LLukas22/scidocs huggingface dataset:
Sofosbuvir with peginterferon-ribavirin for 12 weeks in previously treated patients with hepatitis C genotype 2 or 3 and cirrhosis

UNLABELLED
Sofosbuvir (SOF) in combination with ribavirin (RBV) for 12 or 24 weeks is the current standard of care for patients infected with hepatitis C virus (HCV) genotypes 2 and 3, respectively. However, in clinical trials treatment-experienced patients, particularly those with cirrhosis, had suboptimal sustained virological response (SVR) rates. We assessed the efficacy and safety of sofosbuvir plus peginterferon and ribavirin (SOF+Peg-IFN+RBV) administered for 12 weeks to treatment-experienced patients with HCV genotypes 2 and 3, with and without cirrhosis. We enrolled 47 patients in this open-label, nonrandomized, uncontrolled phase 2 study. The primary endpoint was the proportion of patients with SVR at 12 weeks after cessation of study treatment (SVR12). The overall rate of SVR12 was 89% (95% confidence interval [CI]: 77-97). Rates of SVR12 were higher in patients with genotype 2 than in those with genotype 3, 96% (95% CI: 78-100) and 83% (95% CI: 62-95), respectively. Rates of SVR12 were similar in patients with and without cirrhosis: for genotype 2, 93% of patients with cirrhosis and 100% of patients without cirrhosis achieved SVR12, and for genotype 3, the SVR12 rate was 83% in patients both with and without cirrhosis. One patient discontinued study treatment because of an adverse event and four patients experienced serious adverse events. The most common adverse events were influenza-like illness, fatigue, anemia, and neutropenia.


CONCLUSION
In treatment-experienced patients with HCV genotypes 2 and 3, 12-week administration of SOF+Peg-IFN+RBV provided high SVR rates, irrespective of cirrhosis status. No safety concerns were identified.
A Survey on Botnet Command and Control Traffic Detection

Internet users have been attacked by widespread email viruses earlier, but now scenario has been changed. Now attackers are no more interested to just attract media attention by infecting a large number of computers on the network; in fact, their interest has been shifted to compromising and controlling the infected computers for their personal profits. This new attack trend brings the concept of botnets over the global network of computers. With the high reported infection rates, the vast range of illegal activities and powerful comebacks, botnets are one of the main threats against the cyber security. This paper provides the readers with a background on botnet life-cycle, architecture and malicious activities. It also classifies botnet detection techniques, reviews the recent research works on botnet traffic detection and finally indicates some challenges posed to future work on botnet detection. Keywords—Cyber security, malware, botnet, C&C server, intrusion detection system.
Structure of the archaebacterial 7S RNA molecule

The genes encoding the 7S RNAs of the archaebacteria Archaeoglobus fulgidus, Methanosarcina acetivorans, Sulfolobus solfataricus, and Thermococcus celer have been isolated. All four genes occur as single genomic copies and are flanked by sequences containing potential signals for transcriptional promotion and termination. The genes encode RNA molecules approximately 300 nucleotides in length which conform strictly to a model of secondary structure common to all described archaebacterial 7S RNAs. Archaebacterial 7S RNAs exhibit a strong similarity to eukaryotic 7S RNAs in terms of overall secondary structure, while primary sequence conservation is limited to a specific structural domain of the molecule. This domain displays strong primary and secondary structural similarity to features of small eubacterial RNAs, including the small cytoplasmic (sc) RNA of Bacillus subtilis and the 4.5S RNA of Escherichia coli. Conservation of this structural domain among divergent RNA molecules across three kingdoms suggests that these RNAs are the descendants of a unique subcellular structure present before the divergence of the archaebacterial, eubacterial and eukaryotic kingdoms.
Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis.

