Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene polymorphism of DNA repair gene X‐ray repair cross complementing group 1 and xeroderma pigmentosum group D and environment interaction in non‐small‐cell lung cancer for Chinese nonsmoking female patients

An association between genetic polymorphisms in encoding X‐ray repair cross complementing group 1 (XRCC1) and encoding xeroderma pigmentosum group D (XPD) and risks of non‐small‐cell lung cancer (NSCLC) in East Chinese Han population has been observed. Herein we hypothesized that genetic polymorphisms in these two DNA repair genes are likely to be important in the NSCLC in Chinese nonsmoking female patients. We recruited 327 nonsmoking female patients with NSCLC and 342 individuals with benign lung diseases or healthy controls. Genotype frequencies of XRCC1 T‐77C, Arg194Trp, Arg280His and Arg399Gln, Pro206Pro, and XPD Asp312Asn and Lys751Gln were calculated after Polymerase Chain Reaction amplification and sequencing. Generalized multifactor dimensionality reduction (GMDR) was used to detect the interactive effect of XRCC1 and XPD gene polymorphisms. The ratio of cooking oil mist exposure history and soot exposure history, and the gene frequencies of XRCC1 T‐77C TC + CC, XRCC1 AG + GG, XRCC1 399Gln/Gln, and XPD 751Gln/Gln were higher in female patients with NSCLC than those with benign lung diseases or healthy controls. The haplotypes of XRCC1 T‐Arg‐Arg‐Gln and XRCC1 C‐Arg‐Arg‐Arg were positively associated with the NSCLC occurrence in nonsmoking female patients. GMDR discovered that there was an interactive model of XRCC1 and XPD genes in multiple gene loci. Logistic regression analysis showed that XRCC1 T‐77C, XRCC1 Pro206Pro polymorphism, cooking oil mist and soot exposure history and tumor‐node‐metastasis (TNM) stage were related to NSCLC occurrence for nonsmoking female patients. Taken together, XRCC1 and XPD polymorphisms, cooking oil mist, and soot exposure history may be interactively correlated with NSCLC incidence for nonsmoking female patients.
Color Image Quality Assessment Based on CIEDE2000

Combining the color difference formula of CIEDE2000 and the printing industry standard for visual verification, we present an objective color image quality assessment method correlated with subjective vision perception. An objective score conformed to subjective perception (OSCSP) Q was proposed to directly reflect the subjective visual perception. In addition, we present a general method to calibrate correction factors of color difference formula under real experimental conditions. Our experiment results show that the present DE2000-based metric can be consistent with human visual system in general application environment.
Quantum-critical conductivity of the Dirac fluid in graphene

Electron hydrodynamics in graphene Electrons can move through graphene in a manner reminiscent of fluids, if the conditions are right. Two groups studied the nature of this hydrodynamic flow in different regimes (see the Perspective by Lucas). Gallagher et al. measured optical conductivity using a waveguide-based setup, revealing signatures of quantum criticality near the charge neutrality point. Berdyugin et al. focused on electron transport in the presence of a magnetic field and measured a counterintuitive contribution to the Hall response that stems from hydrodynamic flow. Science, this issue p. 158, p. 162; see also p. 125 Coplanar waveguide–based measurements of optical conductivity in graphene reveal signatures of quantum criticality. Graphene near charge neutrality is expected to behave like a quantum-critical, relativistic plasma—the “Dirac fluid”—in which massless electrons and holes collide at a rapid rate. We used on-chip terahertz spectroscopy to measure the frequency-dependent optical conductivity of clean, micrometer-scale graphene at electron temperatures between 77 and 300 kelvin. At charge neutrality, we observed the quantum-critical scattering rate characteristic of the Dirac fluid. At higher doping, we detected two distinct current-carrying modes with zero and nonzero total momenta, a manifestation of relativistic hydrodynamics. Our work reveals the quantum criticality and unusual dynamic excitations near charge neutrality in graphene.
Longitudinal pathways linking family risk, neural risk processing, delay discounting, and adolescent substance use.

