Miracle-dz/UniFAR-FTUs huggingface dataset:
Tropical forests post-logging are a persistent net carbon source to the atmosphere

Significance Logged tropical forests are counted as important carbon sinks in global carbon budgets due to the woody biomass they regain when they regrow following disturbance, but this assumption ignores the simultaneous carbon losses from the ecosystem. We found that, when quantifying all the source and sink terms of the ecosystem carbon budget, logged tropical forests are a net source of carbon to the atmosphere. This source persists at least 10 y following logging, meaning rates of carbon sequestration in recovering tropical forests are likely much lower than estimated.
Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland

Abstract Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.
Partition Functions and Thermodynamic Properties of Nitrogen and Oxygen Plasmas

The equilibrium chemical composition and thermodynamic properties of nitrogen and oxygen plasmas have been calculated for six pressures (0.01, 0.1, 0.5, 1.0, 2.0, and 5.0 atm) at 100° K increments for the temperature range 2000–35 000° K. The plasma is assumed to be a perfect gas complex consisting of seven components for nitrogen (i.e., molecules, singly ionized molecules, atoms, electrons, and the first three atomic ions) and eight components for oxygen (same as for nitrogen plus the first negative atomic ion). The internal partition functions for nitrogen molecular species were calculated by an approximate technique proposed by Mayer and Mayer using the most recent spectroscopic data available. For oxygen molecular species, the method of Stupochenko et al. was employed to determine the intermolecular potential curves, and the internal partition function was computed by direct summation over the energy states so determined. The electronic partition functions for atoms and atomic ions were computed using.
Effects of Sirolimus treatment on patients with β‐Thalassemia: Lymphocyte immunophenotype and biological activity of memory CD4 + and CD8 + T cells

Inhibitors of the mammalian target of rapamycin (mTOR) have been proposed to improve vaccine responses, especially in the elderly. Accordingly, testing mTOR inhibitors (such as Sirolimus) and other geroprotective drugs might be considered a key strategy to improve overall health resilience of aged populations. In this respect, Sirolimus (also known as rapamycin) is of great interest, in consideration of the fact that it is extensively used in routine therapy and in clinical studies for the treatment of several diseases. Recently, Sirolimus has been considered in laboratory and clinical studies aimed to find novel protocols for the therapy of hemoglobinopathies (e.g. β‐Thalassemia). The objective of the present study was to analyse the activity of CD4+ and CD8+ T cells in β‐Thalassemia patients treated with Sirolimus, taking advantages from the availability of cellular samples of the NCT03877809 clinical trial. The approach was to verify IFN‐γ releases following stimulation of peripheral blood mononuclear cells (PBMCs) to stimulatory CEF and CEFTA peptide pools, stimulatory for CD4+ and CD8+ T cells, respectively. The main results of the present study are that treatment of β‐Thalassemia patients with Sirolimus has a positive impact on the biological activity and number of memory CD4+ and CD8+ T cells releasing IFN‐γ following stimulation with antigenic stimuli present in immunological memory. These data are to our knowledge novel and in our opinion of interest, in consideration of the fact that β‐Thalassemia patients are considered prone to immune deficiency.
UBC9 deficiency enhances immunostimulatory macrophage activation and subsequent antitumor T cell response in prostate cancer

The role of tumor-associated macrophages (TAMs), along with the regulatory mechanisms underlying distinct macrophage activation states, remains poorly understood in prostate cancer (PCa). Herein, we report that PCa growth in mice with macrophage-specific Ubc9 deficiency is substantially suppressed compared with that in wild-type littermates, an effect partially ascribed to the augmented CD8+ T cell response. Biochemical and molecular analyses revealed that signal transducer and activator of transcription 4 (STAT4) is a crucial UBC9-mediated SUMOylation target, with lysine residue 350 (K350) as the major modification site. Site-directed mutation of STAT4 (K350R) enhanced its nuclear translocation and stability, thereby facilitating the proinflammatory activation of macrophages. Importantly, administration of the UBC9 inhibitor 2-D08 promoted the antitumor effect of TAMs and increased the expression of PD-1 on CD8+ T cells, supporting a synergistic antitumor efficacy once it combined with the immune checkpoint blockade therapy. Together, our results demonstrate that ablation of UBC9 could reverse the immunosuppressive phenotype of TAMs by promoting STAT4-mediated macrophage activation and macrophage–CD8+ T cell crosstalk, which provides valuable insights to halt the pathogenic process of tumorigenesis.
Type D Personality as a Marker of Poorer Quality of Life and Mood Status Disturbances in Patients with Skin Diseases: A Systematic Review

