Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Monitoring of Changes in Fecal Flora of Giant Pandas in Mice: Co-Occurrence Network Reconstruction

The giant panda is a unique vulnerable mammal in western China, and its main cause of death is digestive system diseases regardless of whether these animals are in the wild or in captivity. The relationship between the intestinal flora and the host exerts a significant impact on the nutrition and health of the giant pandas. ABSTRACT Giant pandas are uniquely vulnerable mammals in western China. It is important to develop an animal model to explore the intestinal flora of giant pandas to understand the relationship between digestive diseases and flora. Existing animal models of intestinal flora focus on human flora-associated animals, such as mice, and there is a very limited amount of knowledge regarding giant panda flora-associated animals. To fill this gap, fecal microorganisms from giant pandas were transplanted into pseudosterile and germfree mice using single and multiple gavages. Fecal samples were collected from mice at four time points after transplantation for microbial community analysis. We determined that compared to pseudosterile mice, the characteristics of intestinal flora in pandas were better reproduced in germfree mice. There was no significant difference in microbial diversity between germfree mice and giant panda gut microbes from day 3 to day 21. Germfree mice at the phylum level possessed large amounts of Firmicutes and Proteobacteria, and at the genus level, Escherichia-Shigella, Clostridium sensu stricto 1, and Streptococcus dominated the intestinal flora structure. The microbial community co-occurrence network based on indicator species indicated that germfree mice transplanted with fecal bacteria tended to form a microbial community co-occurrence network similar to that of giant pandas, while pseudosterile mice tended to restore the microbial community co-occurrence network originally present in these mice. Our data are helpful for the study of giant panda flora-associated animals and provide new insights for the in vitro study of giant panda intestinal flora. IMPORTANCE The giant panda is a unique vulnerable mammal in western China, and its main cause of death is digestive system diseases regardless of whether these animals are in the wild or in captivity. The relationship between the intestinal flora and the host exerts a significant impact on the nutrition and health of the giant pandas. However, the protected status of the giant panda has made in vivo, repeatable, and large-sample sampling studies of their intestinal flora difficult. This greatly hinders the research depth of the giant panda intestinal flora from the source. The development and utilization of specific animal models to simulate the structure and characteristics of the intestinal flora provide another means to deal with these research limitations. However, current research examining giant panda flora-associated animals is limited. This study is the first to reveal dynamic changes in the fecal flora of giant pandas in mice after transplantation.
What does it mean to flourish? Piloting the flourishing measure with adolescents and young adults with mood and anxiety disorders

Introduction: Treatment for adolescents and young adults with mood and anxiety disorders typically focuses on recovery of symptoms and improvement in functioning. Measuring positive states of health—using self-report surveys such as the Flourishing Measure—may help to promote holistic treatment. We piloted the Flourishing Measure—Adolescent Version in a clinical sample of adolescents and young adults with mood and/or anxiety disorders to determine appropriateness and acceptability in this population. Methods: We recruited adolescents (age 12–18) and young adults (age 19–25) with mood and/or anxiety disorders from an outpatient psychiatry clinic associated with an academic hospital. We used cognitive interviewing, a method used in survey development that determines whether respondents’ understanding aligns with instrument intention. Participants completed the Flourishing Measure and answered questions about their impressions of items. Results: Sixteen participants (10 adolescents and 6 young adults) participated in the study. Participants generally understood the concept of flourishing and the intention of individual items. The items were generally considered clear and participants offered minor suggestions for improvement in wording of the items. Discussion: Participants in our study understood the meaning of flourishing, as well as individual items in the measure. The Flourishing Measure may be suitable for use in clinical and research settings for adolescents and young adults, though piloting with larger, more diverse samples is needed.
Transient methionine deprivation triggers histone modification and potentiates differentiation of induced pluripotent stem cells.