BACKGROUND Current theories in neuroscience emphasize the crucial role of individual differences in the brain contributing to the development of risk taking during adolescence. Yet, little is known about developmental pathways through which family risk factors are related to neural processing of risk during decision making, ultimately contributing to health risk behaviors. Using a longitudinal design, we tested whether neural risk processing, as affected by family multi-risk index, predicted delay discounting and substance use. METHOD One hundred and fifty-seven adolescents (aged 13-14 years at Time 1, 52% male) were assessed annually three times. Family multi-risk index was measured by socioeconomic adversity, household chaos, and family risk-taking behaviors. Delay discounting was assessed by a computerized task, substance use by questionnaire data, and risk-related neural processing by blood-oxygen-level-dependent (BOLD) responses in the amygdala during a lottery choice task. RESULTS Family multi-risk index at Time 1 was related to adolescent substance use at Time 3 (after controlling for baseline substance use) indirectly through heightened amygdala sensitivity to risks and greater delay discounting. CONCLUSIONS Our results elucidate the crucial role of neural risk processing in the processes linking family multi-risk index and the development of substance use. Furthermore, risk-related amygdala activation and delay discounting are important targets in the prevention and treatment of substance use among adolescents growing up in high-risk family environments.
Association of Polymorphisms Modulating Low-density Lipoprotein Cholesterol with Susceptibility, Severity, and Progression of Rheumatoid Arthritis

Objective. Dyslipidemia, a risk factor for cardiovascular diseases, is more prevalent in patients with rheumatoid arthritis (RA) than in the general population. We investigated whether single-nucleotide polymorphisms (SNP) modulating low-density lipoprotein (LDL) cholesterol affect susceptibility, severity, and progression of RA. Methods. We enrolled 302 patients with RA and 1636 healthy controls, and investigated the SNP modulating LDL cholesterol. Clinical characteristics of RA, serum adipocytokine concentrations, and radiographic severity were analyzed according to genotype score based on the number of unfavorable alleles. The influence of genotype score on radiographic progression was also investigated using multivariable logistic models. Results. We identified 3 SNP (rs688, rs693, and rs4420638) modulating LDL cholesterol in Koreans, which correlated well with LDL cholesterol levels in both patients with RA and controls. Among them, 2 SNP, rs688 and rs4420638, were more prevalent in patients with RA than in controls. In patients with RA carrying more unfavorable alleles (genotype score ≥ 3), disease activity measures, serum adipocytokine levels, and radiographic severity were all increased. The genotype score was an independent risk factor for radiographic progression of RA over 2 years, and its effect was greater than the influence of conventional risk factors. Conclusion. SNP modulating LDL cholesterol influence the risk, activity, and severity of RA. These results provide the first evidence that genetic mechanisms linked to dyslipidemia may directly contribute to the susceptibility and prognosis of RA, a representative of chronic inflammatory diseases, explaining the high incidence of dyslipidemia in RA.
Periphytic diatom colonization and litter decomposition in an intermittent stream of South India

We examined the dynamic of periphytic diatom colonization and litter decompositional pattern in an intermittent stream of South India. Litter bags containing 5 g of fresh fallen leaves (belongs to five different species of angiosperms) were fixed in the five stream pools and they were collected after 7, 14, 21, and 28 days of incubation. This experiment showed the diversity, richness, and abundance of diatoms developed on leaf litter. In total, 131 µl−1 cells of diatoms under four species in three families were collected from decomposing leaves in benthic area of stream pools. During experiment, 142 µl−1 cells representing 11 taxa in 10 families were observed in litter bags. The colonization of epiphytic diatom was rapid in early stage of litter decomposition. The higher number of colonization made by Asterionella and Stenopterobia found in litter bags of all experimental weeks. These findings suggest that the rapid microbial colonization (ephiphytic algae) was occurred in the early stage of litter decomposition in an intermittent tropical stream and a comprehensive ecological investigation in perennial natural streams in India is needed.
Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8+ T Cells and Evolve at the Population Level