Type D personality is characterized by social inhibition and negative affectivity. Poorer outcomes and worse quality of life have been linked to type D personality in patients with a variety of non-dermatological diseases. Despite increasing evidence of the importance of type D personality in skin diseases, there are no reviews on this subject. The aim of this review is to summarize the current evidence regarding type D personality and skin diseases. A systematic search was performed using Medline and Web of Science databases from inception to 11 October 2022. Studies addressing the presence of type D personality, its associated factors, its impact on the outcomes of the disease or the quality of life of the patients were included in the systematic review. A total of 20 studies, including 3,124 participants, met the eligibility criteria and were included in the review. Acne, hidradenitis suppurativa, psoriasis, melanoma, atopic dermatitis, chronic spontaneous urticaria and pruritic disorders were the main diseases assessed. Type D personality was more frequent among patients with skin diseases than among controls. Type D personality was found to be associated with poorer quality of life and higher rates of psychological comorbidities in patients with skin diseases. In conclusion, type D personality appears to be a marker of patients with increased risk of poorer quality of life and higher rates of psychological comorbidities. Screening for type D personality in specialized dermatology units might be beneficial to identify patients who are more psychologically vulnerable to the consequences of chronic skin diseases.
Regulation of Lysozyme Activity by Human Hormones

Background: Lysozyme is a part of human and animal noncellular immunity. The regulation of its activity by hormones is poorly studied. The aim of this study was to test the in vitro activity of lysozyme in the presence of catecholamines, natriuretic hormones, and E2. Methods: Hormones were incubated with lysozyme, and the activity of lysozome was further determined using a test culture of Micrococcus luteus in the early exponential growth stage. The activity of lysozyme was assessed based on the rate of change in the OD of the test culture. Molecular docking was performed using SwissDock server (http://www.swissdock.ch/docking), and molecular structures were further analyzed and visualized in the UCSF Chimera 1.15rc software. Results: According to the results, EPN and NE increased lysozyme activity up to 180% compared to the hormone-free enzyme. Changing the pH of the medium from 6.3 to 5.5, increased the lysozyme activity in the presence of E2 up to 150-200 %. The results also showed that exposure to hormones could modify lysozyme activity, and this effect depends on the temperature and pH value. The molecular docking revealed a decrease in the activation energy of the active site of enzyme during the interaction of catecholamines with the amino acid residues, asp52 and glu35 of the active site. Conclusion: Our findings demonstrate an additional mechanism for the involvement of lysozyme in humoral regulation of nonspecific immunity with respect to human pathogenic microflora and bacterial skin commensals by direct modulation of its activity using human hormones.
INTspect: Interrupt Latencies in the Linux Kernel

Interrupt handling with predictably low latency is a must for systems to respond to external events. System designers of tiny embedded computers to large-scale distributed systems face the challenge of ever-increasing hardware and software complexity. In the absence of precise timing models, measurement-based approaches are required to achieve predictably low latency. In this paper, we present INTspect, a tool that systematically evaluates the interrupt latency, at run-time, in the Linux operating system kernel. We apply INTspect on two distinct platforms (i.e. ARM and Intel) to measure interrupt latencies, identify jitter causes, and reveal interdependencies between interrupt handlers and user-space workloads. Our tool thus provides valuable insight on interrupt timings and interferences.
Chenodeoxycholic Acid-Amikacin Combination Enhances Eradication of Staphylococcus aureus

