Miracle-dz/UniFAR-FTUs huggingface dataset:
The transcription factor osterix (SP7) regulates BMP6‐induced human osteoblast differentiation

The transcription factor Osterix (Sp7) is essential for osteoblastogenesis and bone formation in mice. Genome wide association studies have demonstrated that Osterix is associated with bone mineral density in humans; however, the molecular significance of Osterix in human osteoblast differentiation is poorly described. In this study we have characterized the role of Osterix in human mesenchymal progenitor cell (hMSC) differentiation. We first analyzed temporal microarray data of primary hMSC treated with bone morphogenetic protein‐6 (BMP6) using clustering to identify genes that are associated with Osterix expression. Osterix clusters with a set of osteoblast‐associated extracellular matrix (ECM) genes, including bone sialoprotein (BSP) and a novel set of proteoglycans, osteomodulin (OMD), osteoglycin, and asporin. Maximum expression of these genes is dependent upon both the concentration and duration of BMP6 exposure. Next we overexpressed and repressed Osterix in primary hMSC using retrovirus. The enforced expression of Osterix had relatively minor effects on osteoblastic gene expression independent of exogenous BMP6. However, in the presence of BMP6, Osterix overexpression enhanced expression of the aforementioned ECM genes. Additionally, Osterix overexpression enhanced BMP6 induced osteoblast mineralization, while inhibiting hMSC proliferation. Conversely, Osterix knockdown maintained hMSC in an immature state by decreasing expression of these ECM genes and decreasing mineralization and hMSC proliferation. Overexpression of the Osterix regulated gene OMD with retrovirus promoted mineralization of hMSC. These results suggest that Osterix is necessary, but not sufficient for hMSC osteoblast differentiation. Osterix regulates the expression of a set of ECM proteins which are involved in terminal osteoblast differentiation. J. Cell. Physiol. 227: 2677–2685, 2012. © 2011 Wiley Periodicals, Inc.
Displacement behaviour regulates the experience of stress in men

Behavioural coping strategies represent a key means by which people regulate their stress levels. Attention has recently focused on the potential role in coping of ‘displacement behaviour’ – activities such as scratching, lip biting and face touching. Increased levels of displacement behaviour are associated with feelings of anxiety and stress; however, the extent to which displacement behaviour, as a short-term behavioural response to emotionally challenging stimuli, influences the subsequent experience of stress remains poorly understood. The aim of this study was to investigate the potential role of displacement behaviour in coping with stress. In a study population of 42 healthy adult men (mean age = 28.09 years, SD = 7.98), we quantified displacement behaviour during a Trier Social Stress Test (TSST), and used self-report questionnaires to assess trait and state anxiety before the TSST, and the experience of stress afterwards. We predicted displacement behaviour would diminish the negative impact of the stressful situation, and hence be associated with lower post-TSST stress levels. Furthermore, we predicted displacement behaviour would mediate the link between state and trait anxiety on the one hand and the experience of stress on the other. Results showed the rate of displacement behaviour was positively correlated with state anxiety but unrelated to trait anxiety, and negatively correlated with the self-reported experience of stress, in agreement with the idea that displacement behaviour has a crucial impact on regulation of stress. Moreover, serial mediation analyses using a bias-corrected bootstrapping approach indicated displacement behaviour mediated the relationship between state anxiety and the experience of stress, and that state anxiety and displacement behaviour – in combination, respectively – mediated the link between trait anxiety and experience of stress. These results shed important new light on the function of displacement behaviour, and highlight promising new avenues for research into emotional expression and stress regulation.
Aromatic DNA adducts and breast cancer risk: a case-cohort study within the EPIC-Spain

Epidemiologic evidence linking environmental exposure to polycyclic aromatic hydrocarbons (PAH) with breast cancer is limited. Measurement of DNA adducts formed by aromatic compounds, including PAH, has been carried in breast tissue samples and white blood cells from women with breast cancer and different kinds of controls. However, these studies provide inconsistent results and bias cannot be ruled out. During the 7-year follow-up period, 305 women were diagnosed with first primary breast cancer in the EPIC-Spain cohort, and were compared with a sample of 149 women without breast cancer at recruitment, using a case-cohort approach. Aromatic adducts to DNA from leukocytes collected at recruitment were measured by means of the 32P-post-labelling technique. The relative risk and 95% confidence interval (CI), adjusted by relevant confounders, were estimated by a modified version of Cox proportional hazards model. There was a significant increased risk for developing breast cancer when DNA adduct concentrations were doubled, with adjusted RR of 1.61 (95% CI 1.29-2.01). The increase in breast cancer risk was observed both for pre- and post-menopausal women. There was a significant interaction with tobacco smoking and body mass index, with higher effect of DNA adducts on breast cancer risk among smokers and women with normal weight. The results from our study support the hypothesis that factors leading to higher levels of aromatic DNA adducts in white blood cells may be involved in development of breast cancer.
Components of nucleotide excision repair and DNA damage tolerance in Arabidopsis thaliana