Background & Aims Hepatitis D virus (HDV) superinfection in patients with hepatitis B virus (HBV) is associated with rapid progression to liver cirrhosis and hepatocellular carcinoma. Treatment options are limited, and no vaccine is available. Although HDV-specific CD8+ T cells are thought to control the virus, little is known about which HDV epitopes are targeted by virus-specific CD8+ T cells or why these cells ultimately fail to control the infection. We aimed to define how HDV escapes the CD8+ T-cell–mediated response. Methods We collected plasma and DNA samples from 104 patients with chronic HDV and HBV infection at medical centers in Europe and the Middle East, sequenced HDV, typed human leukocyte antigen (HLA) class I alleles from patients, and searched for polymorphisms in HDV RNA associated with specific HLA class I alleles. We predicted epitopes in HDV that would be recognized by CD8+ T cells and corresponded with the identified virus polymorphisms in patients with resolved (n = 12) or chronic (n = 13) HDV infection. Results We identified 21 polymorphisms in HDV that were significantly associated with specific HLA class I alleles (P < .005). Five of these polymorphisms were found to correspond to epitopes in HDV that are recognized by CD8+ T cells; we confirmed that CD8+ T cells in culture targeted these HDV epitopes. HDV variant peptides were only partially cross-recognized by CD8+ T cells isolated from patients, indicating that the virus had escaped detection by these cells. These newly identified HDV epitopes were restricted by relatively infrequent HLA class I alleles, and they bound most frequently to HLA-B. In contrast, frequent HLA class I alleles were not associated with HDV sequence polymorphisms. Conclusions We analyzed sequences of HDV RNA and HLA class I alleles that present epitope peptides to CD8+ T cells in patients with persistent HDV infection. We identified polymorphisms in the HDV proteome that associate with HLA class I alleles. Some variant peptides in epitopes from HDV were only partially recognized by CD8+ T cells isolated from patients; these could be mutations that allow HDV to escape the immune response, resulting in persistent infection. HDV escape from the immune response was associated with uncommon HLA class I alleles, indicating that HDV evolves, at the population level, to evade recognition by common HLA class I alleles.
Vancomycin-Associated Acute Kidney Injury in Critically Ill Adolescent and Young Adult Patients

Background: Risk factors for the development of vancomycin-associated acute kidney injury (AKI) have been evaluated in both pediatric and adult populations; however, no previous studies exist evaluating this in the critically ill adolescent and young adult patients. Objective: Identify the incidence of AKI and examine risk factors for the development of AKI in critically ill adolescents and young adults on vancomycin. Methods: This retrospective review evaluated the incidence of AKI in patients 15 to 25 years of age who received vancomycin, while admitted to an intensive care unit. Acute kidney injury in this population was defined as an increase in serum creatinine by 0.5 mg/dL or 50% from baseline. Patients who developed AKI were evaluated for specific risk factors compared to those who did not develop AKI. Results: A total of 50 patients (20 developed AKI) were included in the study. There was no difference in vancomycin daily dose or duration of vancomycin therapy. Maximum vancomycin trough (31.15 mg/dL vs 12.5 mg/dL, P = .006), percentage of patients with concurrent nephrotoxic medication (95% vs 60%, P = .012) and concurrent vasopressor (55% vs 23%, P = .029) were higher in those who developed AKI. Percentage of patients who underwent a procedure while on vancomycin (35% vs 6.7%, P = .021) was also higher within the AKI group. Conclusions: Vancomycin-associated AKI occurred in 40% of critically ill adolescent and young adult patients. These patients may be more likely to develop vancomycin-associated AKI if they had undergone a procedure, as well as in the presence of high vancomycin trough levels, concurrent nephrotoxic agents, and concurrent vasopressor therapy.
Ischemic Mitral Regurgitation: A Complex Multifaceted Disease

