Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeting complement C5a to improve radiotherapy sensitivity in non-small cell lung cancer

Background Tumor local and distant relapse recurrence after radiotherapy (RT) is one of the critical factors leading to poor prognosis. The effective antitumor effects of RT are dependent upon the participation of innate and adaptive components of the immune system. C5a/C5aR1 signaling can regulate antitumor immune effect in the tumor microenvironment (TME). Thus, exploring the changes and mechanism in the TME induced by RT-mediated complement activation may provide a novel perspective for reversing radioresistance. Methods First, fractionated radiation of 8 Gy ×3 fractions were targeted at Lewis lung carcinoma (LLC) tumor-bearing female mice to measure the infiltration of CD8+ T cell and analyze the RNA sequencing (RNA-seq) in RT-recruited CD8+ T cells. Second, tumor growth was measured in LLC tumor-bearing mice treated with RT either with or without C5aR1 inhibitor to clarify the antitumor effect of RT combined with C5aR1 inhibitor. Third, we detected the expression of C5a/C5aR1 and their signaling pathways on radiated tumor tissues. Furthermore, we investigated the expression of C5a in tumor cells at different time points after different doses of RT. Results In our system, RT induced the increased infiltration of CD8+ T cells and local activation of complement C5a/C5aR. Concurrent administration of RT and blocking of C5aR improved radiosensitivity and tumor-specific immune response, which was reflected by high C5aR expression in CD8+ T cells. The AKT/NF-κB pathway was found to be an important signaling pathway in C5a/C5aR axis mediation by RT. Conclusions RT promotes the release of C5a from tumor cells and leads to up-regulation of C5aR1 expression via the AKT/NF-κB pathway. Inhibition of the combination of complement C5a and C5aR could improve RT sensitivity. Our work provides evidence that the combination of RT and C5aR blockade opens a new window of opportunity to promote anti-tumor therapeutic effects in lung cancer.
Long‐term subtropical grassland plots take a long time to change: Replacement is more important than richness differences for beta diversity

Abstract We studied β diversity of grasses in a subtropical grassland over 60 years in South Africa. We examined the effects of burning and mowing on 132 large plots. We sought to determine the effects of burning and mowing, and mowing frequency, on the replacement of species and the species richness. We conducted the study at Ukulinga, research farm of the University of KwaZulu‐Natal, Pietermaritzburg, South Africa (29°24′E, 30°24′S) from 1950–2010. Plots were burned annually, biennially, triennially, and a control (unburned). Plots were mowed in spring, late summer, spring plus late summer, and a control (unmowed). We calculated β diversity, with a focus on replacement and richness differences. We also used distance‐based redundancy analyses to examine the relative effects of replacement and richness differences on mowing and burning. We used beta regressions to test for the effect of soil depth and its interactions with mowing and burning. There was no significant change in grass beta diversity until 1995. Thereafter, there were changes in β diversity that demonstrated the primary effects of summer mowing frequency. There was no significant effect of richness differences but a strong effect of replacement post‐1995. There was a significant interaction between mowing frequency and soil depth in one of the analyses. Changes in grassland composition took a long time to manifest themselves and were unapparent prior to 1988. However, there was a change in sampling strategy prior to 1988, from point hits to nearest plants, that may also have influenced the rates of changes in replacement and richness differences. Using β‐diversity indices, we found that mowing was more important than burning that burning frequency was unimportant, and there was a significant interaction effect between mowing and soil depth in one of the analyses.
Outcomes of 8 × 8 mm osteotomy in powered external dacryocystorhinostomy

