READ-BAD: A New Dataset and Evaluation Scheme for Baseline Detection in Archival Documents

Text line detection is crucial for any application associated with Automatic Text Recognition or Keyword Spotting. Modern algorithms perform good on well-established datasets since they either comprise clean data or simple/homogeneous page layouts. We have collected and annotated 2036 archival document images from different locations and time periods. The dataset contains varying page layouts and degradations that challenge text line segmentation methods. Well established text line segmentation evaluation schemes such as the Detection Rate or Recognition Accuracy demand for binarized data that is annotated on a pixel level. Producing ground truth by these means is laborious and not needed to determine a method's quality. In this paper we propose a new evaluation scheme that is based on baselines. The proposed scheme has no need for binarization and it can handle skewed as well as rotated text lines. The ICDAR 2017 Competition on Baseline Detection and the ICDAR 2017 Competition on Layout Analysis for Challenging Medieval Manuscripts used this evaluation scheme. Finally, we present results achieved by a recently published text line detection algorithm.Comment: Submitted to DAS201

a retrospective study

Introduction Emergency treatment of major sub-/total traumatic amputations continue to represent a clinical challenge due to high infection rates and serious handicaps. Effective treatment is based on two columns: surgery and antimicrobial therapy. Detailed identification of pathogen spectrum and epidemiology associated with these injuries is of tremendous importance as it guides the initial empiric antibiotic regimen and prevents adverse septic effents. Methods In this retrospective study 51 patients with major traumatic amputations (n = 16) and subtotal amputations (n = 35) treated from 2001 to 2010 in our trauma center were investigated. All patients received emergency surgery, debridement with microbiological testing within 6 h after admission and empircic antimicrobial therapy. Additionally to baseline patient characteristics, the incidence of positive standardized microbiologic testing combined with clinical signs of infection, pathogen spectrum, administered antimicrobial agents and clinical complications were analyzed. Results 70.6% of the patients (n = 36) acquired wound infection. In 39% wounds were contaminated on day 1, whereas the mean length of duration until first pathogen detection was 9.1 ± 13.4 days after injury. In 37% polymicrobial colonization and 28% Pseudomonas were responsible for wound infections during hospitalization. In 45% the empirc antimicrobial therapy focussed on Gram positive strains did not cover the detected bacteria, according antimicrobial resistogram. It was significantly more often found in infections associated with Pseudomonas (p 0.02) or polymicrobial wound infections. Conclusions This epidemiologic study reveals a pathogen shift from Gram-positive to Gram- negative strains with high incidence of Pseudomonas and polymicrobial infections in sub-/total major traumatic amputations. Therefore, empiric antimicrobial treatment historically focussing on Gram-positive strains must be adjusted. We recommend the use of Piperacillin/Tazobactam for these injuries. As soon as possible antimicrobial treatment should be changed from empiric to goal directed therapy according to the microbiological tests and resistogram results

Impact of high prevalence of pseudomonas and polymicrobial gram-negative infections in major sub-/total traumatic amputations on empiric antimicrobial therapy: a retrospective study

INTRODUCTION: Emergency treatment of major sub-/total traumatic amputations continue to represent a clinical challenge due to high infection rates and serious handicaps. Effective treatment is based on two columns: surgery and antimicrobial therapy. Detailed identification of pathogen spectrum and epidemiology associated with these injuries is of tremendous importance as it guides the initial empiric antibiotic regimen and prevents adverse septic effents. METHODS: In this retrospective study 51 patients with major traumatic amputations (n = 16) and subtotal amputations (n = 35) treated from 2001 to 2010 in our trauma center were investigated. All patients received emergency surgery, debridement with microbiological testing within 6 h after admission and empircic antimicrobial therapy. Additionally to baseline patient characteristics, the incidence of positive standardized microbiologic testing combined with clinical signs of infection, pathogen spectrum, administered antimicrobial agents and clinical complications were analyzed. RESULTS: 70.6% of the patients (n = 36) acquired wound infection. In 39% wounds were contaminated on day 1, whereas the mean length of duration until first pathogen detection was 9.1 ± 13.4 days after injury. In 37% polymicrobial colonization and 28% Pseudomonas were responsible for wound infections during hospitalization. In 45% the empirc antimicrobial therapy focussed on Gram positive strains did not cover the detected bacteria, according antimicrobial resistogram. It was significantly more often found in infections associated with Pseudomonas (p 0.02) or polymicrobial wound infections. CONCLUSIONS: This epidemiologic study reveals a pathogen shift from Gram-positive to Gram-negative strains with high incidence of Pseudomonas and polymicrobial infections in sub-/total major traumatic amputations. Therefore, empiric antimicrobial treatment historically focussing on Gram-positive strains must be adjusted. We recommend the use of Piperacillin/Tazobactam for these injuries. As soon as possible antimicrobial treatment should be changed from empiric to goal directed therapy according to the microbiological tests and resistogram results

Secure Execution Architecture based on PUF-driven Instruction Level Code Encryption

A persistent problem with program execution, despite numerous mitigation attempts, is its inherent vulnerability to the injection of malicious code. Equally unsolved is the susceptibility of firmware to reverse engineering, which undermines the manufacturer\u27s code confidentiality. We propose an approach that solves both kinds of security problems employing instruction-level code encryption combined with the use of a physical unclonable function (PUF). Our novel Secure Execution PUF-based Processor (SEPP) architecture is designed to minimize the attack surface, as well as performance impact, and requires no significant changes to the development process. This is possible based on a tight integration of a PUF directly into the processor\u27s instruction pipeline. Furthermore, cloud scenarios and distributed embedded systems alike inherently depend on remote execution; our approach supports this, as the secure execution environment needs not to be locally available at the developers site. We implemented an FPGA-based prototype based on the OpenRISC Reference Platform. To assess our results, we performed a security analysis of the processor and evaluated the performance impact of the encryption. We show that the attack surface is significantly reduced compared to previous approaches while the performance penalty is at a reasonable factor of about 1.5

Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus

Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E–7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits

Meta-analyses identify DNA methylation associated with kidney function and damage

Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Variant annotation was supported by software resources provided via the Caché Campus program of the InterSystems GmbH to Alexander Teumer

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms