1% with H. daqiaonensis IBRC-M 10931T and 48 and 35.2% with H. ventosae IBRC-M 10566T, respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against H. ventosae Al12T and H. daqiaonensis YCSA28T were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C16 : 0 cyclo, C19 : 0 ω8c, C16 : 1 ω7c and/or iso-C15:0 2-OH, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2)T could be classified as a novel species in the genus Halomonas for which the name Halomonas lysinitropha sp. nov. is proposed. The type strain is 3(2)T (=IBRC M 10929T=LMG 29450T=CIP 111708T).
Vitamin D Supplementation Does Not Impact Resting Metabolic Rate, Body Composition and Strength in Vitamin D Sufficient Physically Active Adults

Supplementation with the most efficient form of Vitamin D (VitD3) results in improvements in energy metabolism, muscle mass and strength in VitD deficient individuals. Whether similar outcomes occur in VitD sufficient individuals’ remains to be elucidated. The aim of this study is to determine the effect of VitD3 supplementation on resting metabolic rate (RMR), body composition and strength in VitD sufficient physically active young adults. Participants completed pre-supplementation testing before being matched for sunlight exposure and randomly allocated in a counterbalanced manner to the VitD3 or placebo group. Following 12 weeks of 50 IU/kg body-mass VitD3 supplementation, participants repeated the pre-supplementation testing. Thirty-one adults completed the study (19 females and 12 males; mean ± standard deviation (SD); age = 26.6 ± 4.9 years; BMI = 24.2 ± 4.1 kg·m2). The VitD group increased serum total 25(OH)D by 30 nmol/L while the placebo group decreased total serum concentration by 21 nmol/L, reaching 123 (51) and 53 (42.2) nmol/L, respectively. There were no significant changes in muscle strength or power, resting metabolic rate and body composition over the 12-week period. Physically active young adults that are VitD sufficient have demonstrated that no additional physiological effects of achieving supraphysiological serum total 25(OH)D concentrations after VitD3 supplementation.
Plant traits related to precipitation sensitivity of species and communities in semi-arid shortgrass prairie.

Understanding how plant communities respond to temporal patterns of precipitation in water-limited ecosystems is necessary to predict inter-annual variation and trends in ecosystem properties, including forage production, biogeochemical cycling, and biodiversity. In North American shortgrass prairie, we measured plant abundance, functional traits related to growth rate and drought tolerance, and aboveground net primary productivity (ANPP) to identify: (1) species-level responsiveness to precipitation (precipitation sensitivity, Sspp ) across functional groups, (2) Sspp relationships to continuous plant traits, and (3) whether continuous trait-Sspp relationships scaled to the community level. Across 32 plant species, we found strong bivariate relationships of both leaf dry matter content (LDMC) and leaf osmotic potential (Ψosm ) with Sspp . Yet, LDMC and specific leaf area (SLA) were retained in the lowest AIC multiple regression model, explaining 59% of Sspp . Most relationships between continuous traits and Sspp scaled to the community-level but were often contingent on the presence/absence of particular species and/or land management at a site. Thus, plant communities in shortgrass prairie may shift towards slower growing, more stress resistant species in drought years and/or chronically drier climate. These findings highlight the importance of both leaf economic and drought tolerance traits in determining species and community responses to altered precipitation.
A Novel Orthotopic Patient-Derived Xenograft Model of Radiation-Induced Glioma Following Medulloblastoma

Simple Summary Radiation-induced glioma (RIG) is a highly aggressive brain cancer arising as a consequence of radiation therapy, for which there is currently no effective treatment. In order to test new drugs in the hope of finding more effective therapies, we need mouse models that faithfully replicate human RIG. Our laboratory collected tumour cells at autopsy from a paediatric patient with RIG following treatment for a different brain tumour. Using these cells, we created a mouse brain tumour model that retains all the characteristics and features of the original patient tumour from which it was derived. This unique model allowed us to study the progression of RIG in the brain, and to identify drugs that may be effective in the treatment of this disease. This mouse model will also allow us to test the efficacy of new treatments, with the hope of improving the prognosis for patients diagnosed with this disease. Abstract Radiation-induced glioma (RIG) is a highly aggressive brain cancer arising as a consequence of radiation therapy. We report a case of RIG that arose in the brain stem following treatment for paediatric medulloblastoma, and the development and characterisation of a matched orthotopic patient-derived xenograft (PDX) model (TK-RIG915). Patient and PDX tumours were analysed using DNA methylation profiling, whole genome sequencing (WGS) and RNA sequencing. While initially thought to be a diffuse intrinsic pontine glioma (DIPG) based on disease location, results from methylation profiling and WGS were not consistent with this diagnosis. Furthermore, clustering analyses based on RNA expression suggested the tumours were distinct from primary DIPG. Additional gene expression analysis demonstrated concordance with a published RIG expression profile. Multiple genetic alterations that enhance PI3K/AKT and Ras/Raf/MEK/ERK signalling were discovered in TK-RIG915 including an activating mutation in PIK3CA, upregulation of PDGFRA and AKT2, inactivating mutations in NF1, and a gain-of-function mutation in PTPN11. Additionally, deletion of CDKN2A/B, increased IDH1 expression, and decreased ARID1A expression were observed. Detection of phosphorylated S6, 4EBP1 and ERK via immunohistochemistry confirmed PI3K pathway and ERK activation. Here, we report one of the first PDX models for RIG, which recapitulates the patient disease and is molecularly distinct from primary brain stem glioma. Genetic interrogation of this model has enabled the identification of potential therapeutic vulnerabilities in this currently incurable disease.
Impaired purine homeostasis plays a primary role in trimethoprim‐mediated induction of virulence genes in Burkholderia thailandensis