Herve cheese is a Belgian soft cheese with a washed rind, and is made from raw or pasteurized milk. The specific microbiota of this cheese has never previously been fully explored and the use of raw or pasteurized milk in addition to starters is assumed to affect the microbiota of the rind and the heart. The aim of the study was to analyze the bacterial microbiota of Herve cheese using classical microbiology and a metagenomic approach based on 16S ribosomal DNA pyrosequencing. Using classical microbiology, the total counts of bacteria were comparable for the 11 samples of tested raw and pasteurized milk cheeses, reaching almost 8 log cfu/g. Using the metagenomic approach, 207 different phylotypes were identified. The rind of both the raw and pasteurized milk cheeses was found to be highly diversified. However, 96.3 and 97.9% of the total microbiota of the raw milk and pasteurized cheese rind, respectively, were composed of species present in both types of cheese, such as Corynebacterium casei, Psychrobacter spp., Lactococcus lactis ssp. cremoris, Staphylococcus equorum, Vagococcus salmoninarum, and other species present at levels below 5%. Brevibacterium linens were present at low levels (0.5 and 1.6%, respectively) on the rind of both the raw and the pasteurized milk cheeses, even though this bacterium had been inoculated during the manufacturing process. Interestingly, Psychroflexus casei, also described as giving a red smear to Raclette-type cheese, was identified in small proportions in the composition of the rind of both the raw and pasteurized milk cheeses (0.17 and 0.5%, respectively). In the heart of the cheeses, the common species of bacteria reached more than 99%. The main species identified were Lactococcus lactis ssp. cremoris, Psychrobacter spp., and Staphylococcus equorum ssp. equorum. Interestingly, 93 phylotypes were present only in the raw milk cheeses and 29 only in the pasteurized milk cheeses, showing the high diversity of the microbiota. Corynebacterium casei and Enterococcus faecalis were more prevalent in the raw milk cheeses, whereas Psychrobacter celer was present in the pasteurized milk cheeses. However, this specific microbiota represented a low proportion of the cheese microbiota. This study demonstrated that Herve cheese microbiota is rich and that pasteurized milk cheeses are microbiologically very close to raw milk cheeses, probably due to the similar manufacturing process. The characterization of the microbiota of this particular protected designation of origin cheese was useful in enabling us to gain a better knowledge of the bacteria responsible for the character of this cheese.
Modeling and Control of Legged Robots

The promise of legged robots over standard wheeled robots is to provide improved mobility over rough terrain. This promise builds on the decoupling between the environment and the main body of the robot that the presence of articulated legs allows, with two consequences. First, the motion of the main body of the robot can be made largely independent from the roughness of the terrain, within the kinematic limits of the legs: legs provide an active suspension system. Indeed, one of the most advanced hexapod robots of the 1980s was aptly called the Adaptive Suspension Vehicle [1]. Second, this decoupling allows legs to temporarily leave their contact with the ground: isolated footholds on a discontinuous terrain can be overcome, allowing to visit places absolutely out of reach otherwise. Note that having feet firmly planted on the ground is not mandatory here: skating is an equally interesting option, although rarely approached so far in robotics.
Enhanced Detection of Early Hepatocellular Carcinoma by Serum SELDI-TOF Proteomic Signature Combined with Alpha-Fetoprotein Marker

Biomarkers for accurate diagnosis of early hepatocellular carcinoma (HCC) are limited in number and clinical validation. We applied SELDI-TOF-MS ProteinChip technology to identify serum profile for distinguishing HCC and liver cirrhosis (LC) and to compare the accuracy of SELDI-TOF-MS profile and alpha-fetoprotein (AFP) level in HCC diagnosis. Serum samples were obtained from 120 HCC and 120 LC patients for biomarker discovery and validation studies. ProteinChip technology was employed for generating SELDI-TOF proteomic features and analyzing serum proteins/peptides. A diagnostic model was established by CART algorithm, which is based on 5 proteomic peaks with m/z values at 3324, 3994, 4665, 4795, and 5152. In the training set, the CART algorithm could differentiate HCC from LC subjects with a sensitivity and specificity of 98% and 95%, respectively. The results were assessed in blind validation using separate cohorts of 60 HCC and 60 LC patients, with an accuracy of 83% for HCC and 92% for LC patients. The diagnostic odd ratio (DOR) indicated that SELDI-TOF proteomic signature could achieve better diagnostic performance than serum AFP level at a cutoff of 20 ng/mL (AFP20) (92.72 vs 9.11), particularly superior for early-stage HCC (87% vs 54%). Importantly, a combined use of both tests could enhance the detection of HCC (sensitivity, 95%; specificity, 98%; DOR, 931). Serum SELDI-TOF proteomic signature, alone or in combination with AFP marker, promises to be a good tool for early diagnosis and/screening of HCC in at-risk population with liver cirrhosis.
Prevalence of Complicated Gastroesophageal Reflux Disease and Barrett’s Esophagus Among Racial Groups in a Multi-Center Consortium

