Miracle-dz/UniFAR-FTUs huggingface dataset:
Racial Differences in Outcomes within the National Lung Screening Trial. Implications for Widespread Implementation.

RATIONALE Black individuals with lung cancer (LC) experience higher mortality because they present with more advanced disease and are less likely to undergo curative resection for early-stage disease. The National Lung Screening Trial (NLST) demonstrated improved LC mortality by screening high-risk patients with low-dose computed tomography (LDCT). The benefit of LDCT screening in black individuals is unknown. OBJECTIVES Examine results of the NLST by race. METHODS This was a secondary analysis of a randomized trial (NCT00047385) performed in 33 U.S. centers. MEASUREMENTS AND MAIN RESULTS Overall and lung cancer-specific mortality were measured. Screening with LDCT reduced LC mortality in all racial groups but more so in black individuals (hazard ratio [HR], 0.61 vs. 0.86). Smoking increased the likelihood of death from LC, and when stratified by race black smokers were twice as likely to die as white smokers (HR, 4.10 vs. 2.25). Adjusting for sociodemographic and behavioral characteristics, black individuals experienced higher all-cause mortality than white individuals (HR, 1.35; 95% confidence interval, 1.22-1.49); however, black individuals screened with LDCT had a reduction in all-cause mortality. Black individuals were younger, were more likely to be current smokers, had more comorbidities, and had fewer years of formal education than white individuals (P < 0.05). CONCLUSIONS Black individuals screened with LDCT had decreased mortality from lung cancer. However, the demographics associated with improved LC survival were less commonly found in black individuals. The overall mortality in the NLST was higher for black individuals than white individuals, but improved in black individuals screened, suggesting that this subgroup may have had improved access to care. To realize the reductions in mortality from LC screening, dissemination efforts need to be tailored to meet the needs of this community.
Aquaporin-1 Promoter Hypermethylation Is Associated with Improved Prognosis in Salivary Gland Adenoid Cystic Carcinoma

Objectives Aquaporin-1 (AQP1) is a candidate oncogene that is epigenetically modified in adenoid cystic carcinoma (ACC). We sought to (1) assess AQP1 promoter methylation and expression in an ACC cohort, (2) identify correlations between AQP1 and clinical outcomes, and (3) explore the role of AQP1 in tumor progression in vitro. Study design Laboratory study, retrospective chart review. Setting Academic medical center. Methods DNA and RNA were isolated from ACC tumors and control salivary gland tissues. Quantitative methylation-specific polymerase chain reaction (PCR) was performed on bisulfite-treated DNA. Quantitative reverse transcription PCR was performed after cDNA synthesis. Cell lines stably overexpressing an AQP1 plasmid or empty vector were generated. Cell scratch and Matrigel invasion assays were performed. Retrospective chart review was performed for collection of clinical information. Results Methylation results from 77 tumors and 30 controls demonstrated that AQP1 was hypomethylated in tumors (P < .0001). Fifty-eight tumors (75.3%) displayed AQP1 hypomethylation compared with controls. AQP1 expression levels assessed in 58 tumors and 23 controls demonstrated a trend toward increased expression in tumors (P = .08). Univariate analysis revealed that AQP1 hypermethylation was associated with increased overall survival. No associations between AQP1 expression level and survival were found. AQP1 overexpression did not affect cell migratory or invasive capacities in vitro. Conclusion AQP1 promoter hypomethylation is common in ACC, and AQP1 tends to be overexpressed in these tumors. Increased AQP1 methylation is associated with improved prognosis on univariate analysis, but expression is not associated with outcomes. Further in vitro studies are necessary to clarify the role of AQP1 in ACC.
Transcriptional Repression from the c-myc P2 Promoter by the Zinc Finger Protein ZF87/MAZ*

