P/Key: PUF based second factor authentication

One-time password (OTP) mechanisms are widely used to strengthen authentication processes. In time-based one-time password (TOTP) mechanisms, the client and server store common secrets. However, once the server is compromised, the client's secrets are easy to obtain. To solve this issue, hash-chain-based second-factor authentication protocols have been proposed. However, these protocols suffer from latency in the generation of OTPs on the client side because of the hash-chain traversal. Secondly, they can generate only a limited number of OTPs as it depends on the length of the hash-chain. In this paper, we propose a second-factor authentication protocol that utilizes Physically Unclonable Functions (PUFs) to overcome these problems. In the proposed protocol, PUFs are used to store the secrets of the clients securely on the server. In case of server compromise, the attacker cannot obtain the seeds of clients' secrets and can not generate valid OTPs to impersonate the clients. In the case of physical attacks, including side-channel attacks on the server side, our protocol has a mechanism that prevents attackers from learning the secrets of a client interacting with the server. Furthermore, our protocol does not incur any client-side delay in OTP generation.

Long-term follow-up of young denim sandblasters in Turkey

BACKGROUND

Denim sandblasting-induced silicosis is a recently identified occupational disease.

AIMS

In this study, we aimed to evaluate pulmonary and radiological changes in the long-term follow-up of former denim sandblasters.

METHODS

Ninety former denim sandblasters were followed from 2007 to 2018. Chest X-rays were evaluated according to the International Labour Organization (ILO) classification. Baseline and final data were compared. Silicosis prevalence, radiological progression and pulmonary dysfunction were evaluated.

RESULTS

All of the sandblasters were men. Their mean age was 34 ± 5 years, mean follow-up time was 9 ± 2 years (mean time since initial exposure: 17 ± 2 years) and mean duration of exposure was 34 ± 25 months. Rates of radiological progression and decline in pulmonary during follow-up were 63% and 39%, respectively. During follow-up, all patients were diagnosed with silicosis. All workers who were ILO category 0 at baseline (n = 26, 29%) progressed to higher categories. The number of patients in Category 2 doubled and the number of patients in Category 3 increased by 2.5-fold. Eleven patients developed new large opacities and the number of patients with category C opacity increased from 4 to 13. Exposure time was an independent determinant of radiological progression (OR: 1.0, P = 0.036) and decline in pulmonary function (OR: 1.3, P = 0.019).

CONCLUSION

The prevalence of silicosis in denim sandblasters increases steadily even after exposure is discontinued. Radiological progression was observed in a higher proportion of workers than a decline in lung function. Duration of exposure was the major determinant of disease progression in our study.

Efficient privacy-preserving whole-genome variant queries

MOTIVATION

Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data.

RESULTS

We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.

AVAILABILITY AND IMPLEMENTATION

https://gitlab.com/DIFUTURE/privacy-preserving-variant-queries.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Identifying disease-causing mutations with privacy protection

Motivation

The use of genome data for diagnosis and treatment is becoming increasingly common. Researchers need access to as many genomes as possible to interpret the patient genome, to obtain some statistical patterns and to reveal disease–gene relationships. The sensitive information contained in the genome data and the high risk of re-identification increase the privacy and security concerns associated with sharing such data. In this article, we present an approach to identify disease-associated variants and genes while ensuring patient privacy. The proposed method uses secure multi-party computation to find disease-causing mutations under specific inheritance models without sacrificing the privacy of individuals. It discloses only variants or genes obtained as a result of the analysis. Thus, the vast majority of patient data can be kept private.

Results

Our prototype implementation performs analyses on thousands of genomic data in milliseconds, and the runtime scales logarithmically with the number of patients. We present the first inheritance model (recessive, dominant and compound heterozygous) based privacy-preserving analyses of genomic data to find disease-causing mutations. Furthermore, we re-implement the privacy-preserving methods (MAX, SETDIFF and INTERSECTION) proposed in a previous study. Our MAX, SETDIFF and INTERSECTION implementations are 2.5, 1122 and 341 times faster than the corresponding operations of the state-of-the-art protocol, respectively.

Availability and implementation

https://gitlab.com/DIFUTURE/privacy-preserving-genomic-diagnosis.

Supplementary information

Supplementary data are available at Bioinformatics online.