Aims The Clinical Outcomes Research Initiative database was used to evaluate ethnic trends in complicated reflux disease and suspected Barrett’s esophagus among various racial groups. Methods Endoscopic findings for procedures performed January 2000–December 2005 for any indication and for reflux-related indications were reviewed by racial group. Results Of 280,075 procedures examined, Hispanics were the most likely to have esophagitis (Hispanic 19.6%, white 17.3%, black 15.8%, Asian/Pacific Islander 9.5%, P-value < 0.0001), and white subjects were most likely to have suspected BE (white 5.0%, Hispanic 2.9%, Asian/Pacific Islander 1.8%, black 1.5%, P-value < 0.0001). Endoscopies performed for reflux-related indications had similar trends for esophagitis and esophageal stricture. Among reflux/Barrett’s screening procedures adjusted for age and gender, Hispanics were most likely to have esophagitis (OR = 1.28, P-value < 0.0001) compared to Caucasians. Conclusion Our results demonstrate an association of suspected Barrett’s esophagus and stricture with white patients and esophagitis with Hispanic patients. These findings need to be followed-up with further study.
Electronic Tongues Employing Electrochemical Sensors

This review presents recent advances concerning work with electronic tongues employing electroanalytical sensors. This new concept in the electroanalysis sensor field entails the use of chemical sensor arrays coupled with chemometric processing tools, as a mean to improve sensors performance. The revision is organized according to the electroanalytical technique used for transduction, namely, potentiometry, voltammetry/amperometry or electrochemical impedance. The significant use of biosensors, mainly enzyme-based is also presented. Salient applications in real problem solving using electrochemical electronic tongues are commented.
Data quality evaluation and improvement for prognostic modeling using visual assessment based data partitioning method

When developing Prognostic and Health Management (PHM) applications for manufacturing systems, data acquired frequently comes with issues which hinder further data analysis. However, there is neither a clear definition of the data quality nor evaluation methods to quantify if acquired data is suitable for these prognostic modeling tasks such as failures detection, diagnosis and prediction. Especially, during health diagnosis modeling of engineering systems, based on data-driven method, acquired data is expected to contain clusters that can be used to differentiate multiple system health conditions. So in most cases, once data is acquired, people would like to intuitively believe that data is able to cluster into subgroups. However, this bias could lead to acceptance of false information in data. Furthermore, most of the existing metrics, such as clustering tendency in statistics and cluster-ability in data mining, only individually evaluate data characteristics without considering prognostic modeling. This paper proposes a new method to evaluate and improve data quality for system health diagnosis modeling. The clusters, as critical data characteristics for modeling multiple system conditions, are first estimated by ‘‘visualization’’ on the dissimilarity spectrum from spectral analysis and then evaluated in terms of their fitness and separation with each others. A visual assessment based outlier detection method is also proposed to recognize outliers from the data, which utilizes the graphic intermediate results from previous evaluation. Finally one group of bearing testing dataset acquired from real industrial applications is used to demonstrate how proposed methods are used to evaluate and improve the data quality. Published by Elsevier B.V.
An open trial of 5-aminolevulinic acid photodynamic therapy for vulvar lichen sclerosus.