Purpose: To study the endoscopic ostium characteristics and outcome of 8 × 8 mm osteotomy in external dacryocystorhinostomy (DCR) using the microdrill system. Methods: This prospective interventional pilot study was performed on 40 eyes of 40 patients with primary acquired nasolacrimal duct obstruction (NLDO) from June 2021 to September 2021 in patients undergoing external DCR. An 8 × 8 mm osteotomy was performed using round, cutting burr attached to a microdrill system. Success was defined as patent ostium on lacrimal syringing (anatomical) and a Munk score <3 (functional) at 12 months. Postoperative endoscopic ostium evaluation was done using a modified DCR ostium (DOS) scoring system at 12 months. Results: The mean age of the study participants was 42.41 ± 11.77 years and the male-to-female ratio was 1:4. The mean duration of surgery was 34.15 ± 1.66 minutes and that for osteotomy creation was 2.5 ± 0.69 minutes. The mean intraoperative blood loss was 83.37 ± 11.89 ml. Anatomical and functional success rates were 95% and 85%, respectively. The mean modified DOS score was “excellent” in 34 patients (85%), “good” in 1 patient (2.5%), “fair” in 4 patients (10%), and “poor” in 1 patient (2.5%). Complications included nasal mucosal injury in 10% (4/40) of patients, complete cicatricial closure of ostium in 2.5% (1/40), incomplete cicatricial closure in 10% (4/40), nasal synechiae in 5% (2/40), and canalicular stenosis in 2.5% (1/40). Conclusion: An 8 × 8 mm–sized osteotomy created by powered drill and covered by lacrimal sac–nasal mucosal flap anastomosis in external DCR is an effective technique that has minimal complications and shorter surgical time.
Comparative analysis of visual outcomes following small-incision lenticule extraction with or without cyclotorsion compensation in eyes with high astigmatism: Contralateral eye study

Purpose: To compare the visual outcomes in patients undergoing small-incision lenticule extraction (SMILE) for correction of myopic astigmatism (≥−1.50 D) with or without manual cyclotorsion compensation. Methods: A prospective, double-blinded, randomized, contralateral study was conducted in the refractive services of a tertiary eye care center. Eligible patients with bilateral high myopic astigmatism (≥1.5 D) and intraoperative cyclotorsion (≥5°) undergoing SMILE between June 2018 and May 2019 were included. Cyclotorsion compensation was performed using triple centration method before femtosecond laser delivery. Uncorrected and corrected distance visual acuity (UDVA and CDVA, respectively) measurement, manifest refraction, slit-lamp biomicroscopy, and corneal tomography were performed preoperatively and at 1 and 3 months' postoperative visit. Astigmatic outcomes were analyzed using Alpins criteria. Results: A total of 30 patients (60 eyes) were included in this study. The patients underwent bilateral SMILE surgery, with manual cyclotorsion compensation in one eye (CC group, n = 30 eyes) and no cyclotorsion compensation in the other eye (NCC group, n = 30 eyes). Preoperative astigmatism and intraoperative cyclotorsion were −2.0 D and 7.03° ± 1.06° (CC) and −1.75 D and 7.24° ± 0.98° (NCC) (P = 0.472 and 0.240, respectively). No significant differences were noted in mean refractive spherical equivalent (MRSE), UDVA, CDVA, and refractive error between the two groups at 3 months' postoperative visit. Astigmatic outcomes measured using Alpins criteria demonstrated no significant difference between the two cohorts. Conclusion: The cyclotorsion compensation technique provided no additional advantage in terms of astigmatic outcomes or postoperative visual quality, in eyes with high preoperative astigmatism and intraoperative cyclotorsion.
The Albumin-Bilirubin Score as a Predictor of Liver-Related Mortality in Primary Biliary Cholangitis with Compensated Cirrhosis

Background: Although several prognostic scores have been reported to correlate with the prognosis of primary biliary cholangitis (PBC) patients, there are limited tools to predict the prognosis of PBC with compensated cirrhosis. This study aimed to evaluate the prognostic performance of the albumin-bilirubin (ALBI) score in PBC patients with compensated cirrhosis. Methods: We conducted a retrospective longitudinal study of 219 patients with compensated PBC cirrhosis to evaluate the prognostic performance of the ALBI using Cox regression model, receiver operating characteristic (ROC) curve, and Kaplan-Meier method. Results: During follow-up, a total of 19 subjects (8.7%) met the primary endpoint of liver-related death or liver transplantation (LT). Patients who died/underwent LT have higher ALBI score (−1.06 vs. −2.06, p < 0.001) at baseline than those who survived. ALBI score (hazard ratio: 15.011, 95% confidence interval [CI]: 5.045–44.665, p < 0.001) was associated with an increase in liver-related mortality or LT. ALBI score had the best discriminative capacity to predict the 5-year liver-related mortality (area under the ROC curve: 0.871, 95% CI [0.820, 0.913]) compared with other prognostic scores. The ROC curve showed that the best cut-off value of ALBI score was −1.47, with 90.0% sensitivity and 76.6% specificity. Also, the probability of transplant-free survival decreased with increasing ALBI grade (log-rank p = 0.003). The 5-year transplant-free survival rates of patients in grade 1, grade 2, and grade 3 were 100.0%, 96.4%, and 89.4%, respectively. Conclusion: ALBI score is a simple and effective predictive factor estimating the clinical outcome of patients with compensated PBC cirrhosis and provides better prognostic performance compared with other prognostic scores.
Demographic, social, and behavioral correlates of SARS-CoV-2 seropositivity in a representative, population-based study of Minnesota residents