One of the most commonly prescribed antibiotics against Burkholderia infections is co‐trimoxazole, a cocktail of trimethoprim and sulfamethoxazole. Trimethoprim elicits an upregulation of the mal gene cluster, which encodes proteins involved in synthesis of the cytotoxic polyketide malleilactone; trimethoprim does so by increasing expression of the malR gene, which encodes the activator MalR. We report that B. thailandensis grown on trimethoprim exhibited increased virulence against Caenorhabditis elegans. This enhanced virulence correlated with an increase in expression of the mal gene cluster. Notably, inhibition of xanthine dehydrogenase by addition of allopurinol led to similar upregulation of malA and malR, with addition of trimethoprim or allopurinol also resulting in an equivalent intracellular accumulation of xanthine. Xanthine is a ligand for the transcription factor MftR that leads to attenuated DNA binding, and we show using chromatin immunoprecipitation that MftR binds directly to malR. Our gene expression data suggest that malR expression is repressed by both MftR and by a separate transcription factor, which also responds to a metabolite that accumulates on exposure to trimethoprim. Since allopurinol elicits a similar increase in malR/malA expression as trimethoprim, we suggest that impaired purine homeostasis plays a primary role in trimethoprim‐mediated induction of malR and in turn malA.
JCPyV VP1 Mutations in Progressive Multifocal Leukoencephalopathy: Altering Tropism or Mediating Immune Evasion?

Polyomaviruses are ubiquitous human pathogens that cause lifelong, asymptomatic infections in healthy individuals. Although these viruses are restrained by an intact immune system, immunocompromised individuals are at risk for developing severe diseases driven by resurgent viral replication. In particular, loss of immune control over JC polyomavirus can lead to the development of the demyelinating brain disease progressive multifocal leukoencephalopathy (PML). Viral isolates from PML patients frequently carry point mutations in the major capsid protein, VP1, which mediates virion binding to cellular glycan receptors. Because polyomaviruses are non-enveloped, VP1 is also the target of the host’s neutralizing antibody response. Thus, VP1 mutations could affect tropism and/or recognition by polyomavirus-specific antibodies. How these mutations predispose susceptible individuals to PML and other JCPyV-associated CNS diseases remains to be fully elucidated. Here, we review the current understanding of polyomavirus capsid mutations and their effects on viral tropism, immune evasion, and virulence.
Hodgkin lymphoma arising in patients with chronic lymphocytic leukemia: outcomes from a large multi-center collaboration

Chronic lymphocytic leukemia (CLL) patients who develop Hodgkin lymphoma (HL) have limited survival. No current therapeutic standard of care exists. We conducted a multi-center retrospective study of patients with Hodgkin transformation (HT) of CLL. Clinicobiologic characteristics, treatment type, and survival outcomes were analyzed and compared with historic case series. Ninety-four patients were identified. Median age at HT was 67 years (range, 38-85). Median time from CLL diagnosis to HT was 5.5 years (range, 0-20.2). Prior to HT, patients received a median of two therapies for CLL (range, 0-12). As initial therapy for HT, 61% (n=62) received ABVD-based regimens (adriamycin, bleomycin, vinblastine, and dacarbazine). Seven (7%) patients received hematopoietic cell transplantation (HCT) while in first complete remission (CR1). The median number of treatments for HT per patient was one (range, 0-5) with 59 (61%) patients only receiving one line of therapy. After HT, patients had a median follow-up of 1.6 years (range, 0-15.1). Two-year overall survival (OS) after HT diagnosis was 72% (95% Confidence Interval: 62-83). The patients who received standard ABVD-based therapy had a median OS of 13.2 years. Although limited by small sample size, the patients who underwent HCT for HT in CR1 had a similar 2-year OS (n=7; 67%) compared to patients who did not undergo HCT for HT in CR1 (n=87; 72%; P=0.46). In this multi-center study, HT patients treated with ABVD-based regimens had prolonged survival supporting the use of these regimens as standard of care for these patients.
Crystal Structure of Mannose Specific IIA Subunit of Phosphotransferase System from Streptococcus pneumoniae