Human induced pluripotent stem cells (iPSCs) require high levels of methionine (Met). Met deprivation results in a rapid decrease in intracellular S-adenosyl-methionine (SAM), poising human iPSCs for differentiation and leading to the apoptosis of undifferentiated cells. Met deprivation triggers rapid metabolic changes, including SAM, followed by reversible epigenetic modifications. Here, we show that short-term Met deprivation impairs the pluripotency network through epigenetic modification in a 3D suspension culture. The trimethylation of lysine 4 on histone H3 (H3K4me3) was drastically affected compared with other histone modifications. Short-term Met deprivation specifically affects the transcription start site (TSS) region of genes, such as those involved in the transforming growth factor β pathway and cholesterol biosynthetic process, besides key pluripotent genes such as NANOG and POU5F1. The expression levels of these genes decreased, correlating with the loss of H3K4me3 marks. Upon differentiation, Met deprivation triggers the upregulation of various lineage-specific genes, including key definitive endoderm genes, such as GATA6. Upon differentiation, loss of H3K27me3 occurs in many endodermal genes, switching from a bivalent to a monovalent (H3K4me3) state. In conclusion, Met metabolism maintains the pluripotent network with histone marks, and their loss potentiates differentiation.
Development of a Peripheral Blood Transcriptomic Gene Signature to Predict Bronchopulmonary Dysplasia.

BACKGROUND Bronchopulmonary dysplasia (BPD) is the most common lung disease of extreme prematurity, yet mechanisms that associate with or identify neonates with increased susceptibility for BPD are largely unknown. Combining artificial intelligence with gene expression data is a novel approach that may assist in better understanding mechanisms underpinning BPD. OBJECTIVE Develop an early peripheral blood transcriptomic signature that can predict preterm neonates at risk for developing BPD. METHODS Secondary analysis of whole blood microarray data from 97 very low birth weight neonates day of life 5 was performed. BPD was defined as positive pressure ventilation or oxygen requirement at 28 days of age. Participants were randomly assigned into a training (70%) and testing cohort (30%). Four gene-centric machine learning models were built, and their discriminatory abilities were compared to gestational age or birthweight. RESULTS Neonates with BPD (n=62) exhibited a lower median gestational age (26.0 weeks vs. 30.0 weeks p<0.01) and birthweight (800 grams vs 1,280 grams, p<0.01) compared to non-BPD neonates. From an initial pool (33,252 genes/patient), 4,523 genes exhibited a false discovery rate (FDR) <1%. The area under the receiver operating characteristic curve (AUC) for predicting BPD utilizing gestational age or birthweight were 87.8% and 87.2%, respectively. The machine learning models revealed AUCs ranging between 85.8% and 96.1%. Pathways integral to T cell development and differentiation were most associated with BPD. CONCLUSIONS A derived 5-gene whole blood signature can accurately predict BPD in the first week of life.
The opportunities of research parasitism: A case study using the Barcode of Life Data System (BOLD)

Abstract The Barcode of Life Data System (BOLD) is primarily used to identify biological specimens based on a mitochondrial gene sequence and has been an underpinning resource for life science researchers. Importantly, curators of BOLD archive DNA extracts where possible, and also record contaminant sequences that can be made available on request. This collegial offering of samples and data led to our work describing the serendipitous discovery of new interactions between a Torix Rickettsia bacterium and their arthropod hosts and resulted in winning the 2022 Junior Research Parasite Award. A case study of this work is presented, which discusses the opportunities provided by secondary data and how careful maintenance of such large-scale repositories plays a vital role in scientific research that goes beyond obvious lines of enquiry.
High-Quality Draft Genome Sequence and Characterization of ProBC Plus Weizmannia (Bacillus) coagulans LMG S-31876

