jimnoneill/paper-to-field-training huggingface dataset:
Emerging Challenges In HIV And Aging: Role Of A Glycan-binding Immunomodulatory Lectin

Field: Medicine (Health Sciences)

Despite antiretroviral therapy, people living with HIV have an increased risk for and earlier onset of age-related comorbidities including cardiovascular, kidney, liver, bone, and neurologic disease. About half of the population living with HIV in the U.S. is older than fifty years of age and this trend to an older demographic is expected to continue. Although multifactorial, evidence suggests chronic inflammation and immune activation, thought to stem from occult viral replication and the senescence, exhaustion, and premature aging of the immune system, are key drivers of early development of these comorbidities. Identifying reliable biomarkers to predict disease progression, determining key pathways in comorbidity development, and developing novel interventions to mitigate these complications are warranted as people with HIV age. One key regulator of immunological functions is interactions between cell-surface glycans and glycan-binding proteins, particularly galectins, a family of soluble β-galactoside-binding lectins. In particular, galectin-9 (Gal-9), a pleiotropic mediator of innate and adaptive immune responses, is elevated in the plasma during early HIV infection and remains high after ART suppression compared to people without HIV. Gal-9 is associated with HIV disease progression, the severity of age-related comorbidities, and can induce HIV transcription and reactivate latent virus. Investigating the significance of Gal-9 in the older HIV+ population could lead to the development of novel therapies to improve immune functionality, and reduce inflammation-associated co-morbidities, during ART-suppressed HIV infection. Our in vitro and ex vivo data show that Gal-9 mediates both HIV transcription and T cell activation through Lck-dependent mechanisms, indicative of a TCR activation pathway. We determined the potential of Gal-9 to serve as a biomarker of morbidity and mortality risk in HIV. Our data illustrate a link between cerebrospinal levels of Gal-9 with poor cognitive performance central nervous system immune activation, as well as plasma Gal-9 levels and mortality risk and the burden of comorbid disease among older people living with HIV. Finally, given that the functionality of endogenous Gal-9 during the course of HIV infection is not fully known and targeting Gal-9-induced pathways in vivo are limited, we generated anti-Gal-9 monoclonal antibodies with high specificity and limited off-target effects that can be used to target Gal-9 pathways in vivo in various animal models of HIV infection. Our work provides a framework in guiding the understanding of glycan-galectin interactions in the pathogenic mechanisms of age-related disorders in older HIV-infected individuals on suppressive ART and the relationship between aging, HIV, and inflammation.
LHD Langmuir #53589.1

Field: Physics and Astronomy (Physical Sciences)

Langmuir probes on divertor plates to investigate divertor plasma parameters and fluctuation characteristics of ion flux near the divertor plates. Total 400 Langmuir probes embedded on 20 divertor plates on each of which 20 electrodes are aligned every 6 mm. Sweeping and sampling frequency is normally 250 kHz.
Water-Rock Interaction: Proceedings. Volume 1, Low temperature environments

Field: Earth and Planetary Sciences (Physical Sciences)

The 7th International Symposium on Water-Rock Interaction (WRI-7), sponsored by the International Association of Geochemistry and Cosmochemistry (IAGC), was held in Park City, Utah, USA, 13--18 July 1992. The published papers describe research on water-rock interactions in a wide spectrum of geochemical environments ranging from permafrost zones to hydrothermal and magmatic systems. Many papers describe the recent advances in theories and methodologies, including instrumental techniques, isotopes, and geochemical codes. Although the environments and systems covered represent a continuum spatially and thermally, the papers were split into two volumes based on classical geochemical divisions: low and high temperature geochemistry. Volume I: Low Temperature Environments includes papers dealing with water-rock interactions that take place on the Earth`s surface and in groundwater environments at temperatures generally less than about 100{degree}C. The large number of papers on the `hot`` topic of Mineral-Fluid Interface Geochemistry in general and Kinetics of Geochemical Reactions in particular are included in this volume regardless of temperature. Volume I also contains all the papers in the field of organic geochemistry, including those discussing and organic-inorganic interactions. Selected papers were indexed separately for inclusion in the Energy Science and Technology Database.
Co-prevalence of Human Parvovirus 4 and Primate Erythroparvovirus 1 (B19) in Sickle Cell Disease and Healthy Populations

Field: Medicine (Health Sciences)