Streptococcus pneumoniae is a frequent bacterial pathogen of the human respiratory tract causing pneumonia, meningitis and sepsis, a serious healthcare burden in all age groups. S. pneumoniae lacks complete respiratory chain and relies on carbohydrate fermentation for energy generation. One of the essential components for this includes the mannose phosphotransferase system (Man-PTS), which plays a central role in glucose transport and exhibits a broad specificity for a range of hexoses. Importantly, Man-PTS is involved in the global regulation of gene expression for virulence determinants. We herein report the three-dimensional structure of the EIIA domain of S. pneumoniae mannose phosphotransferase system (SpEIIA-Man). Our structure shows a dimeric arrangement of EIIA and reveals a detailed molecular description of the active site. Since PTS transporters are exclusively present in microbes and sugar transporters have already been suggested as valid targets for antistreptococcal antibiotics, our work sets foundation for the future development of antimicrobial strategies against Streptococcus pneumoniae.
Analysis of Trace Compositions of Meilanchun Sesame-flavor Liquor

The measurement results of trace compositions of Meilanchun sesame-flavor liquor were analyzed and compare with other famous liquors.The results showed that,Meilanchun sesame-flavor liquor not only has the unique sesame-flavor components but also contains many kinds of organic acids,fatty acids(ester),alcohols,phenols,pyrazines etc.Among conventional flavoring compounds,the content of aldehyde acetal is 1.2～4.9 times,the content of ethyl lactate and ethyl acetate is 1.3～3.5 times,and the content of linolic acid,oleic acid and ethyl palmitate is 1.4～4.4 times as much as that of other famous liquors.Among trace flavoring compositions,the content of tetramethylpyrazine is higher than that of other sesame-flavor liquor,but lower than some other famous liquors.The content of lactic acid and acetic acid is more than 2 times of that of other liquors but the content of butyrate is lower.
Novel Bioformulations Developed from Pseudomonas putida BSP9 and Its Biosurfactant for Growth Promotion of Brassica juncea (L.)

In this study, Pseudomonas putida BSP9 isolated from rhizosphere of Brassica juncea was investigated for its plant growth promoting and biosurfactant producing activities. The isolate showed the ability to produce indole acetic acid, siderophore, phosphate solubilization activity and was an efficient producer of biosurfactant. Purification (of the biosurfactant) by thin layer chromatography (TLC) and further characterization by Fourier transform infrared spectroscopy (FTIR) revealed that biosurfactant produced by the isolate belonged to the glycolipid category, which is largely produced by Pseudomonas sp. In addition, liquid chromatography-mass spectroscopy (LC-MS) analysis showed the presence of a mixture of six mono-rhamnolipidic and a di-rhamnolipidic congeners, confirming it as a rhamnolipid biosurfactant. Bioformulations were developed using BSP9 and its biosurfactant to check their impact on promoting plant growth in B. juncea. It was noted from the study that bioformulations amended with biosurfactant (singly or in combination with BSP9) resulted in enhancement in the growth parameters of B. juncea as compared to untreated control. Maximum increment was achieved by plants inoculated with bioformulation that had BSP9 plus biosurfactant. The study also suggested that growth promotion was significant up to a threshold level of biosurfactant and that further increasing the concentration did not further enhance the growth parameter values of the plant. The study proves that novel bioformulations can be developed by integrating plant growth promoting rhizobacteria (PGPR) and their biosurfactant, and they can be effectively used for increasing agricultural productivity while minimizing our dependence on agrochemicals.
Molecular Modeling of µ Opioid Receptor Ligands with Various Functional Properties: PZM21, SR-17018, Morphine, and Fentanyl—Simulated Interaction Patterns Confronted with Experimental Data

Molecular modeling approaches are an indispensable part of the drug design process. They not only support the process of searching for new ligands of a given receptor, but they also play an important role in explaining particular activity pathways of a compound. In this study, a comprehensive molecular modeling protocol was developed to explain the observed activity profiles of selected µ opioid receptor agents: two G protein-biased µ opioid receptor agonists (PZM21 and SR-17018), unbiased morphine, and the β-arrestin-2-biased agonist, fentanyl. The study involved docking and molecular dynamics simulations carried out for three crystal structures of the target at a microsecond scale, followed by the statistical analysis of ligand–protein contacts. The interaction frequency between the modeled compounds and the subsequent residues of a protein during the simulation was also correlated with the output of in vitro and in vivo tests, resulting in the set of amino acids with the highest Pearson correlation coefficient values. Such indicated positions may serve as a guide for designing new G protein-biased ligands of the µ opioid receptor.
Automated Embryo Manipulation and Rotation via Robotic nDEP-Tweezers