Evaluation of lung densitometric and volumetric changes in silicosis patients using three-dimensional software for multidetector CT and the relationship with profusion scores

AIM

To evaluate the density and volume changes in the lungs of silicosis patients and their relationship with the disease severity classification of the International Labor Organization (ILO).

MATERIALS AND METHODS

The multidetector computed tomography (CT) images of 44 patients diagnosed with silicosis and 32 controls that underwent thoracic CT due to trauma were evaluated. Patients with silicosis were divided into three categories according to the ILO classification. Data related to the total lung volume, total lung mean density, lung opacity score, percentage of lung high opacity, and mean density in the lower and upper lobes were obtained using three-dimensional (3D) software.

RESULTS

There was no significant difference between the total lung mean densities of the silicosis and control groups (p=0.213); however, a significant difference was observed between the two groups in terms of the total lung volume (p<0.0001). According to the ILO classification, there was a significant difference between the disease severity categories in relation to the percentage of lung high opacity (p=0.000005). A strong correlation was detected between disease severity and high opacity percentage (p<0.0001, r=0.804). According to the ILO classification, there was also a significant difference between disease severity categories in terms of the lung opacity score (p=0.000144), as well as a moderate correlation between disease severity and opacity score (p<0.0001, r=0.580).

CONCLUSION

Total lung volume is a CT finding that shows variation in exposure to crystalline silica. The percentage of high opacity determined using multidetector CT is an effective parameter in evaluating disease severity.

Comparison of noise effects to state anxiety levels of patients and nurses

Introduction

An quiet environment is comfortable and peaceful. Also, healthy and safety environment is a human right. But, exposure to noise may cause negative effects on psychology and performance. Also, it is a problem in public hospitals, because, noise is an important issue for both nurses and patients.

Objectives

The study was designed to determine decibel levels on the hospital's four unified clinics and compare noise effects to state anxiety levels of patients and nurses.

Methods

Information Form, Spielberger State-Trait Anxiety Inventory (STAI) were applied to participating 40 patients and 14 nurses. A measurement of the sound level of unified clinics was performed for two days in the morning and after lunch for two days.

Results

The range of minimum to maximum decibel levels was significantly greater in nurses’ station (38.66 dB versus 82.48 dB) than patient rooms (24.61 dB versus 74.2 dB) (P < .05). 25 patients and 14 nurses stated that there was noise in the clinic. 19 patients and 10 nurses expressed that it caused a headache. The state anxiety levels were 39.29 ± 5.61 for nurses and 45.4 ± 4.86 for patients. The state anxiety level of patients were 44.83 ± 3.86 in 1. Clinic, 48.8 ± 4.37 in 2. Clinic, 43.82 ± 4.9 in 3. clinic, 44 ± 5.57 in 4. Clinic.

Conclusions

We should reduce the noise level to reduce the level of state anxiety. This study describes one reason to reduce peak noise levels on unified clinics. Standards applied across studies to measure and characterize acoustic environments are urgently needed.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

FMFilter: A fast model based variant filtering tool

The availability of whole exome and genome sequencing has completely changed the structure of genetic disease studies. It is now possible to solve the disease causing mechanisms within shorter time and budgets. For this reason, mining out the valuable information from the huge amount of data produced by next generation techniques becomes a challenging task. Current tools analyze sequencing data in various methods. However, there is still need for fast, easy to use and efficacious tools. Considering genetic disease studies, there is a lack of publicly available tools which support compound heterozygous and de novo models. Also, existing tools either require advanced IT expertise or are inefficient for handling large variant files. In this work, we provide FMFilter, an efficient sieving tool for next generation sequencing data produced by genetic disease studies. We develop a software which allows to choose the inheritance model (recessive, dominant, compound heterozygous and de novo), the affected and control individuals. The program provides a user friendly Graphical User Interface which eliminates the requirement of advanced computer techniques. It has various filtering options which enable to eliminate the majority of the false alarms. FMFilter requires negligible memory, therefore it can easily handle very large variant files like multiple whole genomes with ordinary computers. We demonstrate the variant reduction capability and effectiveness of the proposed tool with public and in-house data for different inheritance models. We also compare FMFilter with the existing filtering software. We conclude that FMFilter provides an effective and easy to use environment for analyzing next generation sequencing data from Mendelian diseases.

Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica

BACKGROUND

Fasciola hepatica causes chronic liver disease, fasciolosis, leading to significant losses in the livestock economy and concerns for human health in many countries. The identification of F. hepatica genes involved in the parasite's virulence through modulation of host immune system is utmost important to comprehend evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, to identify the parasite's putative virulence genes which are associated with host immunomodulation, we explored whole transcriptome of an adult F. hepatica using current transcriptome profiling approaches integrated with detailed in silico analyses. In brief, the comparison of the parasite transcripts with the specialised public databases containing sequence data of non-parasitic organisms (Dugesiidae species and Caenorhabditis elegans) or of numerous pathogens and investigation of the sequences in terms of nucleotide evolution (directional selection) and cytokine signaling relation were conducted.

RESULTS

NGS of the whole transcriptome resulted in 19,534,766 sequence reads, yielding a total of 40,260 transcripts (N₅₀ = 522 bp). A number of the parasite transcripts (n = 1,671) were predicted to be virulence-related on the basis of the exclusive homology with the pathogen-associated data, positive selection or relationship with cytokine signaling. Of these, a group of the virulence-related genes (n = 62), not previously described, were found likely to be associated with immunomodulation based on in silico functional categorisation, showing significant sequence similarities with various immune receptors (i.e. MHC I class, TGF-β receptor, toll/interleukin-1 receptor, T-cell receptor, TNF receptor, and IL-18 receptor accessory protein), cytokines (i.e. TGF-β, interleukin-4/interleukin-13 and TNF-α), cluster of differentiations (e.g. CD48 and CD147) or molecules associated with other immunomodulatory mechanisms (such as regulation of macrophage activation). Some of the genes (n = 5) appeared to be under positive selection (Ka/Ks > 1), imitating proteins associated with cytokine signaling (through sequence homologies with thrombospondin type 1, toll/interleukin-1 receptor, TGF-β receptor and CD147).

CONCLUSIONS

With a comparative transcriptome profiling approach, we have identified a number of potential immunomodulator genes of F. hepatica (n = 62), which are firstly described here, could be employed for the development of better strategies (including RNAi) in the battle against both zoonotically and economically important disease, fasciolosis.

Generating a detailed protein profile of Fasciola hepatica during the chronic stage of infection in cattle

Fasciola hepatica is a trematode helminth causing a damaging disease, fasciolosis, in ruminants and humans. Comprehensive proteomic studies broaden our knowledge of the parasite's protein profile, and provide new insights into the development of more effective strategies to deal with fasciolosis. The objective of this study was to generate a comprehensive profile of F. hepatica proteins expressed during the chronic stage of infection in cattle by building on previous efforts in this area. The approach included an improved sample preparation procedure for surface and internal layers of the parasite, the application of nano-UPLC-ESI-qTOF-MS (nano-ultra-performance LC and ESI quadrupole TOF MS) integrated with different acquisition methods and in silico database search against various protein databases and a transcript database including a new assembly of publically available EST. Of a total of 776 identified proteins, 206 and 332 were specific to the surface and internal layers of the parasite, respectively. Furthermore, 238 proteins were common to both layers, with comparative differences of 172 proteins detected. Specific proteins not previously identified in F. hepatica, but shown to be immunomodulatory or potential drug targets for other parasites, are discussed.

Doppler ultrasound assessment and serum cancer antigen 125 in the diagnosis of ovarian tumors

OBJECTIVE

To differentiate benign from malignant ovarian tumors based on sonographic detection of a solid component.

METHOD

Sixty-three women with ovarian masses were evaluated preoperatively by gray scale and power/color Doppler ultrasonographic examination, with specific predefined criteria for the solid component. Sensitivity, specificity, and positive and negative predictive values were calculated and assessed against the histopathologic outcome. The contribution of cancer antigen (CA) 125 levels to the diagnostic accuracy was also assessed.

RESULT

Sensitivity, specificity, and positive and negative predictive values were 100%, 95.2%, 91.3% and 100%, respectively, with two false-positive results. Had an elevated CA 125 level (>35 U/mL) been included in the malignancy criteria, the false-positive results would have been eliminated, giving an accuracy of 100%.

CONCLUSION

Sonographic evaluation with predefined specific criteria for the detection of a solid tumor component is an accurate method of preoperative discrimination between benign and malignant ovarian tumors. A serum CA 125 assay may assist in eliminating false-positive results.

