Towards a comprehensive open source platform for management and analysis of High Content Screening data

As High Content Screening (HCS) has moved into the main stream for biological and pharmaceutical investigations, a lag of well integrated pipelines for automated acquisition, management and analysis of HCS results turns out to be a bottleneck for fully leveraging the wealth of information contained in a screen and moving to higher throughput. For many applications, monolithic pipelines can not deliver the flexibility and versatility needed. Laboratories and scientific service providers instead usually look into integrating components from both, the open source world and the commercial software world into best-of-breed data pipelines. In this article, we will present two open source components that can be used as flexible and powerful building blocks for such a pipeline

Viewpoint on Emv2, the onlhy endogenous ecotropic murine leukemia virus of C57BL/6 mice

Here I comment on the articles by Lee and colleagues (Retrovirology 2011, 8:82) and Lee and Cho (Retrovirology 2012, 9:23) dealing with an endogenous ecotropic mouse leukemia virus found in C57BL mice

Aktywność fizyczna dziewcząt w okresie dojrzewania = Physical activity in girls at puberty

Pilewska–Kozak Anna B., Łepecka–Klusek Celina, Stadnicka Grażyna, Dobrowolska Beata, Pawłowska–Muc Agnieszka K., Kozak Łukasz A., Ulan Agnieszka, Wagner Emilia. Aktywność fizyczna dziewcząt w okresie dojrzewania = Physical activity in girls at puberty. Journal of Education, Health and Sport. 2015;5(9):305-316. ISSN 2391-8306. DOI10.5281/zenodo.30805http://dx.doi.org/10.5281/zenodo.30805http://ojs.ukw.edu.pl/index.php/johs/article/view/2015%3B5%289%29%3A305-316https://pbn.nauka.gov.pl/works/623257Formerly Journal of Health Sciences. ISSN 1429-9623 / 2300-665X. Archives 2011–2014http://journal.rsw.edu.pl/index.php/JHS/issue/archive Deklaracja.Specyfika i zawartość merytoryczna czasopisma nie ulega zmianie.Zgodnie z informacją MNiSW z dnia 2 czerwca 2014 r., że w roku 2014 nie będzie przeprowadzana ocena czasopism naukowych; czasopismo o zmienionym tytule otrzymuje tyle samo punktów co na wykazie czasopism naukowych z dnia 31 grudnia 2014 r.The journal has had 5 points in Ministry of Science and Higher Education of Poland parametric evaluation. Part B item 1089. (31.12.2014).© The Author (s) 2015;This article is published with open access at Licensee Open Journal Systems of Kazimierz Wielki University in Bydgoszcz, Poland and Radom University in Radom, PolandOpen Access. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium,provided the original author(s) and source are credited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License(http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited.This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercialuse, distribution and reproduction in any medium, provided the work is properly cited.The authors declare that there is no conflict of interests regarding the publication of this paper.Received: 25.08.2015. Revised 05.09.2015. Accepted: 08.09.2015. Aktywność fizyczna dziewcząt w okresie dojrzewaniaPhysical activity in girls at puberty Anna B. Pilewska–Kozak1, Celina Łepecka–Klusek1, Grażyna Stadnicka2, Beata Dobrowolska3, Agnieszka K. Pawłowska–Muc4, Łukasz A. Kozak5, Agnieszka Ulan6, Emilia Wagner6 1Katedra i Klinika Ginekologii i Endokrynologii Ginekologicznej Wydział Nauk o Zdrowiu, Uniwersytet Medyczny w Lublinie2Samodzielna Pracownia Umiejętności Położniczych Wydział Nauk o Zdrowiu, Uniwersytet Medyczny w Lublinie3Katedra Rozwoju Pielęgniarstwa Wydział Nauk o Zdrowiu, Uniwersytet Medyczny w Lublinie4Ośrodek Kształcenia Podyplomowego Pielęgniarek i Położnych Radomski Szpital Specjalistyczny im. dr Tytusa Chałubińskiego w Radomiu5Oddział Chirurgii Urazowo – Ortopedycznej z Chirurgią Kręgosłupa, Samodzielny Publiczny Zakład Opieki Zdrowotnej w Puławach6Studentka III roku kierunku położnictwo, Studenckie Koło Naukowe przy Katedrze i Klinice Ginekologii i Endokrynologii Ginekologicznej, Wydział Nauk o Zdrowiu Uniwersytet Medyczny w Lublinie Streszczenie Wstęp         Sprawność fizyczna ukształtowana w wieku młodzieńczym ma swoje odzwierciedlenie w życiu dorosłym. Wpływa na ogólny dobrostan, na elastyczne przystosowywanie się do ról w życiu zawodowym, na równowagę emocjonalną i większą odporność na stres. Warunkuje odpowiedzialność, wytrwałość w dążeniu do wyznaczonych celów oraz zdyscyplinowanie, a także pozwala na podtrzymanie dobrej kondycji w wieku dojrzałym i w okresie starości.Cel pracy         Sprawdzenie, czy dziewczęta w okresie dojrzewania ćwiczą na lekcjach wychowania fizycznego i są aktywne ruchowo