Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbamylated Lipoproteins and Progression of Diabetic Kidney Disease.

BACKGROUND AND OBJECTIVES Protein carbamylation is a consequence of uremia and carbamylated lipoproteins contribute to atherogenesis in CKD. Proteins can also be carbamylated by a urea-independent mechanism, and whether carbamylated lipoproteins contribute to the progression of CKD has not been investigated. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A case-control study was performed to determine whether there were changes in plasma levels of carbamylated lipoproteins in individuals with type 2 diabetes with eGFR >60 ml/min per 1.73 m2 compared with a group of age- and sex-matched healthy controls. A cohort of 1320 patients with type 2 diabetes with baseline eGFR ≥30 ml/min per 1.73 m2 was longitudinally followed up to evaluate the association between carbamylated lipoproteins and progression of CKD. The primary kidney outcome was defined as doubling of serum creatinine and/or initiation of KRT during follow-up. Plasma carbamylated LDLs and HDLs was measured by ELISA. RESULTS In individuals with diabetes with eGFR >60 ml/min per 1.73 m2, both plasma carbamylated LDL and HDL levels were higher compared with healthy controls (P<0.001). After a mean follow-up of 9 years of the diabetic cohort, individuals in the top quartile of carbamylated LDL (hazard ratio, 2.21; 95% confidence interval, 1.42 to 3.46; P<0.001) and carbamylated HDL (hazard ratio, 4.53; 95% confidence interval, 2.87 to 7.13; P<0.001) had higher risk of deterioration of kidney function compared with those in the lowest quartile. On multivariable Cox regression analysis, plasma carbamylated LDL was no longer associated with kidney outcome after adjusting for baseline eGFR and potential confounding factors. However, the association between plasma carbamylated HDL and kidney outcome remained significant and was independent of HDL cholesterol. CONCLUSIONS Plasma carbamylated HDL but not carbamylated LDL was independently associated with progression of CKD in patients with type 2 diabetes.
Differential effects of acute and chronic treatment with the flavonoid chrysin on anxiety-like behavior and Fos immunoreactivity in the lateral septal nucleus in rats

Abstract The aim of this study was to compare the effects of acute (a single injection) and chronic (21 consecutive days) treatments with chrysin 2, 4, and 8 μmol kg−1 on anxiety-like behavior and Fos immunoreactivity in the lateral septum nucleus (LSN), a structure that is involved in the regulation of anxiety, in male Wistar rats. These effects were compared with the clinically effective anxiolytic diazepam 7 μmol kg−1. The results showed that acute, but not chronic treatment, with 4 μmol kg−1 chrysin exerted anxiolytic- and anti- depressant-like effects with these effects being similar to that of diazepam. Also, none of the above-mentioned treatments did alter Fos immunoreactivity in the LSN, but a tendency towards the reduction of this variable was detected with chrysin 4 μmol kg−1 and diazepam 7 μmol kg−1. Altogether, results suggest that chrysin exerts anxiolytic-like effects, however, it can produce pharmacological tolerance after repeated use, similar to benzodiazepines.
Time-Dependent Response of Human Deciduous Tooth-Derived Dental Pulp Cells Treated with TheraCal LC: Functional Analysis of Gene Interactions Compared to MTA

Pulp capping material should facilitate hard tissue regeneration on the injured pulp tissue. TheraCal LC (TC) was recently developed. Although TC has shown reliable clinical outcomes after direct pulp capping, there are still remaining concerns regarding its detrimental effect on pulp cells. Therefore, this study aimed to identify the gene expression of human deciduous tooth-derived dental pulp cells exposed to TC compared to mineral trioxide aggregate (MTA). The cells were cultured and exposed to TC and MTA for 24 and 72 h. Next, total RNA was isolated. QuantSeq 3′ mRNA-sequencing was used to examine differentially expressed genes (DEGs) in exposed to TC and MTA. Functional analysis of DEGs was performed using bioinformatics analysis. In gene ontology (GO) functional enrichment analysis, cells in TC for 24 h presented significantly enriched immune response (p < 0.001) and inflammatory response (p < 0.01) compared to MTA. TC showed enriched positive regulation of cell migration at 72 h (p < 0.001). In Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, neuroactive ligand–receptor interaction (p = 1.19 × 10−7) and calcium signaling pathway (p = 2.96 × 10−5) were confirmed in the shared DEGs in TC. In conclusion, DEGs in TC may be involved in pathways associated with osteoclastogenesis and osteoclastic differentiation.
ALK inhibitors for non-small cell lung cancer: A systematic review and network meta-analysis