Background: Human Parvovirus 4 (P4) is a non-enveloped, single-stranded DNA virus belonging to the Tetraparvovirus genus within the Parvoviridae family. Epidemiologically, P4 exhibits similarities with its well-established family member, primate erythroparvovirus 1 (known as B19), a blood-borne virus implicated in causing aplastic crises in individuals with sickle cell disease (SCD). Despite the acknowledged association with B19, there is a dearth of prior investigations into the prevalence and clinical significance of P4 in SCD patients. Objectives: This study aims to ascertain the prevalence and outcomes of P4, along with exploring the co-prevalence of P4 with B19 in individuals with SCD. Methods: A total of 165 participants were enrolled, comprising 120 individuals with SCD and 45 healthy controls. The prevalence of P4 and B19 DNA was determined utilizing a nested-PCR method. Sequencing was performed on positive samples to validate the diagnosis, and a phylogenetic tree was constructed based on the sequencing results. Correlations in the data were analyzed using statistical methods. Results: The prevalence of P4 and B19, as well as the co-prevalence of these viruses, was significantly higher in SCD patients than in healthy individuals. Moreover, the prevalence of P4 did not exhibit a significant correlation with variables such as age, sex, aplastic crises, or specific complications associated with SCD. Conclusions: Sickle cell disease patients represent a susceptible population for P4 infection, as indicated by the heightened prevalence observed in this study.
<i>In silico</i> evaluation of new affine interactions of methylcoumarin with cytochromes P450

Field: Chemistry (Physical Sciences)

4-methyl-7-methoxycoumarin (CumOMe) has been synthesized and in silico calculations demonstrated localization of methoxy group within 0.4 nm from Fe ion of hem groups for some structures of human CYP19 & CYP46 as well as CYP152 S. paucimobilis , CYP158 St. coelicolor , HMUO C. diphtheriae , XPLA R. rhodochrous , CYP199A4 Rh. palustris , CYP101A1 Ps. putida and CYP51 M. tuberculosis .
Toxicological evaluation of the herbicide Palace® inDrosophila melanogaster

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Drosophila melanogaster is a suitable model for toxicological studies of environmental pollutants including pesticides, which are known to produce adverse effects on the ecosystem. The aim of the present study was to investigate the adverse influence of the pesticide Palace®, a mixture of 2,4-dichlorophenoxyacetic acid (2,4-D) and picloram, using D. melanogaster as a model organism. D. melanogaster larvae were exposed to 0.011%, 0.022%, 0.112%, 0.224%, and 1.12% of Palace® and development examined. Adult flies were treated with 0.224%, 1.12%, 2.24%, 11.2%, and 22.4% of Palace® and the following analyzed survival, locomotor behavior, acetylcholinesterase (AchE) activity, reactive oxygen species (ROS) production, total and non-protein thiol levels, and mitochondrial function. Data demonstrated that exposure of flies during larval stage to Palace® significantly affected development of larvae to the adult stage. In adults, treatment with Palace® resulted in dose-dependent progressive adverse effects on survival and behavior with males more sensitive than females. In both males and females, ROS production and AchE activity were not markedly affected by Palace®. However, total thiol levels increased in female heads treated with highest dilution of Palace®, while decreased levels of non-protein thiols were detected in heads of male flies following Palace® exposure. In females and males flies exposed to Palace® reduced mitochondrial oxygen consumption related to oxidative phosphorylation (OXPHOS) state, mitochondrial capacity of excess (E-P) and respiratory control ratio (RCR) was noted, indicating that the pesticide mixture altered mitochondrial complexes functionality with consequences on bioenergetics. In summary, Palace® exposure produced adverse effects on D. melanogaster affecting survival, development, behavior and mitochondrial function, which may exert ecotoxicological consequences which poses risks to different organisms in the ecosystem.
A comparison between two image reconstructions on the measures of prostate-specific membrane antigen–positive tumor volume in 18F-PSMA-JK-7-PET/computed tomography

Field: Medicine (Health Sciences)