was positive for malignant cells. Although the numbers are small, cervical cytology appears to be a helpful screening tool. In many countries, population-based cervical cancer screening programs exist. Should patients with breast cancer be screened more frequently? According to international guidelines, routine follow-up is not carried out for detection of non-symptomatic distant metastases. It is important, however, to instruct patients to report symptoms promptly, as treatment of disseminated disease can prolong life expectancy and increase the quality of life in often relatively young women. Moreover, only when the patient is fully informed about her current condition she can make the best decision regarding her further treatment. In conclusion, it is important to be aware of the possibility of cervical involvement in breast cancer. Cytology can be helpful in detecting distant metastases.
Safe trajectory planning for autonomous intersection management by using vehicle to infrastructure communication

The development of autonomous vehicle or self-driving car integrates with the wireless communication technology which would be a forward step for road transportation in the near future. The autonomous crossing of an intersection with an autonomous vehicle will play a crucial role in the future of intelligent transportation system (ITS). The fundamental objectives of this work are to manage autonomous vehicles crossing an intersection with no collisions, maintaining that a vehicle drives continuously, and to decrease the waiting time at an intersection. In this paper, a discrete model of the one-way single intersection is designed. The vehicle-to-infrastructure (V2I) communication is implemented to exchange information between a vehicle and an intersection manager which is the roadside infrastructure. The safe trajectory of autonomous vehicles for the autonomous intersection management is determined and presented by using discrete mathematics.
Mouth opening: a new angle.

BACKGROUND
The authors hypothesized that craniocervical extension occurs during normal mouth opening.


METHODS
Twenty volunteers were studied. Interdental distance was measured at four different degrees of craniocervical extension.


RESULTS
Interdental distance increased from 28 mm (95% confidence interval, 25-30) in slight flexion to 46 mm (95% confidence interval, 42-49) at full extension. Nearly maximal mouth opening was obtained with 26 degrees (95% confidence interval, 22-30) of craniocervical extension from neutral.


CONCLUSION
Craniocervical extension is an integral part of complete mouth opening in conscious subjects. Fixation of the craniocervical junction by disease, an internal or external fixation device, or technique may restrict mouth opening, with consequences for airway management.
R2CNN: Rotational Region CNN for Orientation Robust Scene Text Detection

In this paper, we propose a novel method called Rotational Region CNN (R2CNN) for detecting arbitrary-oriented texts in natural scene images. The framework is based on Faster R-CNN [1] architecture. First, we use the Region Proposal Network (RPN) to generate axis-aligned bounding boxes that enclose the texts with different orientations. Second, for each axis-aligned text box proposed by RPN, we extract its pooled features with different pooled sizes and the concatenated features are used to simultaneously predict the text/non-text score, axis-aligned box and inclined minimum area box. At last, we use an inclined non-maximum suppression to get the detection results. Our approach achieves competitive results on text detection benchmarks: ICDAR 2015 and ICDAR 2013.
Management innovation

This publication contains reprint articles for which IEEE does not hold copyright. Full text is not available on IEEE Xplore for these articles.
[Contribution of PCR for detection and identification of intestinal microsporidia in HIV-infected patients].

AIM
Intestinal microsporidiosis are among the most frequent opportunistic diseases in immunocompromised subjects. This study aimed to evaluate the contribution of PCR for a better detection and species identification of microsporidia in stool specimens of HIV-infected patients.


PATIENTS AND METHODS
Stool samples obtained from 119 HIV-infected Tunisian subjects were screened for intestinal microsporidiosis by light microscopy using Weber's modified Trichrome stain and by a PCR method using universal primers V1/PMP2 which amplified a common fragment of the small subunit rRNA gene of microsporidia. The obtained PCR products were then sequenced using an ABI PRISM 377 DNA sequencer.