ZF87/MAZ is a zinc finger-containing transcription factor that was cloned based on its ability to bind to a site within the c-myc P2 promoter. However, its role in the control of c-myc transcription has not yet been well established. Here we have analyzed the effect of ZF87/MAZ overexpression on transcription from the murine c-myc P2 promoter. It was found that when overexpressed in COS cells, ZF87/MAZ significantly represses transcription from P2. The repression is mediated through the ME1a2 element, located at position −86 relative to the P2 transcriptional start site, and is not mediated through either the E2F or the ME1a1 sites. ZF87/MAZ functions as a true transcriptional repressor since it can repress transcription independently of the c-myc promoter, as part of a fusion with the GAL4 protein. The repressive domain within ZF87/MAZ is located in the amino-terminal half of the protein, a region rich in proline and alanine residues. ZF87/MAZ therefore shares features (i.e.a Pro/Ala-rich region) with those of known transcriptional repressor proteins.
Data mining information visualisation - beyond charts and graphs

Data mining has become a major academic research area over the last ten years. However, in the transition from academic prototypes to commercial products there have been few successes with commercial data mining applications failing to make any significant impact in the marketplace. In this paper it is argued that most data mining applications concentrate on the model-building phase of the data mining process and rarely engage the user in other stages. The paper reviews the challenges of producing successful data mining applications and in particular the role of information visualisation. Visualisation in data mining tends to be used to present final results, rather than playing an important part throughout the entire process. We argue that an immersive environment may provide the user with a more suitable interface than is commonly offered. We present a virtual data mining environment which attempts to integrate a data mining application interface and information visualisation in a seamless manner, using the concept of 'liquid data'.
Ethnography of software maintenance activities in an industrial engineering setup

New technical and procedural interventions are less likely to be adopted in industry, unless they are smoothly integrated into the existing practices of professionals. In this paper, we provide a case study of the use of ethnographic methods for studying software bug-fixing activities at an industrial engineering conglomerate. We aimed at getting an in-depth understanding of software developers' everyday practices in bug-fixing related projects and in turn inform the design of novel productivity tools. The use of ethnography has allowed us to look at the social side of software maintenance practices. In this paper, we highlight 1) organizational issues that influence bug-fixing activities, 2) social role of bug tracking systems, and 3) social issues specific to different phases of bug-fixing activities.
Searching for blood DNA methylation markers of breast cancer risk and early detection.

In this issue of the Journal, Xu et al. (1) used prospectively collected blood samples to determine whether epigenome-wide methylation profiles in blood DNA differ between women who subsequently develop breast cancer and those who do not. Potentially, such a profile could predict the risk of developing breast cancer or detect this disease days to several years before it appears clinically. Existing breast cancer risk prediction models have limited discriminatory accuracy for this common disease (2), and improved methods for early detection are also needed (3,4). In this context, the findings of Xu et al. are promising and exemplify the potential value of epigenome-wide association studies (5,6). However, several important considerations temper the initial enthusiasm and highlight challenges for future studies.
Structure of an early native‐like intermediate of β2‐microglobulin amyloidogenesis

To investigate early intermediates of β2‐microglobulin (β2m) amyloidogenesis, we solved the structure of β2m containing the amyloidogenic Pro32Gly mutation by X‐ray crystallography. One nanobody (Nb24) that efficiently blocks fibril elongation was used as a chaperone to co‐crystallize the Pro32Gly β2m monomer under physiological conditions. The complex of P32G β2m with Nb24 reveals a trans peptide bond at position 32 of this amyloidogenic variant, whereas Pro32 adopts the cis conformation in the wild‐type monomer, indicating that the cis to trans isomerization at Pro32 plays a critical role in the early onset of β2m amyloid formation.
Elements involved in oxygen regulation of the Saccharomyces cerevisiae CYC7 gene