As obligate phototrophs, and despite shielding strategies, plants sustain DNA damage caused by UV radiation in sunlight. By inhibiting DNA replication and transcription, such damage may contribute to the detrimental effects of UV radiation on the growth, productivity, and genetic stability of higher plants. However, there is evidence that plants can reverse UV‐induced DNA damage by photoreactivation or remove it via nucleotide excision repair. In addition, plants may have mechanisms for tolerating UV photoproducts as a means of avoiding replicative arrest. Recently, phenotypic characterization of plant mutants, functional complementation studies, and cDNA analysis have implicated genes isolated from the model plant Arabidopsis thaliana in nucleotide excision repair or tolerance of UV‐induced DNA damage. Here, we briefly review features of these processes in human cells, collate information on Arabidopsis homologs of the relevant genes, and summarize the experimental findings that link certain of these plant genes to nucleotide excision repair or damage tolerance. Environ. Mol. Mutagen. , 2005. © 2005 Wiley‐Liss, Inc.
Hepatitis C Virus Infection and de Novo Glomerular Lesions in Renal Allografts

In the present study we examine whether hepatitis C virus (HCV) infection status influences glomerular pathologic findings in renal allografts and its effect on graft outcome. Renal allograft biopsies performed between January 1991 and June 1999 were considered. Exclusion criteria were insufficient sample, unknown HCV serological status at time of biopsy and final diagnosis of acute rejection. Light microscopy and immunofluorescence studies were performed on all biopsies. According to a predefined protocol, electron microscopy was carried out. Of 138 eligible renal allograft biopsies, 42 fulfilled at least one exclusion criterion. Of 96 biopsies selected for the study, 44 (45.8%) were from HCV‐positive and 52 from HCV‐negative recipients. Renal biopsy was performed 74 ± 55 and 60 ± 39 months after transplantation in HCV‐positive and HCV‐negative groups, respectively (p = 0.12). Of 44 HCV‐positive biopsies, 20 (45.4%) showed membranoproliferative glomerulonephritis (MPGN) (16 type I and 4 type III). Conversely, in HCV‐negative biopsies there were only three cases of MPGN (2 type I and 1 type III). De novo membranous GN (MGN) was diagnosed in 8/44 (18.2%) HCV‐positive and in 4/52 (7.7%) HCV‐negative cases. The prevalence of chronic transplant glomerulopathy was similar in HCV‐positive and HCV‐negative groups (11.4% and 11.5%, respectively). The prognosis of de novo GN (either MPGN or MGN) was worse in HCV‐positive than in HCV‐negative recipients (relative risk 4.89; 95% confidence interval, 1.15–20.69; p = 0.03). By multivariate analysis, HCV‐positive serology infection was the only independent predictor of graft loss (relative risk 2.64; 95% confidence interval, 1.35–5.17; p = 0.005). In diagnostic renal allograft biopsies the presence of de novo immune‐mediated glomerulonephritis, especially type I MPGN, is strongly associated with HCV infection and results in accelerated loss of the graft.
hnRNP proteins and the biogenesis of mRNA.

II. THE hnRNP PROTEINS . Definition and Experimental Criteria . Human . Other Organisms . Posttranslational Modifications .
Pneumococcal Capsules and Their Types: Past, Present, and Future

SUMMARY Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.
SOFT‐MI: A novel microfabrication technique integrating soft‐lithography and molecular imprinting for tissue engineering applications

An innovative approach has been employed for the realization of bioactive scaffolds able to mimic the in vivo cellular microenvironment for tissue engineering applications. This method is based on the combination of molecular imprinting and soft‐lithography technology to enhance cellular adhesion and to guide cell growth and proliferation due to presence of highly specific recognition sites of selected biomolecules on a well‐defined polymeric microstructure. In this article polymethylmethacrylate (PMMA) scaffolds have been realized by using poly(dimethylsiloxane) (PDMS) microstructured molds imprinted with FITC‐albumin and TRITC‐lectin. In addition gelatin, an adhesion protein, was employed for the molecular imprinting of polymeric scaffolds for cellular tests. The most innovative aspect of this research was the molecular imprinting of whole cells for the development of substrates able to enhance the cell adhesion processes. Biotechnol. Bioeng. 2010;106: 804–817. © 2010 Wiley Periodicals, Inc.
Dental Status and Oral Hygiene in Patients with Head and Neck Cancer