The whole-genome sequence of a Weizmannia (Bacillus) coagulans (ProBC Plus) strain isolated from fermented rice is reported here. The complete genome analysis of the strain will be helpful in the future to combat multitudinous problems and will be helpful in providing insights regarding potential probiotic properties. ABSTRACT The whole-genome sequence of a Weizmannia (Bacillus) coagulans (ProBC Plus) strain isolated from fermented rice is reported here. The complete genome analysis of the strain will be helpful in the future to combat multitudinous problems and will be helpful in providing insights regarding potential probiotic properties.
Convection driven magnetohydrodynamic dynamos in rotating spherical shells

Abstract Finite amplitude solutions for magnetohydrodynamic dynamos driven by convection in rotating spherical fluid shells with a radius ratio of ηequals; 0.4 are obtained numerically by the Galerkin method. Solutions which are twice periodic in the azimuth (case m equals; 2) are emphasized, but a few cases with higher azimuthal wavenumber have also been considered. An electrically insulating space outside the fluid shell has been assumed. A comparison of the dynamo solutions of both, dipolar and quadrupolar, symmetries with the corresponding non-magnetic solutions shows a strong increase of the amplitude of convection owing to the release of the rotational constraint by the Lorentz force. In some cases at low Taylor number the amplitude of convection is decreased, however, owing to the competition of the magnetic degree of freedom for the same energy source. The strength of differential rotation is usually reduced by the Lorentz force, especially in the case of quadrupolar dynamos which differ in this r.
A sedimentary record of the evolution of the global marine phosphorus cycle

Phosphorus (P) is typically considered to be the ultimate limiting nutrient for Earth's biosphere on geologic timescales. As P is monoisotopic, its sedimentary enrichment can provide some insights into how the marine P cycle has changed through time. A previous compilation of shale P enrichments argued for a significant change in P cycling during the Ediacaran Period (635–541 Ma). Here, using an updated P compilation—with more than twice the number of samples—we bolster the case that there was a significant transition in P cycling moving from the Precambrian into the Phanerozoic. However, our analysis suggests this state change may have occurred earlier than previously suggested. Specifically in the updated database, there is evidence for a transition ~35 million years before the onset of the Sturtian Snowball Earth glaciation in the Visingsö Group, potentially divorcing the climatic upheavals of the Neoproterozoic from changes in the Earth's P cycle. We attribute the transition in Earth's sedimentary P record to the onset of a more modern‐like Earth system state characterized by less reducing marine conditions, higher marine P concentrations, and a greater predominance of eukaryotic organisms encompassing both primary producers and consumers. This view is consistent with organic biomarker evidence for a significant eukaryotic contribution to the preserved sedimentary organic matter in this succession and other contemporaneous Tonian marine sedimentary rocks. However, we stress that, even with an expanded dataset, we are likely far from pinpointing exactly when this transition occurred or whether Earth's history is characterized by a single or multiple transitions in the P cycle.
Adsorption of alkanes on Au(111): Possible origin of STM contrast at the liquid/solid interface

The molecular structure and origin of contrast of monolayers formed at the interface between Au(111) surfaces and solutions containing n-alkanes (C n H 2 n + 2 , n = 10-50) has been studied by in situ scanning tunneling microscopy (STM) at room temperature. At the liquid/solid interface the monolayers consist of a close-packed arrangement of lamellae separated by troughs. It has been found that at the same experimental conditions the STM contrast of boundaries between lamellae can be different for different regions within the same close-packed monolayer island. Also this contrast strongly depends on the tunneling regime (bias voltage. tunneling current) and qualitatively differs for monolayers formed by alkanes with even and odd numbers. The dependence of STM contrast is being explained by the formation of misfit dislocations within the monolayer in association with a interference of different parallel current paths that connect the STM tip with the substrate through ends of the two nearest alkane molecules.
Interfering with lipid metabolism through targeting CES1 sensitizes hepatocellular carcinoma for chemotherapy