poza szkołą oraz czy ma to związek z miejscem ich zamieszkania.Materiał i metoda         Badaniami ankietowymi objęto 169 uczennic gimnazjów (80 mieszkających w mieście i 89 na wsi) w województwie lubelskim. Wiek dziewcząt wahał się w granicach od 11 lat do 17 lat (Mediana = 15 lat). Kryterium włączenia było wystąpienie menarche. Na prowadzenie badań uzyskano zgody Komisji Bioetycznej Uniwersytetu Medycznego w Lublinie nr KE-0254/224/2013 z dnia 26 września 2013r. oraz nr KE-0254/246/2013 z dnia 24 października 2013r.Wyniki badań         Większość uczennic, zarówno ze wsi, jak i z miasta (odpowiednio 66; 74.1% i 59; 73.8%), oświadczyła, że prowadzi aktywny tryb życia. Innych - analogicznie 10 (11.2%) i 8 (10.0%) było przeciwnego zdania, a co piąta (19; 21.3%) dziewczynka z terenów wiejskich i 13 (16,3%) z miejskich nie potrafiła tego ocenić. Regularne uczęszczanie na lekcje wychowania fizycznego potwierdziły 94 (55,6%) badane. Pozostałe oświadczyły, iż czynią to nieregularnie (68; 40.2%) lub mają zwolnienie lekarskie z tych zajęć (7; 4.1%).  Stwierdzono istotną statystycznie zależność między uczęszczaniem na lekcje wychowania fizycznego a miejscem zamieszkania uczennic (p<0,05), na korzyść mieszkanek miast, które częściej czyniły to regularnie. Ponadto stwierdzono istotne statystycznie zależności pomiędzy preferowanymi formami wypoczynku w okresie szkolnym i wakacyjnym (p<0,001). Różnice zarysowały się także, gdy wzięto pod uwagę miejsce zamieszkania badanych – w okresie zajęć szkolnych formy czynne istotnie częściej, niż bierne preferowały mieszkanki miast niż wsi (p=0.005), a w okresie wakacji odwrotnie (p<0.001).WnioskiWiele dziewcząt w okresie dojrzewania nie ćwiczy regularnie na lekcjach wychowania fizycznego, przy czym częściej mieszkanki wsi niż miast.Aktywne formy wypoczynku w okresie szkolnym preferują częściej mieszkanki miast niż wsi, a w okresie wakacji odwrotnie. Słowa kluczowe: aktywność fizyczna, dojrzewanie, dziewczęta. Summary Introduction         Fitness formed in adolescence is reflected in adulthood. It affects general wellbeing, flexibility to adapt to future roles in professional life, emotional balance and greater resistance to stress. It determines responsibility, persistent pursuit of targets and discipline, and also allows to maintain good health through adulthood and old age.Objective         To verify that girls at puberty do physical exercises at physical education (PE) classes and are physically active outside school, and to establish whether it is related to their place of residence.Material and Methods         The survey was conducted in 169 junior high school students, 80 living in the urban area and89 inthe rural region, aged 11 -17 years (median = 15 years) in The Lublin Province. The inclusion criterion was the occurrence of menarche. The  research was approved by the Bioethics Committee of the Medical University of Lublin No. KE-0254/224/2013 of 26 September 2013 and No. KE-0254/246/2013 of 24 October 2013.Results         Most of the students, both from the country as well as from the city (respectively 66, 74.1% and 59; 73.8%) admitted to leading an active lifestyle. The others, respectively 10 (11.2%) and 8 (10.0%) respondents were of the opposite opinion;  in the group of country girls, one girl in five (19; 21.3%), and 13 girls from the town group (16.3%) were unable to evaluate that. Regular attendance at PE classes was confirmed by 94 (55.6%) respondents. Others stated that they did not do it regularly (68; 40.2%) or were exempted from PE classes due to medical reasons (7; 4.1%). A statistically significant correlation between attending PE and place of residence of students was found (p <0.05) in favor of the inhabitants of the cities who more often did exercise regularly. In addition, statistically significant relationship was determined between preferred forms of rest during the school year and in the summer (p <0.001). Differences also emerged when the place of respondents’ residence was taken into account, i.e. in the period of school, the girls from towns preferred active forms to passive significantly more frequently in comparison to the girls from rural areas (p = 0.005); the situation reversed during the holiday period (p <0.001).ConclusionsMany girls at puberty do not exercise regularly at physical education classes, it is more frequent among the girls from rural regions compared to the girls living in town.During the period of school year, the girls living in urban areas more often prefer active forms of recreation compared to the girls from rural regions and the situation is reversed  during the holiday period. Key words: physical activity, girls, puberty

