Balancing SoNaR: IPR versus Processing Issues in a 500-Million-Word Written Dutch Reference Corpus

In The Low Countries, a major reference corpus for written Dutch is beingbuilt. We discuss the interplay between data acquisition and data processingduring the creation of the SoNaR Corpus. Based on developments in traditionalcorpus compiling and new web harvesting approaches, SoNaR is designed tocontain 500 million words, balanced over 36 text types including bothtraditional and new media texts. Beside its balanced design, every text sampleincluded in SoNaR will have its IPR issues settled to the largest extentpossible. This data collection task presents many challenges because everydecision taken on the level of text acquisition has ramifications for the levelof processing and the general usability of the corpus. As far as thetraditional text types are concerned, each text brings its own processingrequirements and issues. For new media texts - SMS, chat - the problem is evenmore complex, issues such as anonimity, recognizability and citation right, allpresent problems that have to be tackled. The solutions actually lead to thecreation of two corpora: a gigaword SoNaR, IPR-cleared for research purposes,and the smaller - of commissioned size - more privacy compliant SoNaR,IPR-cleared for commercial purposes as well

Karyotype analyses of the species of the genus Jurinea Cass. (Compositae) in Turkey

In this study, karyotype analyses of 13 species belonging to the genus Jurinea Cass. (Compositae) and grown naturally in Turkey were conducted. These taxa include Jurinea alpigena C. Koch, Jurinea ancyrensis Bornm., Jurinea aucherana DC., Jurinea cadmea Boiss., Jurinea cataonica Boiss. and Hausskn., Jurinea consanguinea DC., Jurinea cypria Boiss., Jurinea macrocalathia C. Koch., Jurinea macrocephala DC., Jurinea mollis (L.) Reichb., Jurinea pontica Hausskn. and Freyn ex Hausskn., Jurinea pulchella DC., Jurinea ramulosa Boiss. and Hausskn. Karyotype analysis of all the species are introduced to the scientific community for the first time and they were obtained through an Image analysis system. The study has made  contribution to the cytotaxonomic revision of the genus Jurinea in Turkey.Key words: Asteraceae, Image analysis, Jurinea, karyotype, Turkey

Tobacco Xenobiotics Release Nitric Oxide

Many xenobiotic compounds exert their actions through the release of free radicals and related oxidants [1,2], bringing about unwanted biological effects [3]. Indeed, oxidative events may play a significant role in tobacco toxicity from cigarette smoke. Here, we demonstrate the direct in vitro release of the free radical nitric oxide (•NO) from extracts and components of smokeless tobacco, including nicotine, nitrosonornicotine (NNN) and 4-(methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in phosphate buffered saline and human saliva using electron spin resonance and chemiluminescence detection. Our findings suggest that tobacco xenobiotics represent as yet unrecognized sources of •NO in the body

Perceived Visual Direction near an Occluder

When an opaque object occludes a more distant object, the two eyes often see different parts of the distant object. Hering s laws of visual direction make an interesting prediction for this situation: the part seen by both eyes should be seen in a different direction than the part seen by one eye. We examined whether this prediction holds by asking observers to align a vertical monocular line segment with a nearby vertical binocular segment. We found it necessary to correct the alignment data for vergence errors, which were measured in a control experiment, and for monocular spatial distortions, which were also measured in a control experiment. Settings were reasonably consistent with Hering's laws when the monocular and binocular targets were separated by 30 arcmin or more. Observers aligned the targets as if they were viewing them from one eye only when they were separated by 2 arcmin; this behavior is consistent with an observation reported by Erkelens and colleagues. The same behavior was observed when the segments were horizontal and when no visible occluder was present. Perceived visual direction when the two eyes see different parts of a distant target is assigned in a fashion that minimizes, but does not eliminate, distortions of the shape of the occluded object

An analysis of binocular slant contrast

When a small frontoparallel surface (a test strip) is surrounded by a larger slanted surface (an inducer), the test strip is perceived as slanted in the direction opposite to the inducer. This has been called the depth-contrast effect, but we call it the slant-contrast effect. In nearly all demonstrations of this effect, the inducers slant is specified by stereoscopic signals, and other signals, such as the texture gradient, specify that it is frontoparallel. We present a theory of slant estimation that determines surface slant via linear combination of various slant estimators; the weight of each estimator is proportional to its reliability. The theory explains slant contrast because the absolute slant of the inducer and the relative slant between test strip and inducer are both estimated with greater reliability than the absolute slant of the test strip. The theory predicts that slant contrast will be eliminated if the signals specifying the inducers slant are consistent with one another. It also predicts reversed slant contrast if the inducers slant is specified by nonstereoscopic signals rather than by stereo signals. These predictions were tested and confirmed in three experiments. The first showed that slant contrast is greatly reduced when the stereo- and nonstereo-specified slants of the inducer are made consistent with one another. The second showed that slant contrast is eliminated altogether when the stimulus consists of real planes rather than images on a display screen. The third showed that slant contrast is reversed when the nonstereo-specified slant of the inducer varies and the stereo-specified slant is zero. We conclude that slant contrast is a byproduct of the visual systems reconciliation of conflicting information while it attempts to determine surface slant

