Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced biodegradation of diesel oil by a newly identified Rhodococcus baikonurensis EN3 in the presence of mycolic acid

Aims: The aim of the present study was to isolate and characterize a bacterium, strain EN3, capable of using diesel oil as a major carbon and energy source, and to analyse the enhancement of diesel oil degradation by this organism using synthetic mycolic acid (2‐hexyl‐3‐hydroxyldecanoic acid).
Commercial Molecular Panels Are of Limited Utility in the Classification of Pancreatic Cystic Lesions

The PathfinderTG biomarker panel is useful in the evaluation of pancreatic cysts that have clinical features suspicious for malignancy, but its utility in classifying fine-needle aspiration biopsies from small pancreatic cystic lesions is yet to be proven. We used morphology to classify 20 pancreatic cyst cytology aspirates, all of which met radiographic criteria for close observation. Cases were cytologically classified as consistent with pseudocyst, serous cystadenoma, or mucinous neoplasm with low-grade, intermediate-grade, or high-grade dysplasia and analyzed for carcinoembryonic antigen. Redpath Integrated Pathology Inc. rendered diagnoses of nonmucinous (reactive/indolent or serous) or mucinous (low-risk or at risk) cyst on the basis of results of the PathfinderTG panel (KRAS mutations, DNA content, and loss of heterozygosity at microsatellites linked to tumor suppressor genes). Cytologic and commercial laboratory diagnoses were concordant in only 7 (35%) cases. Seven cysts classified as mucinous with low-grade dysplasia by cytology were interpreted as nonmucinous on the basis of the PathfinderTG panel, 2 of which were resected mucinous cysts. Two pancreatitis-related pseudocysts were misdiagnosed as low-risk mucinous cysts; 1 mucinous cyst with low-grade dysplasia was considered at risk for neoplastic progression using the PathfinderTG panel. Only 1 cyst misclassified as pseudocyst by cytology, but low-risk mucinous cyst by molecular analysis, proved to be a mucinous cystic neoplasm with low-grade dysplasia after surgical resection. We conclude that the PathfinderTG panel may aid the classification of pancreatic lesions, but is often inaccurate and should not replace cytologic evaluation of these lesions.
Indeterminate findings on imaging-guided biopsy: should additional intervention be pursued?

OBJECTIVE Our purpose was to determine the outcome of patients in whom the results of imaging-guided biopsies were indeterminate and to examine factors that may affect outcome. MATERIALS AND METHODS During a 25-month period, 619 consecutive imaging-guided biopsies (CT, n = 268 [43%]; sonography, n = 351 [57%]) were performed on abdominal lesions. Of these biopsies, findings from 454 biopsies (73%) were positive for malignancy, findings from 21 biopsies (3%) yielded a benign diagnosis, and findings from 15 biopsies (2%) were nondiagnostic. Findings from the remaining 129 biopsies (21%) were considered indeterminate because the pathologic diagnosis revealed benign tissue, inflammation, stromal elements, or atypical cells. The frequency of malignancy in lesions of patients in this indeterminate group was determined. RESULTS Thirty-eight of the 129 patients were lost to follow-up. Of the remaining 91 patients, 55 (60%) had true-negative (benign) results, and 36 (40%) had false-negative (malignant) results. A history of malignancy had no significant effect on the true- or false-negative rate (p = .799). However, the guidance technique had a statistically significant effect: CT and sonographic guidance yielded 25 (49%) and 11 (28%) false-negative results, respectively (p = .037). The number of needle passes, needle type and gauge, and biopsy site did not have a statistically significant correlation with the false-negative rate. The presence of atypical cells in the cytologic aspirate was highly predictive, with a 71% false-negative rate (p = .008). CONCLUSION We found a high incidence of malignancy (40%) in lesions deemed indeterminate at the time of biopsy. Thus, close follow-up or additional intervention should be pursued in such cases. Sonographic guidance resulted in a statistically significant decrease in the false-negative rate when compared with CT guidance; however, a history of malignancy, the biopsy site, the needle gauge and type, and the number of passes did not have a significant effect on the false-negative rate.
Colonisation of the oral cavity by periodontopathic bacteria in complete denture wearers.

OBJECTIVE The purpose of this study was to investigate colonisation by periodontopathic bacteria and the sites of colonisation in elderly upper and lower complete denture wearers. We also investigated the relationship between level of oral hygiene and colonisation by periodontopathic bacteria. MATERIALS AND METHODS Forty edentulous and 37 dentate volunteers participated in this study. Samples were collected from whole saliva, and levels of Aggregatibacter actinomycetemcomitans, Prevotella intermedia, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia and Fusobacterium nucleatum were determined by PCR Invader technology. Detection of these species on oral mucosal and denture surfaces was performed by PCR. Fisher's exact test was used for the statistical analysis. Cluster analysis was employed to investigate trends in the periodontopathic bacteria flora in each sampling area. RESULTS Detection rates of periodontopathic bacteria in whole saliva were lower under edentulous conditions than under dentulous conditions, except for A. actinomycetemcomitans and F. nucleatum (p < 0.01). Detection rate of F. nucleatum was the highest in all areas. A positive correlation was observed between DNA quantification of P. gingivalis and number of Candida species in saliva. Cluster analysis of the test species identified two clusters. Tongue-coating status was associated with the detection rate of all periodontopathic bacteria investigated, and denture plaque status was associated with the detection rate of T. denticola and F. nucleatum. CONCLUSION Results indicate the presence of periodontopathic bacteria under edentulous conditions and that the status of oral hygiene of the mucosal or denture surfaces affects colonisation by T. denticola and F. nucleatum.
Tumor Suppressor Interferon-Regulatory Factor 1 Counteracts the Germinal Center Reaction Driven by a Cancer-Associated Gammaherpesvirus

ABSTRACT Gammaherpesviruses are ubiquitous pathogens that are associated with the development of B cell lymphomas. Gammaherpesviruses employ multiple mechanisms to transiently stimulate a broad, polyclonal germinal center reaction, an inherently mutagenic stage of B cell differentiation that is thought to be the primary target of malignant transformation in virus-driven lymphomagenesis. We found that this gammaherpesvirus-driven germinal center expansion was exaggerated and lost its transient nature in the absence of interferon-regulatory factor 1 (IRF-1), a transcription factor with antiviral and tumor suppressor functions. Uncontrolled and persistent expansion of germinal center B cells led to pathological changes in the spleens of chronically infected IRF-1-deficient animals. Additionally, we found decreased IRF-1 expression in cases of human posttransplant lymphoproliferative disorder, a malignant condition associated with gammaherpesvirus infection. The results of our study define an unappreciated role for IRF-1 in B cell biology and provide insight into the potential mechanism of gammaherpesvirus-driven lymphomagenesis. IMPORTANCE Gammaherpesviruses establish lifelong infection in most adults and are associated with B cell lymphomas. While the infection is asymptomatic in many hosts, it is critical to identify individuals who may be at an increased risk of virus-induced cancer. Such identification is currently impossible, as the host risk factors that predispose individuals toward viral lymphomagenesis are poorly understood. The current study identifies interferon-regulatory factor 1 (IRF-1) to be one of such candidate host factors. Specifically, we found that IRF-1 enforces long-term suppression of an inherently mutagenic stage of B cell differentiation that gammaherpesviruses are thought to target for transformation. Correspondingly, in the absence of IRF-1, chronic gammaherpesvirus infection induced pathological changes in the spleens of infected animals. Further, we found decreased IRF-1 expression in human gammaherpesvirus-induced B cell malignancies.
Aging and Social Networks in Spain: The Importance of Pubs and Churches

We examined whether the social convoy model and socioemotional selectivity theory apply in collectivistic cultures by examining the contextual factors which are hypothesized to mediate age-related differences in social support in a collectivist European country. Five hundred Spanish community-dwelling older adults (Mean age = 74.78, SD = 7.76, range = 60–93) were interviewed to examine structural aspects of their social networks. We found that age showed highly complex relationships with network size and frequency of interaction, depending on the network circle and the mediation of cultural factors. Family structure was important for social relations in the inner circle, while pubs and churches were important for peripheral relations. Surprisingly, pub attendance was the most important variable for maintenance of social support of peripheral network members. In general, the results support the applicability of the social convoy and socioemotional selectivity constructs to social support among Spanish older adults.
State production of cultural nationalism: political leaders and preservation policies for historic buildings in France and Italy