Багатогранна постать Івана Яковича Горбачевського

Introduction. Ivan Horbachevsky, native of the Ternopil region, is an outstanding figure in the Ukrainian history. Despite the fact that he had spent almost all his life in the foreign land, he was the faithful son of his Motherland. Ivan Horbachevsky was the first ethnic Ukrainian, who was appointed the health minister in the government of the Austro-Hungarian Empire. The name of Ivan Horbachevsky was being forgotten for a long time inequitably, even though his figure has high historical importance not only forGalicia, but also for wholeUkraine. It should be underlined, that his name has the same significance for Ukrainians as the famous names of Ivan Franko and Solomia Krushelnytska. Taking into account Horbachevsky’s contibutions to our country, in 1992 Cabinet of Ministers of Ukraine took the decision to give the name of this great scientist to the Ternopil Medical Institute. And in this year I. HorbachevskyTernopilStateMedicalUniversity celebrates its 60th anniversary.The aim of the study – to highlight scientific achievements and outline the main milestones in the life of such outstanding person, as Ivan Horbachevsky. This will be the invaluable gift for both present and future generations.Conclusions. The life of Ivan Horbachevsky could be an example for all of us, for all contemporaries, and his scientific contributions will be alive forever and will be continued in the numerous works of his followers. No doubt that every scientist and student of the institution should not only know and remember him, but also followed working and citizenship position of our great compatriot Ivan Horbachevsky.Вступление. Иван Яковлевич Горбачевский, уроженец Тернопольской земли, является неординарной фигурой в украинской истории, ведь, проведя практически всю свою жизнь на чужбине, он навеки остался верным сыном своего Отечества. Иван Яковлевич был первым этническим украинцем, которого назначили министром здравоохранения в правительстве Австро-Венгерской империи. Это имя долгое время оставалось несправедливо забытым, хотя его фигура по исторической значимости для Галичины в том числе и для Украины в целом не уступает знаменитым Ивану Франко и Соломии Крушельницкой. Несмотря на немалые заслуги перед Родиной, имя знаменитого ученого увековечено в названии Тернопольского медицинского института в1992 г. по решению Кабинета Министров Украины. А именно в этом году Тернопольский государственный медицинский университет имени Ивана Яковлевича Горбачевского отметил свое 60-летие.Цель исследования – осветить научные достижения и наметить основные вехи становления такой величественной личности, как Иван Яковлевич Горбачевский, что является неоценимым подарком как сегодняшнему, так и будущему поколению.Выводы. Жизненный путь Ивана Яковлевича Горбачевского является образцом для подражания современниками, а его научные достижения навеки остаются с нами и продолжают свою жизнь в многочисленных трудах последователей. Без сомнения, каждый ученый и студент учебного заведения должен не только помнить, но и подражать как в трудовой, так и в гражданской позиции нашего великого земляка Ивана Яковлевича Горбачевского.Вступ. Іван Якович Горбачевський, уродженець Тернопільської землі, є неординарною постаттю в українській історії, адже, провівши практично все своє життя на чужині, він навіки залишився вірним сином своєї Вітчизни. Іван Якович був першим етнічним українцем, якого призначили міністром охорони здоров’я в уряді Австро-Угорської імперії. Це ім’я тривалий час залишалося несправедливо забутим, хоча його постать за історичною значимістю для Галичини зокрема і для України загалом не поступається славетним Івану Франкові та Соломії Крушельницькій. Зважаючи на чималі заслуги перед Батьківщиною, ім’я славетного вченого увіковічено у назві Тернопільського медичного інституту в 1992 р. за рішенням Кабінету Міністрів України. А саме в цьому році Тернопільський державний медичний університет імені Івана Яковича Горбачевського відзначив своє 60-річчя. Мета дослідження – висвітлити науковий доробок та окреслити основні віхи становлення такої величної особистості, як Іван Якович Горбачевський, що є неоціненним дарунком як теперішньому, так і майбутньому поколінню.Висновки. Життєвий шлях Івана Яковича Горбачевського є взірцем для наслідування сучасниками, а його наукові досягнення навіки залишаються з нами і продовжують своє життя в численних працях послідовників. Без сумніву, кожен науковець і студент навчального закладу повинен не лише пам’ятати, але й наслідувати як у трудовій, так і в громадянській позиції нашого великого земляка Івана Яковича Горбачевського.