RESULTS
The results showed a better sensitivity of PCR in the detection of microsporidia with an infection rate of 14.3% significantly higher than that of 6.7% obtained by light microscopy (p=0.03). As previously described, intestinal microsporidiosis was associated with low CD4 cell counts; 23.9% infection rate in patients having CD4 cell count under 200/mm(3) against 5.6% in patients with higher CD4 cell count (p=0.008). The sequencing of 15 out of the 17 positive PCR products has confirmed in all cases the species identified based on the PCR fragment size i.e., 250pb for Enterocytozoon bieneusi (seven cases) and about 270pb for Encephalitozoon intestinalis (nine cases); one case revealed a double infection.


CONCLUSION
PCR proved to be more effective than classical Trichrome stain for the diagnosis of intestinal microsporidiosis. Moreover, the ability of PCR to identify the species involved could also be useful for cases management.
Anti-racism and indigenous Australians

Indigenous Australians constitute approximately 2.4% of the Australian population and suffer from disadvantage across a range of social, economic, and health indicators compared to other Australians, including exposure to racism across all domains of contemporary Australian society. However, there has been relatively little research conducted on anti-racism in relation to Indigenous Australians. This article begins with an overview of theoretical issues pertinent to the empirical study and public policy of anti-racism. Empirical findings, from social psychology, on effective approaches to anti-racism at the cognitive, individual, interpersonal, and societal level as well as for the targets of racism are detailed with a particular focus on Indigenous Australians. Recommendations for improving and expanding institutional and legal policies to implement these approaches in relation to education and child-rearing, public service, law enforcement and media, as well as monitoring racism and promoting anti-racism in civil society, are then presented. To conclude, strategies for engendering political will to combat racism in the current neoliberal capitalist climate are explored.
Recovering the interleaver of an unknown turbo-code

We give here an efficient algorithm for recovering the permutation of an unknown turbo-code when several noisy codewords are given. The algorithm presented here uses the same information as some other algorithms given previously for this problem but in an optimal fashion. This paper also clarifies the link between this problem and the BCJR decoding algorithm.
NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei

UNLABELLED
NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.


AVAILABILITY AND IMPLEMENTATION
Dataset of nuclei is available at https://www.gred-clermont.fr/media/WorkDirectory.zip. NucleusJ is available at http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start.


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Product identification and kinetic data for the reaction of S(IV) with N(III) oxoacids in aqueous solution in the absence and presence of metal ions

Abstract The reaction of S(IV) with N(III) oxoacids was studied in the pH range 3.5–5.2, and in the absence and presence of metal ions, using ion-pair chromatography (IPC), and stopped-flow and conventional spectroscopy. Product identification and distribution of the sulphur-nitrogen oxides formed during this reaction was determined by IPC. The empirical rate law suggests that HONO and HSO − 3 are the main reactive species in the investigated pH range, and the data are compared to that available from the literature. Hydroxylaminedisulphonate was found to be the only identifiable sulphur-nitrogen oxoanion produced during the reaction. The effect of Mn(II/III) and Fe(II/III) on the reaction was studied and a meaningful catalytic effect was found for Fe(II). This is ascribed to the interaction of Fe(II) with HONO to produce a nitrosyl complex that can react with HSO − 3 according to the Boedeker reaction.
Parental literacy predicts children's literacy: a longitudinal family-risk study.

This family-risk (FR) study examined whether the literacy skills of parents with dyslexia are predictive of the literacy skills of their offspring. We report data from 31 child-parent dyads where both had dyslexia (FR-D) and 68 dyads where the child did not have dyslexia (FR-ND). Findings supported the differences in liability of FR children with and without dyslexia: the parents of the FR-D children had more severe difficulties in pseudoword reading and spelling accuracy, in rapid word recognition, and in text reading fluency than the parents of the FR-ND children. Finally, parental skills were found to be significant predictors of children's Grade 3 reading and spelling. Parental skills predicted children's reading and spelling accuracy even after controlling for children's preschool skills. Our findings suggest that the literacy skills of a parent with dyslexia might be valuable in assessing early on their child's liability to dyslexia.