Hepatocellular carcinoma (HCC) is the most common lethal form of liver cancer. Apart from surgical removal and transplantation, other treatments have not yet been well established for patients with HCC. In this study, we found that carboxylesterase 1 (CES1) is expressed at various levels in HCC. We further revealed that blockage of CES1 by pharmacological and genetical approaches leads to altered lipid profiles that are directly linked to impaired mitochondrial function. Mechanistically, lipidomic analyses indicated that lipid signaling molecules, including polyunsaturated fatty acids (PUFAs), which activate PPARα/γ, were dramatically reduced upon CES1 inhibition. As a result, the expression of SCD, a PPARα/γ target gene involved in tumor progression and chemoresistance, was significantly downregulated. Clinical analysis demonstrated a strong correlation between the protein levels of CES1 and SCD in HCC. Interference with lipid signaling by targeting the CES1-PPARα/γ-SCD axis sensitized HCC cells to cisplatin treatment. As a result, the growth of HCC xenograft tumors in NU/J mice was potently slowed by coadministration of cisplatin and CES1 inhibition. Our results, thus, suggest that CES1 is a promising therapeutic target for HCC treatment.
The effectiveness of a theory-based intervention program for pregnant women with anemia: A randomized control trial

Anemia in pregnancy is a public health concern. It has been diagnosed in 27% of pregnant women in Malaysia and up to 40% of pregnant women globally. This study aimed to develop and evaluate the effectiveness of an intervention initiative based on the health belief model. The MyPinkMom program was disseminated through a mobile messaging application to pregnant women to educate them on the prevention of anemia in pregnancy. We conducted a two-arm cluster-assignment, single-blinded, randomized control trial at two government antenatal clinics in Selangor. One clinic was randomly chosen as the intervention group, and the other was chosen as the control group. Sixty pregnant women with anemia from the intervention group received the MyPinkMom intervention program in the form of six infographic video clips, and 60 pregnant women with anemia from the control group received routine counseling on anemia in pregnancy. Pregnant women who had anemia secondary to hemoglobinopathy or other chronic diseases were excluded from this study. MANOVA showed significant increases in hemoglobin, knowledge, attitude, subjective norms, and perceived behavioral control scores for adherence to iron supplements, dietary iron, and dietary vitamin C intake (p < 0.001) in the intervention group at week 6. A significant reduction also occurred in dietary tannin intake (p < 0.001) in the intervention group at week 6. The intervention group at week 6 showed a large effect on hemoglobin level increments (partial eta squared, Ƞp2 0.268), dietary iron intake (Ƞp2 0.213), knowledge of anemia in pregnancy (Ƞp2 0.622), subjective norm scores for adherence to iron supplements (Ƞp2 0.167), and reduction in dietary tannin intake (Ƞp2 0.353). Similarly, repeated measures ANOVA showed that changes in hemoglobin levels were significantly different over time (i.e., at baseline, week 6, and week 12) between the intervention and control groups (p < 0.001). Hemoglobin increased rapidly over time among participants in the intervention group but gradually in the control group. To conclude, the newly developed MyPinkMom program that was delivered through a messaging application showed effectiveness in preventing anemia during pregnancy.
Perceptions and Attitudes Toward an Interactive Voice Response Tool (Call for Life Uganda) Providing Adherence Support and Health Information to HIV-Positive Ugandans: Qualitative Study

