Nanopore sequencing simulator for DNA data storage

The exponential increase of digital data and the limited capacity of current storage devices have made clear the need for exploring new storage solutions. Thanks to its biological properties, DNA has proven to be a potential candidate for this task, allowing the storage of information at a high density for hundreds or even thousands of years. With the release of nanopore sequencing technologies, DNA data storage is one step closer to become a reality. Many works have proposed solutions for the simulation of this sequencing step, aiming to ease the development of algorithms addressing nanopore-sequenced reads. However, these simulators target the sequencing of complete genomes, whose characteristics differ from the ones of synthetic DNA. This work presents a nanopore sequencing simulator targeting synthetic DNA on the context of DNA data storage

Facial conformation characteristics in Persian and Exotic Shorthair cats

ObjectivesThe primary objectives of the study were to examine the diversity in facial conformation characteristics within a group of Persian (PER) and Exotic Shorthair (EXO) show cats, and to contrast the results to findings within a group of non-purebred domestic shorthair (DSH) and domestic longhair (DLH) cats. The secondary objectives were to determine the PER/EXO show cat owners' perceptions of the breathing status of their cats, and to evaluate if remarks from the cat show judges concerning the cats' head and facial conformation were exclusively related to the aesthetic features of the cats.MethodsSixty-four PER and 12 EXO show cats were prospectively examined at five international cat shows, and 20 DSH/DLH cats were examined at an animal hospital. Facial conformation characteristics were evaluated by examining photos of the cats. Owners of the PER/EXO show cats answered a questionnaire concerning their cats' health status, and they were encouraged to send in the judges' score sheets from the cat shows.ResultsThe PER/EXO show cats had higher diversity in facial conformation characteristics than the DSH/DLH cats, and high incidences of hypoplasia of the nose leather (95%), the nose leather top positioned above the level of the lower eyelid (93%), moderate-to-severe stenotic nares (86%), epiphora (83%) and entropion (32%). Owners of 6/76 PER/EXO show cats stated that their cat had increased respiratory sounds and/or trouble breathing at least once a week. The cat show judges' written comments were exclusively related to aesthetic features of the cats' head and facial conformation details.Conclusions and relevanceHypoplasia of the nose leather, high position of the nose leather top, stenotic nares, epiphora and entropion were common findings in the PER/EXO show cats but not in the DSH/DLH cats. Few of the cat owners perceived that their cat had problems related to the airways

A transcriptomic approach for evaluating the relative potency and mechanism of action of azoles in the rat Whole Embryo Culture.

We evaluated the effect of six azoles on embryonic development in the rat whole embryo culture (WEC). Using the total morphological scoring system (TMS), we calculated the ID10concentration (effective dose for 10% decrease in TMS). For evaluating gene specific responses, we combined previously and newly collected transcriptomics data of rat WEC exposed to a total of twelve azoles at their ID10for 4h. Results revealed shared expressions responses in genes involved in the retinoic acid (RA) and sterol biosynthesis pathways, which are respectively representatives of developmental toxicity and targeted fungicidal action of the azoles. Azoles with more pronounced effects on the regulation of RA-associated genes were generally characterized as more potent embryotoxicants. Overall, compounds with strong sterol biosynthesis related responses and low RA related responses were considered as more favourable candidates, as they specifically regulated genes related to a desired target response. Among the identified sterol associated genes, we detected that methylsterol monooxygenase 1 (Msmo1) was more sensitively induced compared to Cyp51, a classical biomarker of this pathway. Therefore, we suggest that Msmo1 could be a better biomarker for screening the fungicidal value of azoles. In summary, we conclude that the embryonic regulation of RA and sterol metabolic pathways could be indicators for ranking azoles as embryotoxicants and determining their drug efficacy

High-resolution measurement of the time-modulated orbital electron capture and of the β+\beta^+ decay of hydrogen-like 142^{142}Pm60+^{60+} ions