Multidrug resistance (MDR) is spreading globally with increasing speed. The search for new antibiotics is one of the key strategies in the fight against MDR. ABSTRACT The rise of antibiotic resistance and dearth of novel antibiotics have posed a serious health crisis worldwide. In this study, we screened a combination of antibiotics and nonantibiotics providing a viable strategy to solve this issue by broadening the antimicrobial spectrum. We found that chenodeoxycholic acid (CDCA), a cholic acid derivative of the traditional Chinese medicine (TCM) Tanreqing (TRQ), synergizes with amikacin against Staphylococcus aureus in vitro, and this synergistic killing was effective against diverse methicillin-resistant S. aureus (MRSA) variants, including small-colony variants (SCVs), biofilm strains, and persisters. The CDCA-amikacin combination protects a mouse model from S. aureus infections. Mechanistically, CDCA increases the uptake of aminoglycosides in a proton motive force-dependent manner by dissipating the chemical potential and potentiates reactive oxygen species (ROS) generation by inhibiting superoxide dismutase activity. This work highlights the potential use of TCM components in treating S. aureus-associated infections and extend the use of aminoglycosides in eradicating Gram-positive pathogens. IMPORTANCE Multidrug resistance (MDR) is spreading globally with increasing speed. The search for new antibiotics is one of the key strategies in the fight against MDR. Antibiotic resistance breakers that may or may not have direct antibacterial action and can either be coadministered or conjugated with other antibiotics are being studied. To better expand the antibacterial spectrum of certain antibiotics, we identified one component from a traditional Chinese medicine, Tanreqing (TRQ), that increased the activity of aminoglycosides. We found that this so-called agent, chenodeoxycholic acid (CDCA), sensitizes Staphylococcus aureus to aminoglycoside killing and protects a mouse model from S. aureus infections. CDCA increases the uptake of aminoglycosides in a proton motive force-dependent manner by dissipating the chemical potential and potentiates ROS generation by inhibiting superoxide dismutase activity in S. aureus. Our work highlights the potential use of TCM or its effective components, such as CDCA, in treating antibiotic resistance-associated infections.
Application of optimal control theory to diabetes mellitus

The metabolic control of hospitalized diabetic subjects is critical. It may involve the infusion of the hormone insulin so that plasma glucose levels return to (and stay at) some desired value. Unfortunately, such control is often on a trial and error basis. The use of such methods of mathematical modelling and optimal control theory as grid search techniques and discrete segment approaches to derive closed-loop insulin infusion algorithms for the metabolic control of hospitalized, non-insulin producing subjects is described.
Spectroscopic observations of post-common envelope binaries

We present spectroscopy of three post-common envelope binaries, with complete orbital coverage of RE 1016-053. For the latter target we have measured the radial velocities and line strengths and mapped the line emissivity on the surface of the secondary star using both these observational constraints simultaneously. We find that the emissivity is non-uniform over the surface of the star and, accounting for this, Kr=134 km s-1, the mass ratio q=0.5 and orbital inclination is 67 °. We find a secondary star mass of 0.285 M⊙ that corresponds to a spectral type of M3. For PG 1026+002 and RE 2013+400 we were able to update the ephemerides and investigate the widths of the Balmer emission lines. The width of the Balmer emission lines in RE 1016-053 and RE 2013+400 is such that they must be intrinsically broad with σintrin∼ 30-40 km s-1. Surprisingly this is not true for PG 1026+002 where the emission is unresolved. In PG 1026+002 the emission lines may be due to starspots rather than irradiation. The Ca ii emission in RE 1016-053 is also unresolved, as is expected. However, there appears to be no intrinsic Ca ii emission, contrary to expectations based on rotation rate--line strength relationships.
Computer-aided diagnosis for optical diagnosis of diminutive colorectal polyps including sessile serrated lesions: a real-time comparison with screening endoscopists