Background We sought to assess the relative effects of individual anaplastic lymphoma kinase (ALK) inhibitors for the treatment of non-small cell lung cancer (NSCLC). Methods We searched MEDLINE, Embase, Cochrane CENTRAL, and grey literature (July 23, 2019) for randomized controlled trials (RCTs) that included participants with ALK- or ROS1-positive NSCLC who received any ALK inhibitor compared with placebo, another ALK inhibitor, or the same ALK inhibitor at a different dose. The primary outcome was treatment-related death. Secondary outcomes were overall survival (OS), progression-free survival (PFS), and serious adverse events. Data were pooled via meta-analysis and network meta-analysis, and risk of bias was assessed. PROSPERO: CRD42017077046. Results Thirteen RCTs reporting outcomes of interest among participants with ALK-positive NSCLC were identified. Treatment-related deaths were rare, with 10 deaths attributed to crizotinib (risk difference v. chemotherapy: 0.49, 95% credible interval [CrI] –0.16 to 1.46; odds ratio 2.58 (0.76–11.37). All ALK inhibitors improved PSF relative to chemotherapy (hazard ratio [95% CrI]: crizotinib 0.46 [0.39–0.54]; ceritinib 0.52 [0.42–0.64]; alectinib 300 BID 0.16 [0.08–0.33]; alectinib 600 BID 0.23 [0.17–0.30]; brigatinib 0.23 [0.15–0.35]), while alectinib and brigatinib improved PFS over crizotinib and ceritinib (alectinib v. crizotinib 0.34 [0.17–0.70]; alectinib v. ceritinib 0.30 [0.14–0.64]; brigatinib v. crizotinib 0.49 [0.33–0.73]; brigatinib v. ceritinib 0.43 [0.27–0.70]). OS was improved with alectinib compared with chemotherapy (HR 0.57 [95% CrI 0.39–0.83]) and crizotinib (0.68 [0.48–0.96]). Use of crizotinib (odds ratio 2.08 [95% CrI 1.56–2.79]) and alectinib (1.60 [1.00–2.58]) but not ceritinib (1.25 [0.90–1.74), increased the risk of serious adverse events compared with chemotherapy. Results were generally consistent among treatment-experienced or naïve participants. Conclusion(s) Treatment-related deaths were infrequent among ALK-positive NSCLC. PFS may be improved by alectinib and brigatinib relative to other ALK inhibitors; however, the assessment of OS is likely confounded by treatment crossover and should be interpreted with caution.
Examining Bone, Muscle and Fat in Middle-Aged Long-Term Endurance Runners: A Cross-Sectional Study

Aerobic exercise training has many known cardiovascular benefits that may promote healthy aging. It is not known if long-term aerobic exercise training is also associated with structural benefits (e.g., lower fat mass, higher areal bone mineral density (BMD) and greater muscle mass). We evaluated these parameters in middle-aged long-term endurance runners compared to sex-, age-, height-, and weight-matched non-running controls. Total and regional lean and fat mass and areal BMD were assessed by dual-energy X-ray absorptiometry. Sagittal magnetic resonance images captured the cross-sectional area and thickness of the lumbar multifidus. Runners (n = 10; all male) had a mean (standard deviation; SD) age of 49 (4) years, height of 178.9 (4.9) cm, weight of 67.8 (5.8) kg, body mass index (BMI) of 21.4 (1.4) kg/m2 and had been running 82.6 (27.9) km/week for 23 (13) years. Controls (n = 9) had a mean (SD) age of 51 (5) years, height of 176.0 (5.1) cm, weight of 72.8 (7.1) kg, and BMI of 23.7 (2.1) kg/m2. BMI was greater in controls (p = 0.010). When compared to controls on average, runners had a 10 percentage-point greater total body lean mass than controls (p = 0.001) and 14% greater trunk lean mass (p = 0.010), as well as less total body (8.6 kg; p < 0.001), arm (58%; p = 0.002), leg (52%; p < 0.001), trunk (73%; p < 0.001), android (91%; p < 0.001), and gynoid fat mass (64%; p < 0.001). No differences were observed between groups for BMD outcomes or multifidus size. These results underscore the benefits of endurance running to body composition that carry over to middle-age.
Functional connectivity and structural analysis of trial spinal cord stimulation responders in failed back surgery syndrome