Ischemic mitral regurgitation (MR) is a complex multifactorial disease that involves global and regional left ventricular remodeling as well as dysfunction and distortion of the components of the mitral valve including the chordae, annulus and leaflets. This is a frequent (13–59%) complication of myocardial infarction, which is associated with a poor prognosis. The suboptimal results obtained with the most commonly used surgical strategy, that is, restrictive annuloplasty combined with coronary artery bypass graft, emphasize the need to develop alternative or concomitant surgical techniques that directly target the causal mechanisms of the disease. A comprehensive assessment of mitral valve configuration and left ventricular geometry and function prior to surgery as well as an accurate quantification of MR severity at rest and during exercise may help improve patient risk stratification and better individualize the surgical strategy based on the patient’s specific characteristics. The purpose of this review is to summarize the current state of knowledge with regard to the definition, prevalence, mechanisms, outcome and treatment of ischemic MR.
Parental Disengagement in Childhood and Adolescent Male Gun Carrying

Childhood parental disengagement predicts mid- to late-adolescent gun carrying, in part because parental disengagement is associated with higher peer delinquency and externalizing problems during early adolescence. BrightcoveDefaultPlayer10.1542/6138655494001PEDS-VA_2018-1552 Video Abstract OBJECTIVES: To examine the association between parental disengagement in childhood and adolescent gun carrying and determine whether this association is accounted for by externalizing problems and affiliation with delinquent peers during early adolescence. METHODS: The sample included 503 boys (55.7% African American, 40.6% white, 3.7% other) recruited from first-grade classrooms in Pittsburgh public schools. Multi-informant assessments were conducted regularly (semiannually then annually) from approximately ages 7.5 to 20 years. Latent factors were constructed by using parent-reported parental disengagement (ie, poor parental involvement, poor parent-son communication, poor parent-son relationship quality) collected from ages 7.5 to 10 years, youth-reported peer delinquency from ages 10.5 to 13 years, and teacher-reported externalizing problems from ages 10.5 to 13 years. The outcome was youth-reported gun carrying from ages 14 to 20 years. RESULTS: Twenty percent of individuals sampled reported carrying a gun during adolescence. Childhood parental disengagement was significantly associated with adolescent gun carrying (β = .22; 95% confidence interval: 0.08 to 0.36). Furthermore, the association between parental disengagement and gun carrying was partially mediated through peer delinquency and externalizing problems during early adolescence. The 2 indirect paths accounted for ∼29% of the total effect of parental disengagement. CONCLUSIONS: Boys exposed to poorer parental engagement during childhood are more likely to affiliate with delinquent peers and exhibit externalizing problems during early adolescence, which (in turn) increases their risk of carrying a firearm in later adolescence. This suggests that gun violence prevention efforts with children should work to enhance aspects of parental engagement.
Molecular Characterization of Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolated from Swine Farms in Malaysia.

AIMS The high prevalence of multidrug resistance (MDR) and extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae associated with nosocomial infections has caused serious therapeutic challenges. The objectives of this study were to determine the genotypic and phenotypic characteristics of K. pneumoniae strains isolated from Malaysian swine farms and the transferability of ESBL genes by plasmids. RESULTS A total of 50 K. pneumoniae strains were isolated from 389 samples, which were collected from healthy and unhealthy pigs (swine rectum and oral cavities), healthy farmers (human rectum, urine, and nasal cavities), farm's environment, and animal feeds from seven Malaysian swine farms. Antimicrobial susceptibility analysis of these 50 K. pneumoniae strains showed that the majority (86%) were resistant to tetracycline, while 44% and 36% of these strains were MDR and ESBL producers, respectively. PCR and DNA sequencing of the amplicons showed the occurrence of blaTEM (15/18), blaSHV (15/18), blaCTX-M-1 group (7/18), and blaCTX-M-2 group (2/18), while only class 1 integron-encoded integrase was detected. Conjugation experiments and plasmid analysis indicated that the majority of the ESBL genes were plasmid encoded and the plasmids in 11 strains were conjugative. Genotyping by pulsed-field gel electrophoresis and repetitive extragenic palindrome-polymerase chain reaction (REP-PCR) showed that these 50 strains were genetically diverse with 44 pulsotypes and 43 REP-PCR subtypes. CONCLUSIONS ESBL-producing K. pneumoniae strains showed high resistance to tetracycline as this antibiotic is used for prophylaxis and therapeutic purposes at the swine farms. The findings in this study have drawn attention to the issue of increasing MDR in animal husbandry and it should be taken seriously to prevent the spread and treatment failure due to antimicrobial resistance.
Protective Effect of All-Trans Retinoic Acid in Cisplatin-Induced Testicular Damage in Rats