The CYC7 gene of Saccharomyces cerevisiae encodes the minor species, iso-2, of the cytochrome c protein. Its expression is governed by two regulatory sequences upstream from the gene: a positive site which stimulates transcription 240 base pairs 5' from the protein-coding sequence (-240) and a negative site which inhibits transcription at -300. In this study, the nature of the positive site and its relationship to the negative site has been investigated. Expression of the CYC7 gene is weakly inducible by oxygen. This effect was greatly enhanced by the semidominant CYP1-16 mutation in the trans-acting gene CYP1. The weak oxygen regulation in wild-type cells and the enhanced induction in CYP1-16 mutants were found to be mediated through the positive site. A mutational analysis of this site implicated at least part of a tandem, direct repeat of 9 base pairs as essential for the functioning of this site. The relationship between the positive and negative sites was investigated by comparing the expression of the intact gene with that of derivatives lacking either one or the other site. The expression of the gene containing only the negative site was actually stimulated anaerobically, while the gene containing the positive site alone, although having higher expression aerobically than anaerobically, had higher anaerobic expression than did the intact gene. Thus, it appeared that the combination of the positive and negative sites suppressed anaerobic expression. A model which attempts to explain these properties of the two sites and account for the regulation of the expression of the intact gene is presented.
Increasing Diversity within Chlamydiae

In recent years, 16S ribosomal DNA analyses has allowed the recognition of new chlamydia organisms, requiring the creation of new species, genera, and families within this unique, deep lineage of prokaryotes. The trachoma and psittaci groups chlamydiae are now recognized as separate genera, Chlamydia and Chlamydophila, respectively, and biovars of each group have been elevated to the species rank. Simkania and Parachlamydia have been associated with human respiratory infections, while Waddlia seems to be implicated in abortion in bovins. DNA amplification studies targeting the 16S rDNA have revealed a richer diversity within chlamydiae, identifying new lineages from both environmental and clinical samples. Further studies will be of interest to both examine the ecology and evaluate the clinical importance of these novel chlamydiae. Herein, we provide a summary of literature and our data about the novel chlamydial lineages.
Production of Skatole and para-Cresol by a Rumen Lactobacillus sp

The objective of this study was to examine the substrate specificity of several ruminal strains of a Lactobacillus sp. which previously was shown to produce skatole (3-methylindole) by the decarboxylation of indoleacetic acid. A total of 13 compounds were tested for decarboxylase activity. The Lactobacillus strains produced p-cresol (4-methylphenol) by the decarboxylation of p-hydroxyphenylacetic acid, but did not produce either o-cresol or m-cresol from the corresponding hydroxyphenylacetic acid isomers. These strains also decarboxylated 5-hydroxyindoleacetic acid to 5-hydroxyskatole and 3,4-dihydroxyphenylacetic acid to methylcatechol. Skatole and p-cresol were produced in a 0.5:1 ratio, when indoleacetic acid and p-hydroxyphenylacetic acid were combined in equimolar concentrations. Competition studies with indoleacetic acid and p-hydroxyphenylacetic acid suggested that two different decarboxylating enzymes are involved in the production of skatole and p-cresol by these strains. This is the first demonstration of both skatole production and p-cresol production by a single bacterium.
Virus‑like particles as a vaccine delivery system: Myths and facts

Vaccines against viral disease have traditionally relied on attenuated virus strains or inactivation of infectious virus. Subunit vaccines based on viral proteins expressed in heterologous systems have been effective for some pathogens, but have often suffered from poor immunogenicity due to incorrect protein folding or modification. In this review we focus on a specific class of viral subunit vaccine that mimics the overall structure of virus particles and thus preserves the native antigenic conformation of the immunogenic proteins. These virus‑like particles (VLPs) have been produced for a wide range of taxonomically and structurally distinct viruses, and have unique advantages in terms of safety and immunogenicity over previous approaches. With new VLP vaccines for papillomavirus beginning to reach the market place we argue that this technology has now ‘come‑of‑age’ and must be considered a viable vaccine strategy.
A 1V 19.3dBm 79GHz power amplifier in 65nm CMOS

For a highly integrated wireless system including on-chip antennas, high-output- power power amplifiers (PA) are required to cover the desired transmission range. In order to achieve the output power level, power-combining techniques have gained more attention in recent years [1-5]. An efficient power-combining solution is essential since less DC power is needed for the same level of output power, and the difficulties of thermo-dissipation are thus relieved in a high-out- put-power PA. Transformer-based power combining is one of the common tech- niques, which can increase impedance-transformation ratio by increasing the number of input ports and results in a compact layout and reasonable loss [1-3, 5].
Incidence of infectious complications after an ultrasound-guided intervention.