Background The continuing decline in AIDS-related deaths in the African region is largely driven by the steady scale-up of antiretroviral therapy. However, there are challenges to retaining people living with HIV on treatment. Call for Life Uganda (CFLU) is an interactive voice response tool using simple analogue phones. CFLU supports patients with daily pill reminders, preappointment reminders, symptom reporting and management, and weekly health promotion tips. Mobile health tools are being increasingly used in resource-limited settings but are often adopted without rigorous evaluation. Objective This qualitative study conducted at 12 months after enrollment assessed patients’ experiences, perceptions, and attitudes regarding CLFU. Methods We conducted a qualitative substudy within an open-label randomized controlled trial titled “Improving outcomes in HIV patients using mobile phone based interactive software support. ” Data were collected through 6 focus group discussions with participants sampled based on proportion of calls responded to—<25%, between 25% and 50%, and >50%—conducted at the Infectious Diseases Institute, Mulago, and the Kasangati Health Centre IV. NVivo (version 11; QSR International) was used in the management of the data and in the coding of the emerging themes. The data were then analyzed using content thematic analysis. Results There was consensus across all groups that they had more positive than negative experiences with the CFLU system. Participants who responded to >50% of the calls reported more frequent use of the specific elements of the CFLU tool and, consequently, experienced more benefits from the system than those who responded to calls less frequently. Irrespective of calls responded to, participants identified pill reminders as the most important aspect in improved quality of life, followed by health promotion tips. The most common challenge faced was difficulty with the secret personal identification number. Conclusions Findings showed participants’ appreciation, high willingness, and interest in the intervention, CFLU, that demonstrated great perceived potential to improve their access to health care; adherence to treatment; health awareness; and, consequently, quality of life. Trial Registration ClinicalTrials.gov NCT02953080; https://clinicaltrials.gov/ct2/show/NCT02953080
Antioxidant Effects of Rhodoxanthin from Potamogeton crispus L. on H2O2‐Induced RAW264.7 Macrophages Cells

Potamogeton crispus L. (P. crispus) is the type of a widely distributed perennial herbs, which is rich in rhodoxanthin. In this research work, five antioxidant indexes in vitro were selected to study the antioxidant activity of rhodoxanthin from P. crispus (RPC). A model of hydrogen peroxide (H2O2) ‐induced oxidative damage in RAW264.7 cells was established to analyze the antioxidant effect and potential mechanism of RPC. The levels of ROS, MDA and the activities of oxidation related enzymes by H2O2 were determined by enzyme linked immunosorbent assay (ELISA). The mRNA expression of Nrf‐2, HO‐1, SOD1 and SOD2 was measured by qRT‐PCR assay. According to the results, RPC had free radical scavenging ability for 2, 2‐diphenyl‐1‐trinitrohydrazine (DPPH), 2,2’‐azinobis(3‐ethylbenzo‐thiazoline‐6‐sulfonic acid radical ion) (ABTS), hydroxyl radical and superoxide anion. RPC significantly decreased the level of MDA and ROS and LDH activity, while increased GSH level and activities of SOD, GSH−Px and CAT. It was showed that RPC could increase the mRNA expression of Nrf‐2, HO‐1, SOD1 and SOD2 in RAW264.7 cells in a dose‐dependently manner. In summary, RPC treatment could effectively attenuate the H2O2‐induced cell damage rate, and the mechanism is related to the reduction of H2O2 induced oxidative stress and the activation of Nrf‐2 pathway.
“Cinderella was attacked by the big bad wolf, but the police saved her”: intrusions and confabulations on story recall in Korsakoff’s syndrome and alcohol-related cognitive impairments

ABSTRACT Background The relation between confabulations and intrusions in patients with Korsakoff’s syndrome (KS) and patients with alcohol-related cognitive impairments (ARCI) remains under debate. This study examines (1) differences in the production of confabulations and intrusions between patients with KS and ARCI, (2) whether an altered fairy tale induces more intrusions, and (3) whether different types of intrusions were significantly related to confabulations. Methods Twenty-three patients with KS and twenty-two patients with ARCI recalled three different types of stories: a novel story, a fairy tale, and a modified fairy tale. Different types of intrusions were correlated with confabulation measures. Results Patients with KS produced more intrusions in the modified fairy tale condition than patients with ARCI, but these were unrelated to confabulations. Only unrelated intrusions were related to provoked confabulations. Conclusions The results of this study indicate that researchers and clinicians must be aware that in general, intrusions on memory tests should not be interpreted as confabulations. Especially spontaneous confabulations appear to be something completely different from intrusions on any type of story recall. When measuring confabulations it is crucial to use validated instruments.