Background Chronic pain has been associated with alterations in brain structure and function that appear dependent on pain phenotype. Functional connectivity (FC) data on chronic back pain (CBP) is limited and based on heterogeneous pain populations. We hypothesize that failed back surgery syndrome (FBSS) patients being considered for spinal cord stimulation (SCS) therapy have altered resting state (RS) FC cross-network patterns that 1) specifically involve emotion and reward/aversion functions and 2) are related to pain scores. Methods RS functional MRI (fMRI) scans were obtained for 10 FBSS patients who are being considered for but who have not yet undergone implantation of a permanent SCS device and 12 healthy age-matched controls. Seven RS networks were analyzed including the striatum (STM). The Wilcoxon signed-rank test evaluated differences in cross-network FC strength (FCS). Differences in periaqueductal grey (PAG) FC were assessed with seed-based analysis. Results Cross-network FCS was decreased (p<0.05) between the STM and all other networks in these FBSS patients. There was a negative linear relationship (R2 = 0.76, p<0.0022) between STMFCS index and pain scores. The PAG showed decreased FC with network elements and amygdala but increased FC with the sensorimotor cortex and cingulate gyrus. Conclusions Decreased FC between STM and other RS networks in FBSS has not been previously reported. This STMFCS index may represent a more objective measure of chronic pain specific to FBSS which may help guide patient selection for SCS and subsequent management.
Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the long interspersed nuclear element-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of OsNRPD1 would cause sterility in rice. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

This review assessed the molecular characterization of the methicillin-resistant Staphylococcus aureus (MRSA)-ST80 clone with an emphasis on its proportion of total MRSA strains isolated, PVL production, spa-typing, antibiotic resistance, and virulence. A systematic review of the literature was conducted on MRSA-ST80 clone published between 1 January 2000 and 31 August 2019. Citations were chosen for a review of the full text if we found evidence that MRSA-ST80 clone was reported in the study. For each isolate, the country of isolation, the sampling period, the source of isolation (the type of infection, nasal swabs, or extra-human), the total number of MRSA strains isolated, number of MRSA-ST80 strains, antibiotic resistance patterns, PVL production, virulence genes, and spa type were recorded. The data from 103 articles were abstracted into an Excel database. Analysis of the data showed that the overall proportion of MRSA-ST80 has been decreasing in many countries in recent years. The majority of MRSA-ST80 were PVL positive with spa-type t044. Only six reports of MRSA-ST80 in extra-human niches were found. This review summarizes the rise of MRSA-ST80 and the evidence that suggests that it could be in decline in many countries.
Sigmod Officers, Committees, and Awardees Chair Vice-chair Secretary/treasurer Sigmod Executive Com Mittee: Advisory Board: Infor Mation Director: Associate Infor Mation Directors: Sigmod Record Associate Editors: Sigmod Disc and Sigmod Anthology Editor: Awards Com Mittee: Jim Gray Doctoral Disserta