OBJECTIVE The objective of our study was to determine the incidence of infectious complications of common ultrasound-guided procedures including fine-needle aspiration (FNA), drain placement, biopsy, pseudoaneurysm thrombin injection, thoracentesis, and paracentesis. SUBJECTS AND METHODS The infection prevention and control (IPAC) committee at the Mayo Clinic, Rochester, MN, conducts surveillance of selected infections including radiology procedures. When a positive culture, hospital admission, or operating room visit for infection is identified, the patient's electronic records are thoroughly reviewed by an infection control practitioner looking for information about prior interventions. Similarly, the department of radiology prospectively follows all patients who have undergone ultrasound-guided hepatic, renal, and pancreatic biopsies for complications 24 hours, 3 months, and 12 months after biopsy. We reviewed 2 years of these data to determine the incidence of infections after common ultrasound-guided procedures. RESULTS We performed 13,534 ultrasound-guided procedures from January 2006 to December 2007. There were 11 likely and three possible procedure-related infections for an overall incidence of 0.1% (14/13,534). The infections consisted of five abscesses, four bloodstream infections, four cases of peritonitis, and one urinary tract infection. The highest incidence of infections occurred after ultrasound-guided biopsy (0.2%, 10/5,487), with biopsy of a hepatic transplant having the highest incidence (1.0%, 2/192). No infections occurred after thoracentesis and FNA despite the large number of procedures performed (2,489 and 2,340, respectively). Nearly all patients improved on antibiotics. One patient died 5 days after paracentesis; however, death was likely due to multiorgan failure in the setting of fulminant liver failure with hepatorenal syndrome. CONCLUSION The incidence of a serious infectious complication after ultrasoundguided intervention is low. Radiologists can use these data to provide more accurate information to patients when asking for consent before procedures and to reassure their patients.
A hard real-time kernel for Motorola microcontrollers

This paper describes a real-time kernel for running embedded applications on a recent family of Motorola microcontrollers. Both periodic and aperiodic real-time tasks are managed, as well as non real-time tasks. The kernel has been called Yartos, and uses a hard real-time scheduling algorithm based on an EDF approach for the periodic task; aperiodic tasks are executed with a total bandwidth server.
Regional T- and B-cell responses in influenza-infected ferrets

Ferrets were infected with A/Port Chalmers/72 influenza virus and the T- and B-cell responses in the spleen, in lymph nodes draining the upper and lower respiratory tract, and in lung washings were examined in vitro. Lymphocyte responses were measured by using a hemolytic plaque assay for B cells and a proliferation assay for T cells. Virus and antibody levels were measured in respiratory tract washings, and antibody titers were measured in sera from infected animals. Individual B cells secreting specific antibody to A/Port Chalmers/72 virus were detected in regional lymph node and spleen preparations as early as 3 days and as late as 43 days after infection. T-cell assays showed an in vitro response of lymph node cells to A/Port Chalmers/73 virus from day 6 to day 43. Virus was isolated from the respiratory tract up to 7 days after infection. Serum hemagglutination-inhibiting antibody was first detectable on day 6, with maximum titers reached by day 10. These results demonstrated that antibody production and a cellular immune responses were detectable at regional sites at a time when virus was still present and before serum antibody was measured.
A Regularized Locality Projection-Based Sparsity Discriminant Analysis for Face Recognition