Although cultural and political nationalism have often been treated as separate, recent studies argue that they are linked because the state produces policies such as promotion of cultural heritage to further nation building. The article examines the conditions that favour national political leaders adopting policies to protect historic buildings for aims of political nationalism. It compares France and Italy, focusing on the period after 1870. It finds that in both countries, national political leaders have introduced extensive protection of historic buildings when faced with major challenges such as war, regime change or pressures from localism or supporters of cultural nationalism as part of wider strategies to build and reinforce the nation state. But Italy extended protection earlier and more deeply than France, suggesting in a later nation state with strong inherited cultural nationalism but major political weaknesses and, national political leaders may introduce earlier, more far-reaching and more layered legal protection than in states created earlier and with fewer weaknesses.
Evaluation of the Therapeutic Usefulness of Botulinum Neurotoxin B, C1, E, and F Compared with the Long Lasting Type A

Seven types (A–G) of botulinum neurotoxin (BoNT) target peripheral cholinergic neurons where they selectively proteolyze SNAP-25 (BoNT/A, BoNT/C1, and BoNT/E), syntaxin1 (BoNT/C1), and synaptobrevin (BoNT/B, BoNT/D, BoNT/F, and BoNT/G), SNARE proteins responsible for transmitter release, to cause neuromuscular paralysis but of different durations. BoNT/A paralysis lasts longest (4–6 months) in humans, hence its widespread clinical use for the treatment of dystonias. Molecular mechanisms underlying these distinct inhibitory patterns were deciphered in rat cerebellar neurons by quantifying the half-life of the effect of each toxin, the speed of replenishment of their substrates, and the degradation of the cleaved products, experiments not readily feasible at motor nerve endings. Correlation of target cleavage with blockade of transmitter release yielded half-lives of inhibition for BoNT/A, BoNT/C1, BoNT/B, BoNT/F, and BoNT/E (≫31, ≫25, ∼10, ∼2, and ∼0.8 days, respectively), equivalent to the neuromuscular paralysis times found in mice, with recovery of release coinciding with reappearance of the intact SNAREs. A limiting factor for the short neuroparalytic durations of BoNT/F and BoNT/E is the replenishment of synaptobrevin or SNAP-25, whereas pulse labeling revealed that extended inhibition by BoNT/A, BoNT/B, or BoNT/C1 results from longevity of each protease. These novel findings could aid development of new toxin therapies for patients resistant to BoNT/A and effective treatments for human botulism.
Group B Streptococcus colonization by HIV status in pregnant women: prevalence and risk factors.

OBJECTIVES To examine the prevalence of and risk factors for group B Streptococcus (GBS) colonization in an HIV-infected and uninfected pregnant population. METHODS We conducted a retrospective double cohort study comparing the prevalence of GBS colonization between 90 HIV-infected and 1947 uninfected women attending prenatal care at San Francisco General Hospital, an urban public hospital affiliated with the University of California, San Francisco. We investigated risk factors for GBS colonization, including age, ethnicity, obesity, diabetes, alcohol or illicit drug use, tobacco use, degree of immunosuppression, and infectious comorbidities. RESULTS In the multivariable analysis, HIV serostatus was not independently associated with GBS colonization (odds ratio [OR] 1.00, 95% confidence interval [CI] 0.62-1.62). Obesity (OR 1.53, 95% CI 1.13-2.07), white race (OR 1.89, 95% CI 1.30-2.75), and black race (OR 1.78, 95% CI 1.32-2.41) were independently associated with increased maternal GBS colonization. Among HIV-infected women, univariate analysis showed an association between GBS colonization and detectable HIV-1 plasma viral load at the time of rectovaginal culture (p<0.05). Mean CD4 lymphocyte count, infectious comorbidities, and HIV-1 plasma viral load at delivery were not associated with GBS colonization in HIV-infected pregnant women. CONCLUSIONS HIV-1 infection is not a risk factor for GBS colonization among an ethnically diverse pregnant population at San Francisco General Hospital, although our data suggest that among HIV-infected women, plasma HIV-1 viremia may be associated with GBS colonization. Interventions that diminish HIV-1 plasma viral load and, perhaps, genital tract shedding of HIV may be associated with a reduced risk of GBS colonization in future studies.
Brain Changes Following Executive Control Training in Older Adults