The rise of multicore processors and cloud computing is putting enormous pressure on the software community to find solutions to the difficulty of parallel and distributed programming. At the same time, there is more—and more varied—interest in data-centric programming languages than at any time in computing history, in part because these languages parallelize naturally. This juxtaposition raises the possibility that the theory of declarative database query languages can provide a foundation for the next generation of parallel and distributed programming languages. In this paper I reflect on my group’s experience over seven years using Datalog extensions to build networking protocols and distributed systems. Based on that experience, I present a number of theoretical conjectures that may both interest the database community, and clarify important practical issues in distributed computing. Most importantly, I make a case for database researchers to take a leadership role in addressing the impending programming crisis. This is an extended version of an invited lecture at the ACM PODS 2010 conference [32].
The association between vascular access type and depressive symptoms in geriatric hemodialysis population

Objectives A well-functioning vascular access is crucial for hemodialysis treatment, and arteriovenous fistula is the recommended vascular access type. Arteriovenous fistula is superior to other vascular access types in many aspects, but the effect of arteriovenous fistula on patients’ psychiatric state is not well described yet. The aim of this study is to determine whether there is an association between vascular access type and depression scores. Methods This cross-sectional study was conducted at two hemodialysis centers. Geriatric Depression Scale-15 was administered to geriatric hemodialysis patients, using ≥5 score as the cut-off value for the presence of depressive symptoms. Descriptive tests, Kolmogorov–Smirnov test, Pearson’s Chi-square test, Mann–Whitney test, Kruskal–Wallis test, Spearman’s rank correlation calculation, and multiple logistic regression analysis were performed accordingly to analyze the data. Results Of 75 participants, 34 (45.3%) were female and the mean age was 73.4 ± 5.9 years (range: 65–92). The prevalence of depressive symptoms in the geriatric hemodialysis population was 53.3%. Central venous catheter, hypertension, and increased time on hemodialysis have been found to be risk factors for higher depression scores (aOR 10.505 (95% CI 1.435–76.900), p = 0.021; aOR 9.783 (95% CI 2.508–38.169), p = 0.001; aOR 1.019 (95% CI 1.003–1.035), p = 0.017, respectively). Among patients with arteriovenous fistula, those with hypertension had higher depression scores (p = 0.008). Conclusions Geriatric hemodialysis patients were found to have depressive symptoms commonly, and central venous catheter, hypertension, and increased time on hemodialysis have been found to be risk factors for presence of depressive symptoms. To the best of our knowledge, this is the first study highlighting that arteriovenous fistula is associated with lower depression scores and lower prevalence of depressive symptoms.
Reference interval and preanalytical properties of serum neurofilament light chain in Scandinavian adults

Abstract The neurofilament light chain (NfL) is a promising biomarker of neuronal injury which is approaching routine clinical use. With the development of ultra-sensitive technologies, NfL has become measurable in the peripheral blood but the reference interval for serum NfL remains to be established. NfL was measured by a single-molecule array (Simoa™) analysis under internal and external quality control which is established for routine clinical use. Serum samples from 342 reference subjects, 18−87 years were analyzed. The age-partitioned reference interval was established according to Clinical and Laboratory Standards Institute guidelines, an approximation of the upper reference interval limit per 10-year age-groups was performed, and key pre-analytical properties were examined. Serum NfL levels increased 2.9% per year. The non-parametric reference interval for the age groups 18−40, 41−65, and >65 years were 2.8−9.7 ng/L, 4.6 − 21.4 ng/L, and 7.5−53.8 ng/L, respectively. The estimated upper reference interval limits per 10-year intervals corresponded well with the 90% confidence limits of the non-parametric reference interval. The recovery of serum NfL after seven days at room temperature or three freeze-thaw cycles were 93% (95% CI: 89%−97%) and 92% (95% CI: 83%−102%) and levels in serum were only slightly higher than levels in plasma (p < .0001). The study establishes the serum NfL reference interval, provide estimated upper reference intevral limits in 10-year intervals to increase the clinical applicability and uncover pre-analytical properties that make serum NfL feasible for clinical use.
Role of p38-mitogen-activated protein kinase in COPD: pathobiological implications and therapeutic perspectives