Embryo manipulation is a fundamental task in assisted reproductive technology (ART). Nevertheless, conventional pick-place techniques often require proper alignment to avoid causing damage to the embryo and further, the tools have limited capability to orient the embryo being handled. Objective: This paper presents a novel and non-invasive technique that can easily manipulate mouse embryos on a polyvinyl chloride (PVC) Petri dish. Methods: An inverted microchip with quadrupole electrodes was attached to a micromanipulator to become a robotic dielectrophoresis (DEP) tweezers, and a motorized platform provided additional mobility to the embryos lying on a Petri dish. Vision-based algorithms were developed to evaluate relevant information of the embryos from the image, and to provide feedback signals for precise position and orientation control of the embryo. Results: A series of experiments was conducted to examine the system performance, and the embryo can be successfully manipulated to a specified location with the desired orientation for subsequent processing. Conclusion: This system offers a non-contact, low cost, and flexible method for rapid cell handling. Significance: As the DEP tweezers can grasp the embryo without the need for precise alignment, the overall time required to process a large number of embryos can be shortened.
Mid-Task Physical Exercise Keeps Your Mind Vigilant: Evidences From Behavioral Performance and EEG Functional Connectivity

Accumulating efforts have been made to discover effective solutions for fatigue recovery with the ultimate aim of reducing adverse consequences of mental fatigue in real life. The previously-reported behavioral benefits of physical exercise on mental fatigue recovery prompted us to investigate the restorative effect and reveal the underlying neural mechanisms. Specifically, we introduced an empirical method to investigate the beneficial effect of physical exercise on the reorganization of EEG functional connectivity (FC) in a two-session experiment where one session including a successive 30-min psychomotor vigilance task (PVT) (No-intervention session) compared to an insertion of a mid-task 15-min cycling exercise (Intervention session). EEG FC was obtained from 21 participants and quantitatively assessed via graph theoretical analysis and a classification framework. The findings demonstrated the effectiveness of exercise intervention on behavioral performance as shown in improved reaction time and response accuracy. Although we found significantly altered network alterations towards the end of experiment in both sessions, no significant differences between the two sessions and no interaction between session and time were found in EEG network topology. Further interrogation of functional connectivity through classification analysis showed decreased FC in distributed brain areas, which may lead to the significant reduction of network efficiency in both sessions. Moreover, we showed distinct patterns of FC alterations between the two sessions, indicating different information processing strategies adopted in the intervention session. In sum, these results provide some of the first quantitative insights into the complex neural mechanism of exercise intervention for fatigue recovery and lead a new direction for further application research in real-world situations.
Floral specialization for different pollinators and divergent use of the same pollinator among co-occurring Impatiens species (Balsaminaceae) from Southeast Asia

Floral variation among closely related species is thought to often reflect differences in pollination systems. Flowers of the large genus Impatiens are characterized by extensive variation in colour, shape and size and in anther and stigma positioning, but studies of their pollination ecology are scarce and most lack a comparative context. Consequently, the function of floral diversity in Impatiens remains enigmatic. This study documents floral variation and pollination of seven co-occurring Impatiens spp. in the Southeast Asian diversity hotspot. To assess whether floral trait variation reflects specialization for different pollination systems, we tested whether species depend on pollinators for reproduction, identified animals that visit flowers, determined whether these visitors play a role in pollination and quantified and compared key floral traits, including floral dimensions and nectar characteristics. Experimental exclusion of insects decreased fruit and seed set significantly for all species except I. muscicola, which also received almost no visits from animals. Most species received visits from several animals, including bees, birds, butterflies and hawkmoths, only a subset of which were effective pollinators. Impatiens psittacina, I. kerriae, I. racemosa and I. daraneenae were pollinated by bees, primarily Bombus haemorrhoidalis. Impatiens chiangdaoensis and I. santisukii had bimodal pollination systems which combined bee and lepidopteran pollination. Floral traits differed significantly among species with different pollination systems. Autogamous flowers were small and spurless, and did not produce nectar; bee-pollinated flowers had short spurs and large floral chambers with a wide entrance; and bimodally bee- and lepidopteran-pollinated species had long spurs and a small floral chamber with a narrow entrance. Nectar-producing species with different pollination systems did not differ in nectar volume and sugar concentration. Despite the high frequency of bee pollination in co-occurring species, individuals with a morphology suggestive of hybrid origin were rare. Variation in floral architecture, including various forms of corolla asymmetry, facilitates distinct, species-specific pollen-placement on visiting bees. Our results show that floral morphological diversity among Impatiens spp. is associated with both differences in functional pollinator groups and divergent use of the same pollinator. Non-homologous mechanisms of floral asymmetry are consistent with repeated independent evolution, suggesting that competitive interactions among species with the same pollination system have been an important driver of floral variation among Impatiens spp.