Background Monitoring COVID-19 infection risk in the general population is a public health priority. Few studies have measured seropositivity using representative, probability samples. The present study measured seropositivity in a representative population of Minnesota residents prior to vaccines and assess the characteristics, behaviors, and beliefs of the population at the outset of the pandemic and their association with subsequent infection. Methods Participants in the Minnesota COVID-19 Antibody Study (MCAS) were recruited from residents of Minnesota who participated in the COVID-19 Household Impact Survey (CIS), a population-based survey that collected data on physical health, mental health, and economic security information between April 20 and June 8 of 2020. This was followed by collection of antibody test results between December 29, 2020 and February 26, 2021. Demographic, behavioral, and attitudinal exposures were assessed for association with the outcome of interest, SARS-CoV-2 seroprevalence, using univariate and multivariate logistic regression. Results Of the 907 potential participants from the CIS, 585 respondents then consented to participate in the antibody testing (64.4% consent rate). Of these, results from 537 test kits were included in the final analytic sample, and 51 participants (9.5%) were seropositive. The overall weighted seroprevalence was calculated to be 11.81% (95% CI, 7.30%-16.32%) at of the time of test collection. In adjusted multivariate logistic regression models, significant associations between seroprevalence and the following were observed; being from 23–64 and 65+ age groups were both associated with higher odds of COVID-19 seropositivity compared to the 18–22 age group (17.8 [1.2–260.1] and 24.7 [1.5–404.4] respectively). When compared to a less than $30k annual income reference group, all higher income groups had significantly lower odds of seropositivity. Reporting practicing a number of 10 (median reported value in sample) or more of 19 potential COVID-19 mitigation factors (e.g. handwashing and mask wearing) was associated with lower odds of seropositivity (0.4 [0.1–0.99]) Finally, the presence of at least one household member in the age range of 6 to 17 years old was associated with higher odds of seropositivity (8.3 [1.2–57.0]). Conclusions The adjusted odds ratio of SARS-CoV-2 seroprevalence was significantly positively associated with increasing age and having household member(s) in the 6–17 year age group, while increasing income levels and a mitigation score at or above the median were shown to be significantly protective factors.
COVID‐19 infection in myasthenia gravis: Clinical course and outcomes

Myasthenia gravis (MG) patients have been predicted to have high rates of coronavirus disease‐2019 (COVID‐19) complications due to frequent involvement of respiratory muscles in MG and frequent use of immunosuppressive therapies. We investigated outcomes of MG patients infected with SARS‐CoV‐2 to identify risk factors for exacerbation and severe disease.
Exploring the mechanism of BK polyomavirus-associated nephropathy through consensus gene network approach