Abstract Background We aimed to compare the accuracy of the optical diagnosis of diminutive colorectal polyps, including sessile serrated lesions (SSLs), between a computer-aided diagnosis (CADx) system and endoscopists during real-time colonoscopy. Methods We developed the POLyp Artificial Recognition (POLAR) system, which was capable of performing real-time characterization of diminutive colorectal polyps. For pretraining, the Microsoft-COCO dataset with over 300 000 nonpolyp object images was used. For training, eight hospitals prospectively collected 2637 annotated images from 1339 polyps (i. e. publicly available online POLAR database). For clinical validation, POLAR was tested during colonoscopy in patients with a positive fecal immunochemical test (FIT), and compared with the performance of 20 endoscopists from eight hospitals. Endoscopists were blinded to the POLAR output. Primary outcome was the comparison of accuracy of the optical diagnosis of diminutive colorectal polyps between POLAR and endoscopists (neoplastic [adenomas and SSLs] versus non-neoplastic [hyperplastic polyps]). Histopathology served as the reference standard. Results During clinical validation, 423 diminutive polyps detected in 194 FIT-positive individuals were included for analysis (300 adenomas, 41 SSLs, 82 hyperplastic polyps). POLAR distinguished neoplastic from non-neoplastic lesions with 79 % accuracy, 89 % sensitivity, and 38 % specificity. The endoscopists achieved 83 % accuracy, 92 % sensitivity, and 44 % specificity. The optical diagnosis accuracy between POLAR and endoscopists was not significantly different ( P = 0.10). The proportion of polyps in which POLAR was able to provide an optical diagnosis was 98 % (i. e. success rate). Conclusions We developed a CADx system that differentiated neoplastic from non-neoplastic diminutive polyps during endoscopy, with an accuracy comparable to that of screening endoscopists and near-perfect success rate.
Booster vaccination protection against SARS-CoV-2 infections in young adults during an Omicron BA.1-predominant period: A retrospective cohort study

Background While booster vaccinations clearly reduce the risk of severe Coronavirus Disease 2019 (COVID-19) and death, the impact of boosters on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections has not been fully characterized: Doing so requires understanding their impact on asymptomatic and mildly symptomatic infections that often go unreported but nevertheless play an important role in spreading SARS-CoV-2. We sought to estimate the impact of COVID-19 booster doses on SARS-CoV-2 infections in a vaccinated population of young adults during an Omicron BA.1-predominant period. Methods and findings We implemented a cohort study of young adults in a college environment (Cornell University’s Ithaca campus) from a period when Omicron BA.1 was the predominant SARS-CoV-2 variant on campus (December 5 to December 31, 2021). Participants included 15,800 university students who completed initial vaccination series with vaccines approved by the World Health Organization for emergency use, were enrolled in mandatory at-least-weekly surveillance polymerase chain reaction (PCR) testing, and had no positive SARS-CoV-2 PCR test within 90 days before the start of the study period. Robust multivariable Poisson regression with the main outcome of a positive SARS-CoV-2 PCR test was performed to compare those who completed their initial vaccination series and a booster dose to those without a booster dose. A total of 1,926 unique SARS-CoV-2 infections were identified in the study population. Controlling for sex, student group membership, date of completion of initial vaccination series, initial vaccine type, and temporal effect during the study period, our analysis estimates that receiving a booster dose further reduces the rate of having a PCR-detected SARS-CoV-2 infection relative to an initial vaccination series by 56% (95% confidence interval [42%, 67%], P < 0.001). While most individuals had recent booster administration before or during the study period (a limitation of our study), this result is robust to the assumed delay over which a booster dose becomes effective (varied from 1 day to 14 days). The mandatory active surveillance approach used in this study, under which 86% of the person-days in the study occurred, reduces the likelihood of outcome misclassification. Key limitations of our methodology are that we did not have an a priori protocol or statistical analysis plan because the analysis was initially done for institutional research purposes, and some analysis choices were made after observing the data. Conclusions We observed that boosters are effective, relative to completion of initial vaccination series, in further reducing the rate of SARS-CoV-2 infections in a college student population during a period when Omicron BA.1 was predominant; booster vaccinations for this age group may play an important role in reducing incidence of COVID-19.
Serotonin Reuptake Inhibitor Increases Pseudarthrosis Rates in Anterior Cervical Discectomy and Fusions