Evaluation of cerebral vasospasm with transcranial magnetic stimulation: an experimental study

Despite the current use of several different methods for diagnosis and follow-up of cerebral vasospasm after subarachnoid hemorrhage, an easy, quick, reliable, and noninvasive method is still needed for evaluation of this entity. We investigated the value of transcranial magnetically evoked motor potential changes during the vasospasm period in a rabbit experimental subarachnoid hemorrhage model. We also recorded motor evoked potential changes after deferoxamine treatment during vasospasm. Our results reveal a significant increase in latency periods of evoked potentials during the angiographically proven vasospasm period (34.5%) over those in sham-operated rabbits (9.5%). With deferoxamine treatment, only a minor increase in latency periods (4.5%) was detected after subarachnoid hemorrhage. These results suggest the potential value of evoked motor potential recording as a diagnostic tool in cases of cerebral vasospasm.

Effects of deferoxamine and sympathectomy on endothelin-1-induced contraction and acetylcholine-induced relaxation following subarachnoid hemorrhage in carotid artery

The role of endothelium-related factors in the pathogenesis of cerebral vasospasm after subarachnoid hemorrhage (SAH) has gained interest since the discovery of EDRF and of endothelin-1 (ET-1). The effect of SAH and both treatment of deferoxamine (DFO) and sympathectomy on endothelium-dependent vasodilation and ET-1-induced vasoconstriction of isolated rabbit carotid artery was examined using an isometric tension recording method. Thirty-five rabbits were divided into four groups: control animals, 7 days after SAH, treatment with DFO after SAH for 7 days and sympathectomy after SAH. Acetylcholine (10(-8) to 10(-5) M) was used to evoke concentration-dependent vasodilation of isolated arterial rings previously contracted by 10(-6) M phenylephrine. In the animals killed 7 days after SAH, acetylcholine-induced relaxation was suppressed and the degree of relaxation of this group was 50% of the initial contractile tone in response to the 10(-5) M acetylcholine. These relaxant responses did not return to control values in carotid arteries obtained from animals treated with DFO and subjected to sympathectomy. In isolated carotid arteries, ET-1 (10(-10) to 10(-8) M) produced concentration-dependent contractions. These contractile responses were significantly enhanced in animals 7 days after SAH compared with controls and did not return to control values in carotid arteries obtained from animals both treated with DFO and sympathectomized for 7 days after SAH. The present experiments suggest that impairment of endothelium-dependent vasodilation and the hyperreactivity of ET-1 of the carotid artery as well as cerebral arteries may be involved in the pathogenesis of cerebral vasospasm. Both treatment with DFO and sympathectomy during the chronic stage for vasospasm after SAH did not affect these vascular responses of the extradural part of the carotid artery to ET-1 and acetylcholine.

Effect of deferoxamine and sympathectomy on vasospasm following subarachnoid hemorrhage

We examined the effects of subarachnoid hemorrhage (SAH) and treatment with deferoxamine (DFO) or sympathectomy on vascular smooth muscle function, as well as the underlying mechanisms involved, by recording the responses to nor-adrenaline and serotonin in isolated carotid arteries in vitro. All studies were performed before and 7 days after SAH. An experimental subarachnoid hemorrhage model was created in rabbits by injecting autologous arterial blood into the subarachnoid space of the rabbits via cisterna magna punction. During the chronic stage of vasospasm following SAH deferoxamine (DFO) was given to the animals and cervical and periarterial sympathectomy was performed in the other groups of animals. In isolated carotid arteries noradrenaline (10(-8) to 10(-4) mol/l) and serotonin (10(-8) to 10(-4) mol/l) produced concentration-dependent contractions. These contractile responses were significantly enhanced in animals 7 days after SAH compared to controls and did not return to control values in carotid arteries obtained from animals treated with DFO or sympathectomy for 7 days after SAH. These results show that SAH causes supersensitivity in the carotid as well as cerebral arteries during the first week after SAH and could contribute to the development of cerebral vasospasm. Both treatment with DFO and sympathectomy after SAH did not reduce the contractile responses to noradrenaline and serotonin in the carotid arteries. In conclusion, treatment with DFO or sympathectomy during the chronic stage of vasospasm after SAH did not affect the vascular responses of the extradural part of the carotid artery to vasoactive substances.