ABSTRACT Introduction: The p38 serine-threonine kinases are members of the large family of mitogen-activated protein kinases (MAPK). In particular, p38 MAPK subgroup includes four isoforms (α, β, γ, δ), among which p38α and p38β are mainly involved in inflammatory disorders. Indeed, by activating key transcription factors and by inducing the expression of several cytokines and chemokines, p38α plays a central role in the pathobiology of chronic obstructive pulmonary disease (COPD). Areas covered: This concise review focuses on the contribution of p38 MAPK to development, maintenance, and amplification of chronic lung inflammation in COPD. Moreover, we discuss the potential role of p38 MAPK as suitable target for perspective therapeutic approaches under evaluation as potential new COPD treatments. In this regard, an extensive literature search has been conducted throughout PubMed source (1990–2020). Expert opinion: Despite some promising preclinical data, so far the results of clinical trials evaluating p38 MAPK inhibitors have been quite disappointing, thus suggesting a cautious judgment about the future perspectives of these drugs for COPD therapy.
Brevinin-2GHk from Sylvirana guentheri and the Design of Truncated Analogs Exhibiting the Enhancement of Antimicrobial Activity

Brevinins are an important antimicrobial peptide (AMP) family discovered in the skin secretions of Ranidae frogs. The members demonstrate a typical C-terminal ranabox, as well as a diverse range of other structural characteristics. In this study, we identified a novel brevinin-2 peptide from the skin secretion of Sylvirana guentheri, via cloning transcripts, and identifying the expressed mature peptide, in the skin secretion. The confirmed amino acid sequence of the mature peptide was designated brevinin-2GHk (BR2GK). Moreover, as a previous study had demonstrated that the N-terminus of brevinin-2 is responsible for exerting antimicrobial activity, we also designed a series of truncated derivatives of BR2GK. The results show that the truncated derivatives exhibit significantly improved antimicrobial activity and cytotoxicity compared to the parent peptide, except a Pro14 substituted analog. The circular dichroism (CD) analysis of this analog revealed that it did not fold into a helical conformation in the presence of either lipopolysaccharides (LPS) or TFE, indicating that position 14 is involved in the formation of the α-helix. Furthermore, three more analogs with the substitutions of Ala, Lys and Arg at the position 14, respectively, revealed the influence on the membrane disruption potency on bacteria and mammalian cells by the structural changes at this position. Overall, the N-terminal 25-mer truncates demonstrated the potent antimicrobial activity with low cytotoxicity.
Variations in Nitrogen Metabolism are Closely Linked with Nitrogen Uptake and Utilization Efficiency in Cotton Genotypes under Various Nitrogen Supplies

Cotton production is highly sensitive to nitrogen (N) fertilization, whose excessive use is responsible for human and environmental problems. Lowering N supply together with the selection of N-efficient genotypes, more able to uptake, utilize, and remobilize the available N, could be a challenge to maintain high cotton production sustainably. The current study aimed to explore the intraspecific variation among four cotton genotypes in response to various N supplies, in order to identify the most distinct N-efficient genotypes and their nitrogen use efficiency (NUE)-related traits in hydroponic culture. On the basis of shoot dry matter, CCRI-69 and XLZ-30 were identified as N-efficient and N-inefficient genotypes, respectively, and these results were confirmed by their contrasting N metabolism, uptake (NUpE), and utilization efficiency (NUtE). Overall, our results indicated the key role of shoot glutamine synthetase (GS) and root total soluble protein in NUtE. Conversely, tissue N concentration and N-metabolizing enzymes were considered as the key traits in conferring high NUpE. The remobilization of N from the shoot to roots by high shoot GS activity may be a strategy to enhance root total soluble protein, which improves root growth for N uptake and NUE. In future, multi-omics studies will be employed to focus on the key genes and pathways involved in N metabolism and their role in improving NUE.
Optical coherence tomography in diagnosis of inflammatory scalp disorders

The common inflammatory scalp disorders share similar clinical manifestations, and patient work up require invasive, undesirable diagnostic procedures like biopsy to ensure correct diagnosis. Optical coherence tomography (OCT) is a non‐invasive high‐resolution imaging modality that has found a valuable tool to assist in the diagnose and evaluation of different skin diseases.