Manifold learning and classifiers based on sparse representation are widely used in pattern recognition. Most of the conventional manifold learning methods are subjected to the choice of parameters. In this paper, we present a Regularized Locality Projection based on Sparsity Discriminant Analysis (RLPSD) method for Feature Extraction (FE) to understand the high-dimensional data such as face images. In RLPSD, firstly, we show the sparse representation of training samples by collaborative representation-based classification (CRC). Secondly, the idea of part optimization based on sparse representation is used to ensure the within-class compactness which combines with the labels of measurements and the weights of sparse presentation can be as small as possible. Finally, whole optimization can be directly obtained without the iteration of local optimization. Meanwhile, the separability information of between-class can be well discriminated by scatter matrix which is similar to Fisher linear discriminant analy.
A golden calf in sacred space?: The future of St Katherine's monastery, Mount Sinai (Egypt)

Abstract The spectacular fortified monastery of St Katherine, continuously inhabited since the 4th century and with a library second only in historical significance to that of the Vatican, forms the epicentre of a sacred landscape surrounding Mount Sinai, in the southern Sinai desert (Egypt). This site, with religious significance for Jews, Muslims and Christians alike, is currently threatened by very rapid growth in visitation Jrom Egypt's new tourist resorts on the Red Sea coast, less than three hours drive away. Currently, 97,000 visitors per year arrive at St Katherine, 80% of whom are day‐trip visitors and many of whom stay less than half an hour. This represents a 300% increase in the last decade, projected to increase by a further 500% by 2017. Tourism pressure is having a serious effect on the sustainability of monastic life, despite efforts to limit visiting hours and access. This fieldwork‐based case study summarises the current impact of tourism in the Mount Sinai area suggesting that although .
Hepatic Oxidative Stress Following Prolonged Sublethal Microcystin LR Exposure

Microcystin LR (MCLR) is a naturally occurring protein phosphatase inhibitor and potent hepatotoxin produced by strains of Microcystis aeruginosa. Although its acute toxicity has been well characterized, little is known about its chronic effects. In this study, we sought to acquire evidence that oxidative stress may play a role in the pathogenesis of prolonged sublethal MCLR toxicity. Twelve rats (3 per group) weighing on average 185 g were exposed to 1 of 3 different concentrations of MCLR (16, 32, and 48 μg/kg/day) or to saline via intraperitoneal osmotic pumps for 28 days. Histologic evidence of dose-dependent hepatic inflammation was seen, including infiltration of centrilobular regions by lymphocytes, macrophages, and neutrophils, centrilobular fibrosis, apoptosis, and steatosis. Analysis of lipid peroxidation products revealed a dose-dependent increase in malondialdehyde concentrations with an approximate 4-fold increase in the livers of the high-dose rats over those of the saline-treated controls. Livers from MCLR-exposed rats were more sensitive than those of controls to the cytotoxic effects of the organic oxidizing agent tert-butyl hydroperoxide, based on an MTT (3-[dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) viability assay. These histopathologic and biochemical findings indicate that oxidative stress may play a significant role in the pathogenesis of chronic MCLR toxicosis.
Mechanical properties of 7–10 mm bone grafts and small slurry grafts in impaction bone grafting

We compared the mechanical properties of morselized cancellous bone grafts of two sizes: 7–10 mm bone and small slurry bone (about 2 mm). The in vitro test was designed to simulate the hammer and impactor system for impaction bone grafting used in hip arthroplasty clinical practice. The 7–10 mm bone grafts showed higher height, elastic modulus, and massive extrusion strength than those of the small slurry bone grafts. No difference was found in yield strength. The bone mineral density of the 7–10 mm grafts continued to increase during impaction and became higher than that of the small slurry bone grafts after 10 impactions. Our results demonstrated that the small slurry bone grafts exhibit worse mechanical properties as compared with the 7–10 mm bone grafts, which implies that the use of this material in reconstruction of a bone defect in the acetabulum should be limited. © 2011 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 29: 1491–1495, 2011