Poor oral hygiene is believed to play a role as a risk factor for head and neck cancer, especially for oral cancer. Only few epidemiologic data exist about dental status and oral hygiene in these patients. We performed a case-control study involving 100 patients with squamous cell carcinoma of the upper aerodigestlve tract and 214 age- and sex-matched control subjects with no known tumorous disease. In the tumor patients, oral hygiene and dental status proved to be significantly worse: The majority of the tumor patients seldom or never brushed their teeth and the frequency of dental visits was significantly lower. Tartar of 3 mm or more was found in 40.9% of the tumor patients and in 22% of the control subjects. In the tumor group, the incidence of decayed teeth was significantly higher compared with the control subjects. Chronic Inflammation of the gingiva was observed in 28% of the tumor patients vs. 13.5% in the control gorup. Oral hygiene was negatively correlated with alcohol as well as with tobacco consumption. The social status of subjects also correlated with oral hygiene, which was found to be worst in subjects from the lower social strata. The present study revealed a poor dental status and oral hygiene in patients with head and neck cancer. The pathogenetic mechanism being associated with this suspected risk factor remains to be investigated.
Immunocyte Enumeration in Duodenal Biopsies of Migraine Without Aura Patients With or Without Food-Induced Migraine

The possibility of an IgE-mediated allergic mechanism in food-induced migraine remains controversial. Twenty consecutive migraine patients, 11 with food-induced migraine, 9 without, were investigated for determination and counting of immunocyte populations (IgA, IgM, IgE, IgG containing cells) by biopsies at duodenum 2 level. Conventional histology and plasmocyte populations were not significantly different between the two groups of migraine patients. This study does not support the existence of an IgE-mediated allergic mechanism in food-induced migraine.
Retrieval, experimental, and computational assessment of the performance of total knee replacements

Wear mechanisms in polyethylene components for total knee replacements are inherently mechanical; the local stresses or strains exceed some material limit. Retrieval analysis and knee simulators have provided the means to quantify the damage observed in vivo or in vitro. These results have been circumstantially linked to the material stresses obtained from computational simulations using finite element analysis, knee simulator tests, and computational simulations of two condylar knee designs. We hypothesize that if an equivalent loading environment is produced in the computational simulation, we can correlate the distribution of computed stresses with observed damage of simulator specimens and further relate design differences to in vivo performance from retrieval analyses. The finite element model agreed with the knee simulator kinematics and kinetics within 2–13%, and composite FEA contact areas matched 66–90% of the damage areas due to burnishing on the simulator specimens. Burnishing was the primary mode of damage for both the simulator and retrieval specimens corresponding with the relatively low magnitudes of contact stress observed. Both the computational and experimental techniques underpredicted the amount determined from retrieval analysis, but the differences between the two designs were consistent for all three methods. Combining these techniques strengthens the applicability of the computational simulation while highlighting the complementary approach of these methods for preclinical testing and assessing the link between material state and damage. © 2006 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 24:1384–1394, 2006
The Effect of Age on Short-term Outcomes After Pancreatic Resection: A Population-based Study

Objective:To use a large population-based cohort to determine age-dependent short-term outcomes after pancreatic resection. Methods:We identified all pancreatic resections in Texas from 1999 to 2005. Patients were stratified into 4 age groups (<60, 60–69, 70–79, and 80+ years). Bivariate and multivariate analyses were performed to determine the effect of age on mortality, discharge to home versus requiring inpatient nursing care, and length of stay. Results:Three thousand seven hundred and thirty-six patients underwent pancreatic resection. Unadjusted in-hospital mortality increased with each increasing age group from 2.4% in patients <60 to 11.4% in patients 80 years and older (P < 0.0001). Likewise, postoperative lengths of stay increased with each increasing age group (P = 0.02). Age group independently predicted the need for discharge to an inpatient nursing unit rather than home (P < 0.0001), with the odds ration (OR) increasing with each increasing age group. With each increasing age group, patients were less likely to be resected at high-volume (H-V) hospitals (>10 pancreatic resections/y). Whereas low-volume (L-V) hospitals (≤10 pancreatic resections/y) had higher mortality rates (3.2% versus 7.3%, P < 0.0001), the difference in mortality between H- and L-V hospitals was more striking in older patients. With increasing age group, mortality increased from 3.0% to 9.5% to 11.4% to 14.7% at L-V hospitals. It increased from 2.0% to 3.5% to 4.5% to 8.7% at H-V hospitals (P < 0.0001). In the multivariate model controlling for gender, race, hospital volume, year of surgery, diagnosis, risk of mortality, severity of illness, admission status, and procedure type, older age group independently predicted increased mortality. The OR for patients 60–69 years was 2.5 (P = 0.0003), the OR for patients 70–79 years was 1.8 (P = 0.02), and the OR for patients 80+ years was 4.4 (P < 0.0001) when compared with patients <60 years. Conclusions:In contrast to some previous single-institution studies, we found that increased age is an independent risk factor for mortality after pancreatic resection. For all ages, mortality rates were higher at L-V hospitals, but the difference worsened significantly with increasing age. Older patients had longer lengths of stay, were less likely to be discharged home, and more likely to require care at an inpatient nursing or acute care facility at the time of discharge.
Malware Detection based on Graph Classification