BK polyomavirus-associated nephropathy occurs in kidney transplant recipients under immunosuppressive treatment. BK polyomavirus is implicated in cancer development and invasion, and case reports of renal cell carcinoma and urothelial carcinoma possibly associated with BK polyomavirus has been reported. Further, it has been suggested that the immune responses of KT-related diseases could play a role in the pathogenesis and progression of renal cell carcinoma. Thus, we thought to examine the relationship between BK polyomavirus-associated nephropathy and renal cell carcinoma in terms of gene expression. To identify the common and specific immune responses involved in kidney transplantation-related diseases with a specific focus on BK polyomavirus-associated nephropathy, we performed consensus weighted gene co-expression network analysis on gene profile datasets of renal biopsy samples from different institutions. After the identification of gene modules and validation of the obtained network by immunohistochemistry of the marker across kidney transplantation-related diseases, the relationship between prognosis of renal cell carcinoma and modules was assessed. We included the data from 248 patients and identified the 14 gene clusters across the datasets. We revealed that one cluster related to the translation regulating process and DNA damage response was specifically upregulated in BK polyomavirus-associated nephropathy. There was a significant association between the expression value of hub genes of the identified cluster including those related to cGAS-STING pathway and DNA damage response, and the prognosis of renal cell carcinoma. The study suggested the potential link between kidney transplantation-related diseases, especially specific transcriptomic signature of BK polyomavirus associated nephropathy and renal cell carcinoma.
Correlation between Multiparametric MR Imaging and Molecular Genetics in Pontine Pediatric High-Grade Glioma

BACKGROUND AND PURPOSE: Molecular profiling is a crucial feature in the “integrated diagnosis” of CNS tumors. We aimed to determine whether radiomics could distinguish molecular types of pontine pediatric high-grade gliomas that have similar/overlapping phenotypes on conventional anatomic MR images. MATERIALS AND METHODS: Baseline MR images from children with pontine pediatric high-grade gliomas were analyzed. Retrospective imaging studies included standard precontrast and postcontrast sequences and DTI. Imaging analyses included median, mean, mode, skewness, and kurtosis of the ADC histogram of the tumor volume based on T2 FLAIR and enhancement at baseline. Histone H3 mutations were identified through immunohistochemistry and/or Sanger or next-generation DNA sequencing. The log-rank test identified imaging factors prognostic of survival from the time of diagnosis. Wilcoxon rank-sum and Fisher exact tests compared imaging predictors among groups. RESULTS: Eighty-three patients had pretreatment MR imaging and evaluable tissue sampling. The median age was 6 years (range, 0.7–17 years); 50 tumors had a K27M mutation in H3-3A, and 11, in H3C2/3. Seven tumors had histone H3 K27 alteration, but the specific gene was unknown. Fifteen were H3 wild-type. Overall survival was significantly higher in H3C2/3- compared with H3-3A-mutant tumors (P = .003) and in wild-type tumors compared with any histone mutation (P = .001). Lower overall survival was observed in patients with enhancing tumors (P = .02) compared with those without enhancement. H3C2/3-mutant tumors showed higher mean, median, and mode ADC_total values (P < .001) and ADC_enhancement (P < .004), with lower ADC_total skewness and kurtosis (P < .003) relative to H3-3A-mutant tumors. CONCLUSIONS: ADC histogram parameters are correlated with histone H3 mutation status in pontine pediatric high-grade glioma.
Detection of gene clusters for biodegradation of alkanes and aromatic compounds in the Rhodococcus qingshengii VKM Ac-2784D genome

Bacterial species of the genus Rhodococcus are known to be efficient degraders of hydrocarbons in contaminated soil. They are also employed for bioremediation of polluted environments. These bacteria are widely met in soil, water and living organisms. Previously, we have isolated the Rhodococcus qingshengii strain VKM Ac-2784D from the rhizosphere of couch grass growing on oil-contaminated soil. This strain can effectively degrade oil and some model compounds (naphthalene, anthracene and phenanthrene). The results of phylogenetic analysis show that this strain belongs to the species R. qingshengii. To understand the catabolic properties of this strain, we have studied its gene clusters possessing such properties. The alkane destruction genes are represented by two clusters and five separate alkB genes. The destruction of aromatic compounds involves two stages, namely central and peripheral. The R. qingshengii VKM Ac-2784D genome contains four out of eight known central metabolic pathways for the destruction of aromatic compounds. The structure of the gene clusters is similar to that of the known strains R. jostii RHA1 and R. ruber Chol-4. The peripheral pathways include the genes encoding proteins for benzoic acid destruction. The presence of biphenyl 2,3-dioxygeneses as well as gene clusters of benzoate and 2-hydroxypentandienoate pathways suggests that R. qingshengii VKM Ac-2784D could degrade polychlorinated biphenyls. The biodegradation ability can be enhanced by biosurfactants, which are known to be synthesized by Rhodococcus. The R. qingshengii VKM Ac-2784D genome contains the otsA, otsB, treY, treZ genes. The bioinformatics data are supported by the previous biochemical experiments that allow a mixture of species with a wide variation of metabolic pathways to be obtained.
Comparison of myocardial perfusion between the users of two antiepileptic medications: valproate vs. carbamazepine