Purpose To investigate the effects of all-trans retinoic acid (ATRA) in cisplatin (CP)-induced testicular damage in rats. Materials and Methods Twenty-eight male Wistar rats were divided into four groups: Control, ATRA alone, ATRA+CP, and CP alone. Body weight, testicular weight, sperm count, sperm motility, percentage of abnormal sperm, total antioxidant status (TAS), total oxidant status (TOS), oxidative stress index (OSI) in testicular tissue, and testicular histopathology were compared among groups. Results The sperm count and motility significantly decreased and the percentage of abnormal sperm significantly increased in the CP group compared to the control and ATRA groups. CP+ATRA administration significantly increased the sperm count and motility, but reduced the abnormal sperm count. CP administration significantly increased TOS and OSI compared to the control group and the other groups. Administering CP+ATRA significantly decreased TOS and the OSI in testicular tissue and reduced spermatogenesis, but increased the Johnsen score. Conclusions The destructive effects of CP treatment on testicular tissue and spermatogenesis were reduced by administering ATRA.
A role for the microbiome in mother–infant interaction and perinatal depression

Abstract Perinatal depression is a significant public health problem, due to its negative impact on maternal well-being and long-term adverse effects for children. Mother–infant interaction and maternal responsiveness and sensitivity are a hypothesized mechanism by which perinatal depression effects child development, and increasing research in the microbiota–gut–brain axis may provide a new avenue of investigation. There is limited efficacy for treatment of perinatal depression for improving the mother–infant relationship and child outcomes. The maternal microbiota may be the basis of child outcomes through foetal programming and sharing of microbes between mother and infant. There is evidence that less diversity of the intestinal microbial community is associated with neuropsychiatric disorders, including depression and anxiety in mothers and offspring. Assessing the maternal and child’s microbial communities may be an important missing component in mother–infant attachment-based therapies during treatment of perinatal depression. Probiotics and prebiotics require further research as additions to mother–infant interventions. Further research may enable identification of bacterial genes that indicate specific pathways that could be targeted to improve outcomes for mother and child.
Repetitive saliva swallowing test and water swallowing test may identify a COPD phenotype at high risk of exacerbation

Patients with chronic obstructive pulmonary disease (COPD) are known to present with dysphagia from an early stage. Dysphagia leads to swallowing‐related complications, in turn leading to COPD exacerbation. Dysphagia screening is recommended; however little is known of its utility in detecting a COPD phenotype at risk for exacerbation. The simple swallowing provocation test (SSPT), considered to be a standard screening test, requires specific equipment, physician skill and patient discomfort.
Impact of the Gastro-Intestinal Bacterial Microbiome on Helicobacter-Associated Diseases

Helicobacter pylori is a bacterium that selectively infects the gastric epithelium of half of the world population. The microbiome, community of microorganisms gained major interest over the last years, due to its modification associated to health and disease states. Even if most of these descriptions have focused on chronic disorders, this review describes the impact of the intestinal bacterial microbiome on host response to Helicobacter associated diseases. Microbiome has a direct impact on host cells, major barrier of the gastro-intestinal tract, but also an indirect impact on immune system stimulation, by enhancing or decreasing non-specific or adaptive response. In microbial infections, especially in precancerous lesions induced by Helicobacter pylori infection, these modifications could lead to different outcome. Associated to data focusing on the microbiome, transcriptomic analyses of the eukaryote response would lead to a complete understanding of these complex interactions and will allow to characterize innovative biomarkers and personalized therapies.