Objectives Tumor volume in prostate-specific membrane antigen (PSMA-TV)–PET/computed tomography (CT) has shown an emerging impact for prognosis and response evaluation in patients with prostate cancer. We evaluated the robustness of different PSMA-TV delineation methods. Materials and methods A total of 40 18 F-JK-7-PSMA-PET/CT performed on the same scanner were analyzed. PSMA-TV measurements were performed using a standardized uptake value of 4.0 as a fixed threshold (T1), 41% of the single hottest voxel as an adaptive threshold (T2), and a liver-specific threshold (T3) for delineation in two reconstruction methods [four iterations and 12 subsets (R1) and three iterations and 21 subsets while applying a point spread function and a time-of-flight algorithm (R2)]. Differences between the segmentation thresholds in R1 and R2 were gathered and tested for statistical significance. Results PSMA-TV differed significantly between R1Tx and R2Tx for individual segmentation thresholds, with PSMA-TV in R2 being significantly smaller than in R1 using the same segmentation method. Comparing the differences in PSMA-TV between R1 and R2 reconstruction between the three separate segmentation thresholds showed significantly larger absolute volume differences for T2 compared with T3 and significantly larger relative volume differences for T2 compared with T1 and T3. Conclusion Reconstruction settings greatly influence the measurement of PSMA-TV, regardless of the segmentation threshold chosen; however, our results indicate that the fixed thresholds (T1 and T3) are less susceptible to reconstruction-induced volumetry effects than a relative threshold.
The Extended Optical Disk of M101

Field: Physics and Astronomy (Physical Sciences)

We have used deep, wide-field optical imaging to study the faint outskirts of the luminous spiral galaxy M101 (NGC 5457), as well as its surrounding environment. Over six square degrees, our imaging has a limiting surface brightness of mu_B ~ 29.5 mag/arcsec^2, and has revealed the stellar structure of M101's disk out to nearly 25 arcminutes (50 kpc), three times our measured R25 isophotal size of the optical disk. At these radii, the well-known asymmetry of the inner disk slews 180 degrees, resulting in an asymmetric plume of light at large radius which follows the very extended HI disk to the northeast of M101. This plume has very blue colors (B-V ~ 0.2), suggesting it is the somewhat more evolved (few hundred Myr to ~ 1 Gyr) counterpart of the young far ultraviolet emitting population traced by GALEX imaging. We also detect another, redder spur of extended light to the east of the disk, and both structures are reminiscent of features produced during fly-by galaxy interactions. However, we see no evidence of very extended tidal tails around M101 or any of its companions which might be expected from a recent encounter with a massive companion. We consider the properties of M101's outer disk in light of possible past interactions with the nearby companion galaxies NGC 5477 and NGC 5474. The detection of optical starlight at such large radii gives us the ability to study star formation histories and stellar populations in outer disks over a longer timescales than those traced by the UV or Halpha emitting populations. Our data suggest ongoing buildup of the M101's outer disk due to encounters in the group environment triggering extended star formation and tidal heating of existing disk populations.
Zeolite addition in microalgae Chlorella sp. for treatment of bacteria contaminated vinasse

Field: Environmental Science (Physical Sciences)

Abstract Chlorella pyrenoidosa has been grown in artificial vinasse digestate. The method being used is intended to gather data on kinetic parameters that govern the performance of C. pyrenoidosa cultivated in a medium containing bacterial components. This condition was developed by introducing 1000 μL of Bacillus cereus to the medium (5 ppm of vinasse: 15 ppm of NaHCO 3 = 3:2), which was subsequently mixed with C. pyrenoidosa culture at a 1:1 v/v ratio. The cultivation was carried out in batch mode for 15 days. The photosynthesis process of C. pyrenoidosa was conducted in 14 h and supported by 2 mL L −1 Guillard, which was given every 5 days. The study additionally investigated how different amounts of Zeolite (30, 60, and 90 gL −1 ) affected the kinetic parameters of microalgae grown in artificial vinasse digestate. This study demonstrated that the utilization of artificial vinasse digestate as a growing medium for C. pyrenoidosa resulted in growth limitation symptoms of microalgae, as a consequence of unfavorable interaction between C. pyrenoidosa and bacteria that already existed in the medium. This is indicated by low values of growth kinetics parameters, including specific growth rate (0.0259 d −1 ) and biomass productivity (0.51774 gL −1 d −1 ) as compared to the reactor without bacteria in the medium. Therefore, adding a certain quantity of Zeolite to the reactor is a promising alternative for mitigating the negative effects of bacterial presence. With the addition of 90 g L −1 of Zeolite to the reactor, the specific growth rate of C. pyrenoidosa increases by 71%, indicating an appropriate growth. In addition, the total yield of PHB formation and the Melanoidin degradation efficacy of this reactor improved by 70% and 98%, respectively.
IDDF2024-ABS-0100 Integrative analysis of scRNA-Seq and bulk RNA-Seq data revealed T cell marker genes-based molecular subgroups and prognosis in liver cancer

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Background

Liver cancer (LC) is a heterogeneous tumor with unfavorable prognosis. T cells play key roles in tumor surveillance and cancer immunotherapy. The aim of this study is to explore the role of T cell marker genes (TCMGs) in LC based on scRNA-Seq and bulk RNA-Seq data.