Background. While older adults are able to attend to goal-relevant information, the capacity to ignore irrelevant or distracting information declines with advancing age. This decline in selective attention has been associated with poor modulation of brain activity in sensory cortices by anterior brain regions implicated in cognitive control. Objective. Here we investigated whether participation in an executive control training program would result in improved selective attention and associated functional brain changes in a sample of healthy older adults (N = 24, age 60-85 years). Methods. Participants were enrolled in a goal-oriented attentional self-regulation (GOALS) program (n = 11) or a brain health education workshop as an active control condition (n = 13). All participants performed a working memory task requiring attention to or suppression of visual stimuli based on goal-relevance during functional magnetic resonance imaging. Results. We observed a pattern of enhanced activity in right frontal, parietal and temporal brain regions from pre- to posttraining in the GOALS intervention group, which predicted the selectivity of subsequent memory for goal-relevant stimuli. Conclusions. Executive control training in older adults alters functional activity in brain regions associated with attentional control, and selectively predicts behavioral outcome.
Acute Sleep Restriction Reduces Insulin Sensitivity in Adolescent Boys.

BACKGROUND Short sleep duration has been linked to impaired glucose metabolism in many experimental studies. Moreover, studies have reported indications of an increased metabolic stress following sleep restriction. OBJECTIVE We aimed to investigate the effects of partial sleep deprivation on markers of glucose metabolism. Additionally, we aimed to investigate if short sleep duration induces a state of endocrine stress. DESIGN A randomized crossover design, with 2 experimental conditions: 3 consecutive nights of short sleep (SS, 4 h/night) and long sleep (LS, 9 h/night) duration. SUBJECTS AND MEASUREMENTS In 21 healthy, normal-weight male adolescents (mean ± SD age: 16.8 ± 1.3 y) we measured pre- and post-prandial glucose, insulin, C-peptide, and glucagon concentrations. Furthermore, we measured fasting cortisol, 24-h catecholamines, and sympathovagal balance. RESULTS Fasting insulin was 59% higher (P = 0.001) in the SS than the LS condition as was both fasting (24%, P < 0.001) and post-prandial (11%, P = 0.018) C-peptide. Pre- and post-prandial glucose and glucagon were unchanged between conditions. The homeostasis model assessment of insulin resistance (HOMA-IR) index was 65% higher (P = 0.002) and the Matsuda index was 28% lower (P = 0.007) in the SS condition compared to the LS condition. The awakening cortisol response and 24-h norepinephrine were not affected by sleep duration, whereas 24-h epinephrine was 24% lower (P = 0.013) in the SS condition. Neither daytime nor 24-h sympathovagal balance differed between sleep conditions. Short wave sleep was preserved in the SS condition. CONCLUSION Short-term sleep restriction is associated with decreased insulin sensitivity in healthy normal-weight adolescent boys. There were no indications of endocrine stress beyond this. CITATION Klingenberg L; Chaput JP; Holmbäck U; Visby T; Jennum P; Nikolic M; Astrup A; Sjödin A. Acute Sleep Restriction Reduces Insulin Sensitivity in Adolescent Boys. SLEEP 2013;36(7):1085-1090.
Evaluating competing perspectives towards undeclared work: some lessons from Bulgaria

