Engines of liberation

women;technological change

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.National Science Foundation (U.S.) (NSF/NIH BIGDATA Grant R01GM108348-01)National Science Foundation (U.S.) (Graduate Research Fellowship)Simons Foundatio

Parenting and child adjustment: a comparison of Turkish and English families

The links between parenting and child behaviour in cultural context have received increasing research attention. We investigated the effect of parenting on child adjustment using a multi-method design, comparing English and Turkish families. The socioeconomically diverse samples included 118 English and 100 Turkish families, each with two children aged 4–8 years. Mothers completed questionnaires as well as parent–child interaction being assessed using a structured Etch-a-Sketch task with each child separately. Children were interviewed about their relationships with their mothers using the Berkeley Puppet Interview. Multiple-group Confirmatory Analysis was used to test Measurement Invariance across groups, and a multi-informant approach was used to assess parenting. We found partial cross-cultural measurement invariance for parenting and child adjustment. Strikingly, the association between parenting and child adjustment was stronger among English families than Turkish families. Culturally distinct meanings of both parenting and child behaviour must be considered when interpreting their association

Diagnostic algorithm for papillary urothelial tumors in the urinary bladder

Papillary urothelial neoplasms with deceptively bland cytology cannot be easily classified. We aimed to design a new algorithm that could differentiate between these neoplasms based on a scoring system. We proposed a new scoring system that enables to reproducibly diagnose non-invasive papillary urothelial tumors. In this system, each lesion was given individual scores from 0 to 3 for mitosis and cellular thickness, from 0 to 2 for cellular atypia, and an additional score for papillary fusion. These scores were combined to form a summed score allowing the tumors to be ranked as follows: 0–1 = UP, 2–4 = low malignant potential (LMP), 5–7 = low-grade transitional cell carcinoma (TCC), and 8–9 = high-grade TCC. In addition to the scoring system, ancillary studies of MIB and p53 indexes with CK20 expression pattern analyses were compared together with clinical parameters. The MIB index was strongly correlated with disease progression. Four of the 22 LMP patients (18.2%) had late recurrences, two of these four (9.1%) had progression to low-grade carcinoma. The MIB index for LMP patients was strongly associated with recurrence (recurrence vs. non-recurrence, 16.5 vs. 8.1, p < 0.001). The proposed scoring system could enhance the reproducibility to distinguish papillary urothelial neoplasms

Treatment of thromboangiitis obliterans (Buerger's disease) with bosentan

<p>Abstract</p> <p>Background</p> <p>This study assessed the effectiveness and safety of bosentan when administered to thromboangiitis obliterans (Buerger's disease) patients.</p> <p>Methods</p> <p>A clinical pilot study was designed in which patients with ulcer and/or pain at rest were treated with bosentan p.o. at a dose of 62.5 mg twice daily during the first month, which was thereafter up-titrated to 125 mg twice daily. The study endpoints were clinical improvement rate, major or minor amputation rate, haemodynamic changes, changes in endothelial function and angiographic changes.</p> <p>Results</p> <p>Seven out of 12 patients were male (58%). Median age was 39 years (range 29-49). The median follow-up was 20 months (range 11-40). All patients were smokers. With bosentan treatment, new ischaemic lesions were observed in only one patient. Overall, clinical improvement was observed in 12 of the 13 extremities (92%). Only two out of 13 extremities underwent amputation (one major and one minor) after bosentan treatment. After being assessed by digital arteriography with subtraction or angio-magnetic resonance imaging, an increase of distal flow was observed in 10 out of the 12 patients. All patients experienced a statistically significant improvement in their BAFMD values (mean: 1.8 at baseline; 6.6 at the end of the treatment; 12.7 three months after the end of the treatment; p < 0.01).</p> <p>Conclusion</p> <p>Bosentan treatment may result in an improvement of clinical, angiographic and endothelial function outcomes. Bosentan should be investigated further in the management of TAO patients. Larger studies are required to confirm these results.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT01447550">NCT01447550</a></p

Effects of acid leaching on halloysite

A characteristic iron-containing halloysite sample from Turkey was subjected to acid leaching using organic and inorganic acids for removing iron impurities. The aim of this study was to compare the raw hydrated and dehydrated halloysites with the leached products. Hydrochloric acid and oxalic acid were chosen as leaching agents for the removal of iron impurities at 80 °C for 2.5 h. The physicochemical properties of the acid-treated halloysite were analyzed by XRF, XRD, FTIR, TGA, DTA, SEM, and TEM. The XRF results showed that the acid treatment caused the dissolution of minor amounts of Al3+ ions from the clay layer. The XRD results indicated that the crystalline structure was unchanged after the leaching. However, it was observed that the hydrated (1 nm) halloysite readily lost its interlayer water and was transformed to the dehydrated (0.7 nm) form. In addition, no visible effects of the acid treatment on the tubular structure of halloysite were detected in the SEM and TEM images. Typical pores of varying dimensions were observed in all of the samples regardless of their form or treatment. Furthermore, the TG-DTA and FTIR analysis results were similar for both the raw and the acid-treated samples

Localized lipoatrophy due to recombinant growth hormone therapy in a child with 6.7 kilobase gene deletion isolated growth hormone deficiency

Local lipoatrophy is a well known complication of insulin treatment at injection sites and the etiology is thought to be a cross reaction with lipid tissues and insulin antibody. Although mild lipoatrophy during growth hormone treatment has been reported in the literature, severe local lipoatrophy in injection sites in the extremities has not yet been published. We report a patient with isolated GH deficiency due to 6.7 kb gene deletion who received high dose rhGH treatment and developed local lipoatrophies at injection sites without any antibody detection after 6 years of therapy. The etiology of the lipoatrophy is suspected to be by the direct lipolytic effect of high doses of rhGH

Levels: A Rat Model

Technicians often receive chronic magnetic exposures from magnetic resonance imaging (MRI) devices, mainly due to static magnetic fields (SMFs). Here, we ascertain the biological effects of chronic exposure to SMFs from MRI devices on the bone quality using rats exposed to SMFs in MRI examining rooms. Eighteen Wistar albino male rats were randomly assigned to SMF exposure (A), sham (B), and control (C) groups. Group A rats were positioned within 50 centimeters of the bore of the magnet of 1.5 T MRI machine during the nighttime for 8 weeks. We collected blood samples for biochemical analysis, and bone tissue samples for electron microscopic and histological analysis. The mean vitamin D level in Group A was lower than in the other groups (p = 0.002). The mean cortical thickness, the mean trabecular wall thickness, and number of trabeculae per 1 mm(2) were significantly lower in Group A (p = 0.003). TUNEL assay revealed that apoptosis of osteocytes were significantly greater in Group A than the other groups (p = 0.005). The effect of SMFs in chronic exposure is related to movement within the magnetic field that induces low-frequency fields within the tissues. These fields can exceed the exposure limits necessary to deteriorate bone microstructure and vitamin D metabolism

The effect of the position of compression screw in plate-screws method used in fracture treatment on fatigue strength of joint

A number of combination studies on the use of plate-screws, which has become a traditional method in fracture treatment, have been conducted to obtain a more rigid joint. These studies in the literature were reviewed and it was seen that the effect of the position of the compression screw, used with the aim of making the fracture line come closer to each other during fracture fixation, on the fatigue strength of the joint hasn’t been investigated. Within the scope of this study, a screw combination study by including Limited Contact Dynamic Compression Plate (LC-DCP) plates that possess combined hole properties was carried out. Three different combinations were created during the study. In these combinations, the unlocked screw that was located on the part where the force was applied and that was used for compression was placed in different holes and fatigue strengths of the joints were investigated under dynamic bending force. As a result of the study, it was observed that as the compression screw moved away from the fracture line, fatigue strength of the joint consisting of plate, screw and bone decreased. In addition, it was found that all the joints in the 3rd combination got damaged as a result of the fracture of the bone. © Springer Nature Switzerland AG 2019

Chronic Exposure to Static Magnetic Fields from Magnetic Resonance Imaging Devices Deserves Screening for Osteoporosis and Vitamin D Levels: A Rat Model.

Technicians often receive chronic magnetic exposures from magnetic resonance imaging (MRI) devices, mainly due to static magnetic fields (SMFs). Here, we ascertain the biological effects of chronic exposure to SMFs from MRI devices on the bone quality using rats exposed to SMFs in MRI examining rooms. Eighteen Wistar albino male rats were randomly assigned to SMF exposure (A), sham (B), and control (C) groups. Group A rats were positioned within 50 centimeters of the bore of the magnet of 1.5 T MRI machine during the nighttime for 8 weeks. We collected blood samples for biochemical analysis, and bone tissue samples for electron microscopic and histological analysis. The mean vitamin D level in Group A was lower than in the other groups (p = 0.002). The mean cortical thickness, the mean trabecular wall thickness, and number of trabeculae per 1 mm2 were significantly lower in Group A (p = 0.003). TUNEL assay revealed that apoptosis of osteocytes were significantly greater in Group A than the other groups (p = 0.005). The effect of SMFs in chronic exposure is related to movement within the magnetic field that induces low-frequency fields within the tissues. These fields can exceed the exposure limits necessary to deteriorate bone microstructure and vitamin D metabolism