Methods

The scRNA-Seq and bulk RNA-Seq data were from TCGA and GEO databases. The scRNA-Seq data were normalized and annotated with R packages 'Seurat' and 'harmony'. The R packages 'limma' and 'ConsensusClusterPlus' were used to select the differentially expressed genes (DEGs) and identify molecular subgroups. The R package 'immunedeconv' and TIDE algorithm were used to predict the tumor microenvironment and immunotherapy response. The R packages 'pRRophetic' and 'maftools' were used to predict the IC50 level and visualize the somatic mutation. qRT-PCR and Western blot were applied to detect key gene expression.

Results

A total of 8839 cells were classified into 8 kinds of cells, among which T cells were the most numerous (IDDF2024-ABS-0100 Figure 1. Identification of single-cell clusters and 3 subgroups based on TCMGs (A,B)). The DEGs in T cells were screened to intersect with the genes with differential expression and prognostic ability in LC (IDDF2024-ABS-0100 Figure 1. Identification of single-cell clusters and 3 subgroups based on TCMGs (C)). 12 TCMGs were selected and 3 subgroups were identified in LC cohort (IDDF2024-ABS-0100 Figure 1. Identification of single-cell clusters and 3 subgroups based on TCMGs (D,E)). IDDF2024-ABS-0100 Figure 1. Identification of single-cell clusters and 3 subgroups based on TCMGs (F) showed that the overall survival of subgroup G1 was poorest. Distinct immune cell infiltration, immunotherapy response, and immune checkpoint expression were observed among 3 subgroups (IDDF2024-ABS-0100 Figure 2. Immune cell infiltration and somatic mutation analysis among 3 subgroups (A-C)). G1 exhibited the best therapeutic efficacy of Sorafenib (IDDF2024-ABS-0100 Figure 2. Immune cell infiltration and somatic mutation analysis among 3 subgroups (D)). The somatic mutation was visualized in IDDF2024-ABS-0100 Figure 2. Immune cell infiltration and somatic mutation analysis among 3 subgroups (E). Univariate and multiple Cox analysis highlighted ATP6V0B as a key gene among TCMGs (IDDF2024-ABS-0100 Figure 3. Identification and validation of key TCMGs (A,B)). The higher expression of ATP6V0B in LC was further validated by qRT-PCR and Western blot (IDDF2024-ABS-0100 Figure 3. Identification and validation of key TCMGs (C-E)).

Conclusions

Our research explored the role of TCMGs in the molecular classification and prognosis of LC by scRNA-Seq and bulk RNA-Seq analysis and highlighted ATP6V0B as a valuable biomarker in LC.
Influence of vegetation index to the rainfall intensity in Pasuruan Area, East Java Province, Indonesia

Field: Environmental Science (Physical Sciences)

An increase in population increases the rate of urbanization. This results in changes in land cover from vegetation to artificial material. As a result, much of the land surface reflects the sun's energy. Consequently, this increases the surface temperature of the land. An increase in land surface temperature (LST) will increase the intensity of rainfall. Therefore, the present study aimed to investigate the relationship between the increase in LST and rainfall intensity. Changes in land cover can be detected by normalized difference vegetation index (NDVI) and normalized difference built-up index (NDBI) parameters. Landsat satellite imagery was used to detect NDVI, NDBI, and LST. Image processing was done for imageries scanned in 1995, 2015, 2017, and 2021. Two areas in the East Java Province of Indonesia, namely Malang City and Pasuruan Area, were selected. The daily rainfall intensity data were collected from related rainfall stations in the same year. The Mononobe method was applied to analyze hourly and minute rainfall intensity. IDF curves were drawn from the analyzed results. The relationship between both parameters was analyzed by comparing the LST and hourly rainfall intensity from the IDF curve. The studied results showed that the maximum temperature increase from 1995 to 2021 for the Malang City and Pasuruan Area was 2.60 C and 7.60 C, respectively. For rain, the maximum rainfall intensity increased by 58 mm for Malang City and 18 mm for the Pasuruan Area. LST and rainfall intensity change trends of the two areas had a positive coefficient of regression. The findings can be used to predict the rainfall intensity and floods based on the LST data.
Data from IFNγ Markedly Cooperates with Intratumoral Dendritic Cell Vaccine in Dog Tumor Models