The periodic time modulations, found recently in the two-body orbital electron-capture (EC) decay of both, hydrogen-like $^{140}$Pr$^{58+}$ and $^{142}$Pm$^{60+}$ ions, with periods near to 7s and amplitudes of about 20%, were re-investigated for the case of $^{142}$Pm$^{60+}$ by using a 245 MHz resonator cavity with a much improved sensitivity and time resolution. We observed that the exponential EC decay is modulated with a period $T = 7.11(11)$s, in accordance with a modulation period $T = 7.12(11)$ s as obtained from simultaneous observations with a capacitive pick-up, employed also in the previous experiments. The modulation amplitudes amount to $a_R = 0.107(24)$ and $a_P = 0.134(27)$ for the 245 MHz resonator and the capacitive pick-up, respectively. These new results corroborate for both detectors {\it exactly} our previous findings of modulation periods near to 7s, though with {\it distinctly smaller} amplitudes. Also the three-body $\beta^+$ decays have been analyzed. For a supposed modulation period near to 7s we found an amplitude $a = 0.027(27)$, compatible with $a = 0$ and in agreement with the preliminary result $a = 0.030(30)$ of our previous experiment. These observations could point at weak interaction as origin of the observed 7s-modulation of the EC decay. Furthermore, the data suggest that interference terms occur in the two-body EC decay, although the neutrinos are not directly observed.Comment: In memoriam of Prof. Paul Kienle, 9 pages, 1 table, 5 figures Phys. Lett. B (2013) onlin

Observation of Non-Exponential Orbital Electron Capture Decays of Hydrogen-Like 140^{140}Pr and 142^{142}Pm Ions

We report on time-modulated two-body weak decays observed in the orbital electron capture of hydrogen-like $^{140}$Pr$^{59+}$ and $^{142}$Pm$^{60+}$ ions coasting in an ion storage ring. Using non-destructive single ion, time-resolved Schottky mass spectrometry we found that the expected exponential decay is modulated in time with a modulation period of about 7 seconds for both systems. Tentatively this observation is attributed to the coherent superposition of finite mass eigenstates of the electron neutrinos from the weak decay into a two-body final state.Comment: 12 pages, 5 figure

Adverse anthropometric risk profile in biochemically controlled acromegalic patients: comparison with an age- and gender-matched primary care population

GH and IGF-1 play an important role in the regulation of metabolism and body composition. In patients with uncontrolled acromegaly, cardiovascular morbidity and mortality are increased but are supposed to be normalised after biochemical control is achieved. We aimed at comparing body composition and the cardiovascular risk profile in patients with controlled acromegaly and controls. A cross-sectional study. We evaluated anthropometric parameters (height, weight, body mass index (BMI), waist and hip circumference, waist to height ratio) and, additionally, cardiovascular risk biomarkers (fasting plasma glucose, HbA1c, triglycerides, total cholesterol, HDL, LDL, and lipoprotein (a), in 81 acromegalic patients (58% cured) compared to 320 age- and gender-matched controls (ratio 1:4), sampled from the primary care patient cohort DETECT. The whole group of 81 acromegalic patients presented with significantly higher anthropometric parameters, such as weight, BMI, waist and hip circumference, but with more favourable cardiovascular risk biomarkers, such as fasting plasma glucose, total cholesterol, triglycerides and HDL levels, in comparison to their respective controls. Biochemically controlled acromegalic patients again showed significantly higher measurements of obesity, mainly visceral adiposity, than age- and gender-matched control patients (BMI 29.5 ± 5.9 vs. 27.3 ± 5.8 kg/m2; P = 0.020; waist circumference 100.9 ± 16.8 vs. 94.8 ± 15.5 cm; P = 0.031; hip circumference 110.7 ± 9.9 vs. 105.0 ± 11.7 cm; P = 0.001). No differences in the classical cardiovascular biomarkers were detected except for fasting plasma glucose and triglycerides. This effect could not be attributed to a higher prevalence of type 2 diabetes mellitus in the acromegalic patient group, since stratified analyses between the subgroup of patients with acromegaly and controls, both with type 2 diabetes mellitus, revealed that there were no significant differences in the anthropometric measurements. Biochemically cured acromegalic patients pertain an adverse anthropometric risk profile, mainly because of elevated adiposity measurements, such as BMI, waist and hip circumference, compared to an age- and gender-matched primary care population