Phylogenetic relationship analysis of Genista L. (Fabaceae) species from Turkey as revealed by intersimple sequence repeat amplification

Genista L. (Fabaceae) is distributed in Europe, South Africa, and West Asia and consists of almost 90 species in the world. Thirteen species of the genus are distributed in Turkey. Taxonomic problems of the species started to be resolved with recently developed DNA-based molecular methods. These methods, in contrast to phenotypical analyses, are free from the effects of environmental conditions. In this study, DNA of the species which belong to the Genista genus, grown naturally in Turkey and collected from the different localities, were isolated with a commercial kit. Inter-simple sequence repeat (ISSR) is a simple molecular marker system that provides reliable results. Based on ISSR data, genetic similarities anddendrogram demonstrating the phylogenetic relationships among the Genista taxa were prepared by the NTSYSpc 2.0 software. In this study, infrageneric classifications of the Genista taxa belonging to the Flora of Turkey were conducted based on molecular data. ISSR analysis strongly supported the hypothesis that G. aucheri is accepted as the synonym of G. sessilifolia

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.

Common Variable Immunodeficiency Disorders (CVIDs) are the most prevalent cause of primary antibody failure. CVIDs are highly variable and a genetic causes have been identified in <5% of patients. Here, we performed whole genome sequencing (WGS) of 34 CVID patients (94% sporadic) and combined them with transcriptomic profiling (RNA-sequencing of B cells) from three patients and three healthy controls. We identified variants in CVID disease genes TNFRSF13B, TNFRSF13C, LRBA and NLRP12 and enrichment of variants in known and novel disease pathways. The pathways identified include B-cell receptor signalling, non-homologous end-joining, regulation of apoptosis, T cell regulation and ICOS signalling. Our data confirm the polygenic nature of CVID and suggest individual-specific aetiologies in many cases. Together our data show that WGS in combination with RNA-sequencing allows for a better understanding of CVIDs and the identification of novel disease associated pathways

Assessing the influence of health systems on Type 2 Diabetes Mellitus awareness, treatment, adherence, and control: A systematic review.

BACKGROUND: Type 2 Diabetes Mellitus (T2DM) is reported to affect one in 11 adults worldwide, with over 80% of T2DM patients residing in low-to-middle-income countries. Health systems play an integral role in responding to this increasing global prevalence, and are key to ensuring effective diabetes management. We conducted a systematic review to examine the health system-level factors influencing T2DM awareness, treatment, adherence, and control. METHODS AND FINDINGS: A protocol for this study was published on the PROSPERO international prospective register of systematic reviews (PROSPERO 2016: CRD42016048185). Studies included in this review reported the effects of health systems factors, interventions, policies, or programmes on T2DM control, awareness, treatment, and adherence. The following databases were searched on 22 February 2017: Medline, Embase, Global health, LILACS, Africa-Wide, IMSEAR, IMEMR, and WPRIM. There were no restrictions on date, language, or study designs. Two reviewers independently screened studies for eligibility, extracted the data, and screened for risk of bias. Thereafter, we performed a narrative synthesis. A meta-analysis was not conducted due to methodological heterogeneity across different aspects of included studies. 93 studies were included for qualitative synthesis; 7 were conducted in LMICs. Through this review, we found two key health system barriers to effective T2DM care and management: financial constraints faced by the patient and limited access to health services and medication. We also found three health system factors that facilitate effective T2DM care and management: the use of innovative care models, increased pharmacist involvement in care delivery, and education programmes led by healthcare professionals. CONCLUSIONS: This review points to the importance of reducing, or possibly eliminating, out-of-pocket costs for diabetes medication and self-monitoring supplies. It also points to the potential of adopting more innovative and integrated models of care, and the value of task-sharing of care with pharmacists. More studies which identify the effect of health system arrangements on various outcomes, particularly awareness, are needed

Quasi-simultaneous multiplane calcium imaging of neuronal circuits

Two-photon excitation fluorescence microscopy is widely used to study the activity of neuronal circuits. However, the fast imaging is typically constrained to a single lateral plane for a standard microscope design. Given that cortical neuronal networks in a mouse brain are complex three-dimensional structures organised in six histologically defined layers which extend over many hundreds of micrometres, there is a strong demand for microscope systems that can record neuronal signalling in volumes. Henceforth, we developed a quasi-simultaneous multiplane imaging technique combining acousto-optic deflector and static remote focusing to provide fast imaging of neurons from different axial positions inside the cortical layers without the need for the mechanical interference of either the objective lens or the specimen. The hardware and the software are easily adaptable to existing two-photon microscopes. Here, we demonstrated that our imaging method can record, at high speed and high image contrast, the calcium dynamics of neurons in two different imaging planes separated axially, with the in-focus and the refocused planes 120 μm and 250 μm below the brain surface respectively