Field: Medicine (Health Sciences)

<div>Abstract<p>Dendritic cell (DC)–based immunotherapy can trigger effective immune responses against cancer in human patients. Although accompanied by little toxicity, further improvements are needed to optimize immune responses for fully satisfactory clinical outcomes. IFNγ, a potent inducer of T helper type 1 immune responses, is considered an important tool to realize improvements. In this study, we sought to clarify the effect of IFNγ on the maturation and activation of DCs and the clinical outcome of DC-based cancer therapy in dogs. <i>In vitro</i> experiments indicated that IFNγ significantly enhanced the expression of immune stimulatory molecules and interleukin-12 by DCs derived from canine monocytes. IFNγ also significantly strengthened DC-mediated growth suppression against tumor cell lines. DC inoculation with concomitant delivery of IFNγ into primary or recurrent tumors elicited significant clinical responses, including four complete responses and two partial responses against malignant tumors, also eliciting partial responses against benign but actively growing tumors. Together, our results indicate that combining IFNγ and DCs could induce strong immune responses against tumors, significantly improving clinical outcomes. The present study of dogs bearing common types of cancer in humans offers a unique line of support for the development of human cancer therapies. Cancer Res; 70(18); 7093–101. ©2010 AACR.</p></div>
Maize Mo17 SNPs

Field: Agricultural and Biological Sciences (Life Sciences)

Genome resequencing of Mo17 was done as part of the bioMAP project (REF). 477 million 100bp paired-end reads were generated for Mo17 giving an average of 95x coverage. Reads were first trimmed by Trimmomatic (Bolger et al. 2014) and mapped to the maize B73 genome AGPv4 (Jiao et al. 2017) using BWA-MEM (Li and Durbin 2010). PCR duplicates were marked and removed using GATK (McKenna et al. 2010). Variants were called by GATK haplotypecaller and filtered using different filters for SNPs: (QD > 2, FS < 60, MQ > 40, MQRankSum > -12.5, ReadPosRankSum > -8, SOR < 4) and for InDels: (QD > 2, FS < 200, ReadPosRankSum > -20, SOR < 10). Moreover, variants located in regions with unusually high coverage (DP > Mean + 2*SD) and heterozygous calls (GT == '0/1') were also removed. The final variant file containing 8.04 million variants with 164 thousand CDS variants was deposited in DRUM.
Rectangular Strain-Rosette Method For Measuring The Mode I Stress-Intensity Factor Ki And T-Stress

Field: Engineering (Physical Sciences)

In this paper, a new experimental technique for measuring Stress Intensity Factor (SIF) and T-stress under mode I loading is developed. The expressions of the normal and tangential strains close to the crack tip are given using the first five terms of the generalized Westergaard formulation. In order to accurately determine the SIF and T-stress, the method exploits the optimal positioning of a rectangular strain gage rosette near a crack tip in mode I. Thus, errors due to the higher order terms of the asymptotic expansion are eliminated. Finally, a comparison of the analytical results with a finite element calculations, for different specimen dimensions, is carried out.
Impact of high hydrostatic pressure and ultrasounds technologies in the autolytic process of Saccharomyces cerevisiae in a model wine system

Field: Agricultural and Biological Sciences (Life Sciences)

Autolysis plays a crucial role as a technological tool in the ageing process of specific wines. This includes white, red and sparkling wines. During ageing on the lees, yeasts release different compounds that positively modify the composition of the wine. However, traditional autolytic methods can be time-consuming. This work evaluates the use of different ultrasound (US) and high hydrostatic pressure (HHP) treatments to expedite the autolytic process in Saccharomyces cerevisiae in a model wine system. The results suggest that treating yeast cells with US resulted in a faster release of nucleic acids, proteins, and total polysaccharides compared to HHP treatment. The environmental scanning electron microscopy (ESEM) of the treated lees demonstrated that the impact on the yeast cell surface was more pronounced after exposure to US compared to treatments involving HHP. In conclusion, under these conditions the US treatment effectively triggered autolysis in the wine yeast strain, facilitating the release of macromolecules in a model wine.