Malware detection is nowadays a big challenge. The existing techniques for malware detection require a huge effort of engineering to manually extract the malicious behaviors. To avoid this tedious task of manually discovering malicious behaviors, we propose in this paper to apply learning for malware detection. Given a set of malwares and a set of benign programs, we show how learning techniques can be applied in order to detect malware. For that, we use abstract API graphs to represent programs. Abstract API graphs are graphs whose nodes are API functions and whose edges represent the order of execution of the different calls to the API functions (i.e., functions supported by the operating system). To learn malware, we apply well-known learning techniques based on Random Walk Graph Kernel (combined with Support Vector Machines). We can achieve a high detection rate with only few false alarms (98.93% for detection rate with 1.24% of false alarms). Moreover, we show that our techniques are able to detect several malwares that could not be detected by wellknown and widely used antiviruses such as Avira, Kaspersky, Avast, Qihoo-360, McAfee, AVG, BitDefender, ESET-NOD32, F-Secure, Symantec or Panda.
Achieving High Adolescent HPV Vaccination Coverage

BACKGROUND AND OBJECTIVE: Despite national recommendations for adolescent human papillomavirus (HPV) vaccination, rates have lagged behind those of other adolescent vaccines. We implemented interventions and examined rates of vaccination coverage in a large, urban, safety net health care system to understand whether our tactics for achieving high rates of adolescent vaccination were successful. METHODS: Denver Health is an integrated urban safety net health system serving >17 000 adolescents annually. The process for achieving high vaccination rates in our health system includes “bundling” of vaccines, offering vaccines at every visit, and standard orders. Data from vaccine registry and utilization statistics were used to determine vaccination rates in adolescents aged 13 to 17 years from 2004 to 2014, and these findings were compared with state and national rates for 2013. Regression analysis was used to identify characteristics associated with vaccination. RESULTS: In 2013 (N = 11 463), HPV coverage of ≥1 dose was 89.8% (female subjects) and 89.3% (male subjects), compared with national rates of 57.3% and 34.6%. Rates of HPV coverage (≥3 doses) were 66.0% for female subjects and 52.5% for male subjects, versus 37.6% and 13.9% nationally. For both sexes, tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis, adsorbed, vaccine coverage was 95.9% (86.0% nationally), and meningococcal conjugate vaccine coverage was 93.5% (77.8% nationally). Female subjects, Hispanic subjects, non-English speakers, and teenagers <200% below the federal poverty level were more likely to have received 3 doses of HPV. CONCLUSIONS: Through low-cost, system-wide standard procedures, Denver Health achieved adolescent vaccination rates well above national coverage rates. Avoiding missed opportunities for vaccination and normalizing the HPV vaccine were key procedures that contributed to high coverage rates.
Elevated Variance in Heart Rate During Slow-Wave Sleep After Late-Night Physical Activity

This study investigates the effect of mild physical activity before bedtime on the sleep pattern and heart rate during the night. Nine healthy subjects underwent a habituation night, a reference night, and a physical induction night. The physical induction night did not alter the sleep pattern. Physical activity before bedtime resulted in higher heart rate variance during slow-wave sleep. The low-frequency/high-frequency component (LF/HF) ratio during slow-wave sleep in the physical induction night was significantly higher than during the reference night. Increased mean heart rate and higher LF/HF ratio are related to decreased parasympathetic dominance. Exercise up to 1 h before bedtime thus seems to modify the quality of sleep. (Author correspondence: Daniel.Berckmans@biw.kuleuven.be)
Multijam Solutions in Traffic Models with Velocity-Dependent Driver Strategies

The optimal-velocity follow-the-leader model is augmented with an equation that allows each driver to adjust their target headway according to the velocity difference between the driver and the car in front. In this more detailed model, which is investigated on a ring, stable and unstable multipulse or multijam solutions emerge. Analytical investigations using truncated Fourier analysis are confirmed and complemented by a detailed numerical bifurcation analysis. In addition to standard rotating waves, time-modulated waves are found.