Objective(s): The prevalence of coronary artery disease (CAD) is high in patients with epilepsy using antiepileptic drugs (AED). Epilepsy, AED, or the type and duration of AED use , may contribute to higher CAD risk. In this study, myocardial perfusion imaging (MPI) was compared between patients using carbamazepine and valproate. Method: Out of 73 patients receiving carbamazepine or valproate monotherapy for more than 2 years, visited at a tertiary referral clinic, 32 patients participated in a 2-day stress and rest phases MPI. For each phase, 15-25 mCi 99mTc-MIBI was injected, at peak exercise or by pharmacologic stimulation for the stress phase. SPECT with cardiac gating was done by a dual-head gamma camera and processed and quantified. Scans with at least one definite reversible hypo-perfusion segment were considered abnormal. Results: Seventeen patients received carbamazepine monotherapy and 15 valproates. Age and duration of AED use were similar between the groups. Two scans were abnormal (6.3%) both in valproate group (13.3%). Duration of AED use was higher in patients with abnormal scans. In patients receiving monotherapy >2 years, the frequency of abnormal MPI was similar between groups (P-value=0.12). In patients receiving monotherapy > 5 years, prevalence of abnormal MPI was higher in the valproate group (28.6% vs. 0.0%; P-value=0.042). Considering valproate subgroup, ischemic patients had higher duration of AED use, comparing with the normal patients (17.0±4.2 vs. 6.4±4.8, P-value=0.014). Conclusion: MPIs were abnormal in patients receiving valproate after 5 years compared to patients receiving carbamazepine. Long-term valproate use may increase the risk of CAD.
Central Venous Catheter as a Novel Approach to Postoperative Thrombolysis in Patients with Acute Iliofemoral Deep Venous Thrombosis

ABSTRACT Background and aims Percutaneous mechanical thrombectomy (PMT) along with postoperative thrombolysis (POT) has been the standard treatment for acute iliofemoral deep venous thrombosis (IFDVT). However, commonly used catheter directed thrombolysis (CDT) approaches for POT carry certain disadvantages, including the need for a sheath, inferior comfortability, and catheter-related complications. Therefore, we propose a new simplified method of POT using a central venous catheter (CVC). Methods The retrospective study analyzed patients with IFDVT who underwent POT using CVC from January 2020 to August 2021. The treatment modalities included filter placement, thrombus removal, iliac vein obstruction release, postoperative CVC thrombolysis, filter retrieval, and adequate full course anticoagulation. Results A total of 39 patients were included in this retrospective study. All patients underwent PMT surgery with a procedure success rate of 100%. In the post-PMT CVC thrombolysis, the puncture sites were located in the below-knee vein, including 58.97% in the peroneal vein. The mean duration of CVC-directed thrombolysis was 3.69 ± 1.08 days, and the total urokinase dose was 2.27 ± 0.71 MIU. A total of 37 patients (94.87%) had successful thrombolysis with a length of hospital stay of 5.82 ± 2.21 days. During CVC-directed thrombolysis, only four minor bleeding complications occurred, two of which were indwelling catheter-related. During the 12-month follow-up period, the patency rate and post-thrombotic syndrome incidences were 97.44% and 2.56%, respectively. Conclusion Thrombolysis through a CVC is a feasible, safe, and effective POT method, and could be an alternative to the conventional CDT approach for patients with IFDVT.
Incidence and factors associated with chronic chikungunya arthritis following chikungunya virus infection

Chikungunya virus infection is a mosquito‐borne illness. First‐phase symptoms include fever, malaise, rash, and arthritis (self‐limiting). Some patients can have chronic‐phase symptoms, including chronic tenosynovitis, bursitis, and arthritis. This study aimed to determine the incidence and risk factors of chronic arthritis in patients with chikungunya infection.