Structural Stability of Intelectin-1

We study the structural stability of helical and non-helical regions in chain A of human intelectin-1. Using a geometrical model introduced previously, a computational analysis based on the recently reported crystal structure of this protein by Kiessling et al. [Nature Struct. Mole. Bio. 22 (2015), 603] is carried out to quantify the resiliency of the native state to steric perturbations. Response to these perturbations is characterized by calculating, relative to the native state, the lateral, radial and angular displacements of n-residue segments of the polypeptide chain centered on each residue. By quantifying the stability of the protein through six stages of unfolding, we are able to identify regions in chain A of intelectin-1 which are markedly affected by structural perturbations versus those which are relatively unaffected, the latter suggesting that the native-state geometry of these regions is essentially conserved. Importantly, residues in the vicinity of calcium ions comprise a conserved region, suggesting that Ca ions play a role not only in the coordination of carbohydrate hydroxyl groups, but in preserving the integrity of the structure

Measurements of natural radioactivity in the salt cavern of the Polkowice-Sieroszowice copper mine

Due to their low radioactivity background, underground physics laboratories offer a unique possibility for investigating extremely rare phenomena like proton decay, dark matter signals or neutrino physics/astrophysics related issues. The knowledge of the natural radioactivity background is essential for the success of an underground physics experiment. The following measurements of the natural radioactivity background, in the foreseen location of an underground physics laboratory in the salt layer, in the Polkowice–Sieroszowice copper mine are presented: concentration of natural radio-isotopes from in situ obtained gamma-ray spectra and from alpha spectroscopy of rock samples, radon concentration in the air and the dose determination

A Possible Constraint on Regional Precipitation Intensity Changes under Global Warming

Changes in daily precipitation versus intensity under a global warming scenario in two regional climate simulations of the United States show a well-recognized feature of more intense precipitation. More important, by resolving the precipitation intensity spectrum, the changes show a relatively simple pattern for nearly all regions and seasons examined whereby nearly all high-intensity daily precipitation contributes a larger fraction of the total precipitation, and nearly all low-intensity precipitation contributes a reduced fraction. The percentile separating relative decrease from relative increase occurs around the 70th percentile of cumulative precipitation, irrespective of the governing precipitation processes or which model produced the simulation. Changes in normalized distributions display these features much more consistently than distribution changes without normalization. Further analysis suggests that this consistent response in precipitation intensity may be a consequence of the intensity spectrum’s adherence to a gamma distribution. Under the gamma distribution, when the total precipitation or number of precipitation days changes, there is a single transition between precipitation rates that contribute relatively more to the total and rates that contribute relatively less. The behavior is roughly the same as the results of the numerical models and is insensitive to characteristics of the baseline climate, such as average precipitation, frequency of rain days, and the shape parameter of the precipitation’s gamma distribution. Changes in the normalized precipitation distribution give a more consistent constraint on how precipitation intensity may change when climate changes than do changes in the nonnormalized distribution. The analysis does not apply to extreme precipitation for which the theory of statistical extremes more likely provides the appropriate description

A Novel Two-Channel Continuous-Time Time-Interleaved 3rd-order Sigma- Delta Modulator with Integrator-Sharing Topology

this paper presents a 3rd-order two-path Continuous-Time Time-Interleaved (CTTI) delta-sigma modulator which is implemented in standard 90nm CMOS technology. The architecture uses a novel method to resolve the delayless feedback path issue arising from the sharing of integrators between paths. By exploiting the concept of the time-interleaving techniques and through the use time domain equations, a conventional single path 3rd-order Discrete-Time (DT) ΔΣ modulator is converted into a corresponding two-path Discrete-Time Time-Interleaved (DTTI) counterpart. The equivalent Continuous-Time Time-Interleaved version derived from the DTTI ΔΣ modulator by determining the DT loop filters and converting them to the equivalent Continuous-Time (CT) loop filters through the use of the Impulse Invariant Transformation. Sharing the integrators between two paths of the reported modulator makes it robust to path mismatch effects compared to the typical Time-Interleaved (TI) modulators which have individual integrators in all paths. The modulator achieves a dynamic range of 12 bits with an OverSampling Ratio (OSR) of 16 over a bandwidth of 10MHz and dissipates only 28mW of power from a 1.8-V supply. The clock frequency of the modulator is 320MHz but integrators, quantizers and DACs operate at 160MHz

Data visualization in yield component analysis: an expert study

Even though data visualization is a common analytical tool in numerous disciplines, it has rarely been used in agricultural sciences, particularly in agronomy. In this paper, we discuss a study on employing data visualization to analyze a multiplicative model. This model is often used by agronomists, for example in the so-called yield component analysis. The multiplicative model in agronomy is normally analyzed by statistical or related methods. In practice, unfortunately, usefulness of these methods is limited since they help to answer only a few questions, not allowing for a complex view of the phenomena studied. We believe that data visualization could be used for such complex analysis and presentation of the multiplicative model. To that end, we conducted an expert survey. It showed that visualization methods could indeed be useful for analysis and presentation of the multiplicative model