Study Design Retrospective cohort. Purpose To determine (1) the effects of serotonin reuptake inhibitors in pseudarthrosis rates after anterior cervical decompression and fusion (ACDF) and (2) to identify patient-reported outcome measures in patients taking serotonin reuptake inhibitors. Overview of Literature Recent literature suggests that selective serotonin reuptake inhibitors (SSRIs) may inhibit fracture healing via downregulation of osteoblast differentiation. Spinal fusion supplementation with osteoblast-rich substances enhances spinal fusion, thus SSRIs may be detrimental. Methods Patients with 1-year postoperative dynamic cervical spine radiographs following ACDF were grouped into serotonin reuptake inhibitor prescriptions (SSRI, serotonin-norepinephrine reuptake inhibitor [SNRI], or tricyclic antidepressant [TCA]) and no prescription (atypical antidepressant or no antidepressant). Pseudarthrosis was defined as ≥1 mm interspinous process motion on dynamic radiographs. Logistic regression models were controlled for confounding to analyze pseudarthrosis rates. Alpha was set at p-values of <0.05. Results Of the 523 patients who meet the inclusion criteria, 137 (26.2%) were prescribed an SSRI, SNRI, or TCA. Patients with these prescriptions were more likely to have pseudarthrosis (p=0.008) but not a revision surgery due to pseudarthrosis (p=0.219). Additionally, these patients had worse 1-year postoperative mental component summary (MCS)-12 (p=0.015) and Neck Disability Index (NDI) (p=0.006). The multivariate logistic regression analysis identified SSRI/SNRI/TCA use (odds ratio [OR], 1.82; 95% confidence interval [CI], 1.11–2.99; p=0.018) and construct length (OR, 1.91; 95% CI, 1.50–2.44; p<0.001) as pseudarthrosis predictors. A SSRI/SNRI/TCA prescription was a revision surgery predictor due to adjacent segment disease on univariate analysis (OR, 2.51; p=0.035) but not on multivariate logistic regression analysis (OR, 2.24; p=0.10). Conclusions Patients taking serotonin reuptake-inhibiting antidepressants are at increased risk of worse postoperative outcome scores, including NDI and MCS-12, likely due to their underlying depression. This may contribute to their greater likelihood of having adjacent segment surgery. Additionally, preoperative use of serotonin reuptake inhibitors in patients undergoing an ACDF is a predictor of radiographic pseudarthrosis but not pseudarthrosis revision.
Artemether treatment improves islet function and metabolic homeostasis in diabetic nonhuman primates

Highlights Artemether increased the serum concentration of c‐peptide and decreased the usage of insulin in the diabetic monkey. Artemether downregulated the serum concentration of total cholesterol and low‐density lipoprotein cholesterol in the diabetic monkey. Artemether did not induce dramatic changes of the concentration of liver or kidney damage markers in the serum.
Toward a Resolution of the Bump and Beat Cepheid Mass Discrepancies

The extant beat and bump Cepheid mass discrepancy problems are reexamined with the new opacities of Iglesias and Rogers. Compared to calculations with the Los Alamos opacities, the period ratios P 1 /P 0 and P 2 /P 0 (1) are strongly reduced for any fixed stellar parameters (L, M, T eff , X, Z) and (2) exhibit a novel, large sensitivity to luminosity and to metallicity. For the beat Cepheids the P 1 /P 0 period ratios now yield masses between 4 and 7 M ⊙ , in agreement with the other mass determinations