ABSTRACT When explaining and tackling the undeclared economy in Central and Eastern Europe, participants have been conventionally viewed as rational economic actors. They engage in undeclared work when the benefits outweigh the costs. Participation is thus deterred by increasing the sanctions and/or probability of being caught. Recently, however, an alternative social actor approach has emerged which views participants as engaging in undeclared work when their norms, values and beliefs (i.e. citizen morale) do not align with laws and regulations (i.e. state morale). Here, therefore, initiatives to develop greater symmetry between civic and state morale are pursued. To evaluate the validity and effectiveness of these competing explanations and policy approaches, 2,004 face-to-face interviews conducted in Bulgaria in late 2015 are reported. Logit marginal effects regression analysis reveals no association between participation in undeclared work and the perceived level of penalties and risk of detection, but a strong significant association with the level of asymmetry between citizen and state morale; the greater the asymmetry, the higher is the likelihood of participation in undeclared work. The paper concludes by discussing the implications for explaining and tackling undeclared work.
Sound‐evoked network calcium transients in mouse auditory cortex in vivo

Non‐technical summary The coherent activity of a large number of neurons forming functional cell assemblies crucially contributes to neuronal information processing in the brain. It is believed that activity of such populations constitutes a key mechanism linking awareness, stimuli from the external world, memory and behaviour. In this study, we recorded population calcium signals in the auditory cortex of mice using an optical fibre. We found that the population activity was dominated by transients lasting ∼1 s. These calcium transients directly reflected the action potential firing of local clusters of neurons and occurred spontaneously as well as in response to sound stimulation. We characterized in detail the spontaneous and sound‐evoked calcium signals and the relation between the two. Thus, we were able to identify population calcium transients as an important element of sensory signalling.
Treatment Outcomes in Very High-risk Prostate Cancer Treated by Dose-escalated and Combined-Modality Radiation Therapy

Objectives:The aim of this study was to report treatment outcomes in patients with very high-risk prostate cancer (VHRPC) treated with dose-escalated radiotherapy. Methods:We conducted a retrospective multi-institutional review on patients with VHRPC (those with at least 2 high-risk factors of prostate-specific antigen >20 ng/mL, Gleason score 8 to 10, or clinical T3 to T4 stage), treated with either dose-escalated external-beam radiotherapy (EBRT) or combined-modality radiotherapy (CMRT) consisting of pelvic irradiation and permanent interstitial brachytherapy. Results:A total of 238 patients with VHRPC were identified. Of them, 69% of patients received EBRT and 31% received CMRT; 88% received androgen-deprivation therapy (ADT), 56% for ≥24 months (long-term ADT). The majority (69%) of patients were above 65 years old and were less likely to receive CMRT than younger patients (25% vs. 43%, P=0.006), although they did not differ from younger patients in tumor characteristics. Median follow-up was 61 months (interquartile range, 38 to 93 mo). Biochemical progression-free survival (BPFS), distant metastasis-free survival (DMFS), and cancer-specific survival (CSS) for all patients at 8 years were (±SE): 50.6%±4.7%, 68.5%±4.3%, 78.7%±3.8%, respectively, and were similar for patients 65 years and below versus above 65 years old (BPFS: HR=0.88, P=0.56; DMFS: HR=0.79, P=0.40; CSS HR=0.99, P=0.99). After adjustment for patient, tumor, and treatment-related covariates on multivariate analysis, CMRT was associated with improved BPFS (HR=0.44, P=0.012) with trends for DMFS (HR=0.52, P=0.10) and CSS (HR=0.55, P=0.21), whereas long-term ADT was independently associated with improved BPFS (HR=0.40, P=0.019), CSS (HR=0.20, P=0.002), and PCSM (HR=0.25, P=0.004). Conclusions:Dose-escalated EBRT or CMRT with long-term ADT resulted in favorable clinical outcomes for patients with VHRPC.
Panel Data Estimation in Finance: Testable Assumptions and Parameter (In)Consistency

We investigate the strict-exogeneity assumption, a necessary condition for estimator consistency in many finance panel-data applications. We outline tests for strict exogeneity in both traditional (non–instrumental variable (IV)) and IV settings. When we apply these tests in common traditional finance panel regressions, we find that the strict-exogeneity assumption is often strongly rejected, suggesting large inference errors. We test for strict exogeneity in specific finance panel-data IV settings and illustrate the potential for these tests to help confirm, or rule out, the validity of common panel-data IV estimators. We offer recommendations to address the strict-exogeneity issue in finance research.