Competition for hydrogen bond formation in the helix-coil transition and protein folding

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev

Upgraded LED illuminator for colorimetric research

В статье описана экспериментальная осветительная установка с использованием стандартных светоизлучающих диодов. Управление яркостью светодиодных компонентов осуществляется при помощи автоматизированной системы, представляющей собой комплекс драйверов с широтно-импульсной модуляцией. Исследуемая экспериментальная осветительная установка предназначена для регулирования значения индекса цветопередачи при фиксированных цветности и общей яркости, что позволяет управлять визуально-воспринимаемой насыщенностью зелёных и красных цветов отражающих объектов.The article describes an experimental lighting system using standard light-emitting diodes. Brightness of light-emitting iodes components are managed using an automated system, which is a set of drivers with pulse width modulation. The researched experimental lighting system designed to regulate the value of the color rendering index at fixed chromaticity and brightness that makes possible to control visually perceived saturation of green and red colors reflecting objects

Оптимизация диагностической модели для прогнозирования эффективности химиолучевой терапии рака шейки матки на группе пациентов с коморбидными состояниями: когортное одноцентровое ретроспективное исследование

INTRODUCTION: Radiomics is a promising area of diagnostics. In clinical practice, ultrasound and magnetic resonance imaging are widely used for Cervical Cancer (CC). The lack of standards when carrying out examinations entails the problem of distinguishing different signs, i.e. there is no possibility to compare results of different institutions.OBJECTIVE: To review radiological diagnostic procedures and optimize a model to enable expanded large-scale multicentre mathematical analysis of radiological findings in comorbid women with CC.MATERIALS AND METHODS: The data from 362 magnetic resonance imaging (MRI) procedures (Philips Achieva, The Netherlands, 1.5T), 500 pelvic ultrasound procedures (US), and 500 retroperitoneal US in 77 comorbid women with cervical squamous cell cancer and cardiovascular disease, carried out between 2012 and 2022, were retrospectively examined. FIGO pretreatment stage 1А–4А. Age: 48.3±13.1. Follow-up period: 3.7±1.3 years.Statistics: Data analysis was carried out using the Stata 13 program (StataCorpLP, CollegeStation, TX, USA). The normality of the distribution of features was assessed using the Shapiro-Wilk criterion. The condition of equality of variances of the distribution of features was calculated according to the Leven criterion. For descriptive statistics of normally distributed features with equality of variances, the calculation of averages and standard deviations was used. Qualitative variables are represented as numbers (%). Logistic regression is performed. The significance level for all the methods used is set as p<0.05.RESULTS: The possibility of segmentation was 2.6% according to US and 100% according to MRI. We analyzed 1443 T2 TSE, 531 T1 TSE, 563 diffusion-weighted images (DWI), 389 STIR, 1987 post-contrast series (in 272 cases (75%) the study was accompanied by contrast agent administration). An MRI model for subsequent feature extraction in patients with CC should consist of T2TSE in the sagittal plane, DWI in the axial plane with automatic construction of apparent diffusion coefficient (ADC) maps.The most reproducible and valuable components of the model are found to be the DWI with automatic ADC map. The ADC value from the parametral fat significantly increased the probability of recurrence, and the cut-off point for ROC analysis was 1.1×10–3 mm2/sec.DISCUSSION: An analysis of medical ultrasound and MRI images in terms of their value for radiomics was carried out. According to the results, MRI is the preferred method. An important next step is to standardize series to extract additional value from diagnostic studies and to carry out multicentre retrospective studies using a multicomponent model.CONCLUSIONS: MRI is a reproducible and frequently used method with the ability to extract additional value from images. T2 TSE in the sagittal plane and DWI in the axial plane with automatic ADC map, followed by segmentation of the parametral area adjacent to the tumor, are considered the most frequently used techniques. Postcontrast imaging are not a reproducible technique and have no added value. A model MRI procedure to determine additional textural characteristics in patients with СС consists of T2-TSE in the sagittal plane, DWI in the axial plane with automatic ADC map.ВВЕДЕНИЕ: Перспективным направлением в диагностике является радиомика. В клинической практике при злокачественном новообразовании шейки матки (ЗНО ШМ) широко используется ультразвуковая и магнитно-резонансная диагностика. Отсутствие стандартов при проведении исследований влечет проблему выделения различных признаков, то есть отсутствие возможности сопоставления результатов работ разных учреждений.ЦЕЛЬ: Проанализировать процедуры лучевой диагностики и оптимизировать модель для возможности расширенного масштабного многоцентрового математического анализа результатов лучевых методов исследования у коморбидных пациенток со ЗНО ШМ.МАТЕРИАЛЫ И МЕТОДЫ: Ретроспективно изучены данные 362 процедур магнитно-резонансной томографии (МРТ) (Philips Achieva, Нидерланды, 1.5T), 500 процедур ультразвукового исследования (УЗИ) органов малого таза, 500 процедур УЗИ забрюшинного пространства у 77 коморбидных пациенток с плоскоклеточным ЗНО ШМ и сердечно-сосудистой патологией, выполненные в 2012–2022 гг. Стадия по FIGO до лечения — 1А–4А. Возраст — 48,3±13,1 года. Период наблюдения — 3,7±1,3 года.Статистика: Анализ данных проводился с использованием программы Stata 13 (StataCorpLP, CollegeStation, TX, USA). Нормальность распределения признаков оценивалась с помощью критерия Шапиро–Уилка. Условие равенства дисперсий распределения признаков рассчитывалось по критерию Левена. Для описательной статистики нормально распределенных признаков с равенством дисперсий использовалось вычисление средних значений и стандартных отклонений. Качественные переменные представлены в виде чисел (%). Выполнена логистическая регрессия. Уровень значимости для всех использующихся методов установлен как p<0,05.РЕЗУЛЬТАТЫ: По данным УЗИ возможность сегментации была в 2,6%, по данным МРТ — в 100%. Проанализировано 1443 T2 TSE, 531 T1 TSE, 563 диффузионно-взвешенных изображений (ДВИ), 389 STIR, 1987 постконтрастных серий (в 272 случаях (75%) исследование сопровождалось введением контрастного вещества). Модель МРТ для последующего извлечения признаков у больных ЗНО ШМ должна состоять из Т2-взвешенных изображений в сагиттальной плоскости, ДВИ в аксиальной плоскости с автоматическим построением карт измеряемого коэффициента диффузии (ИКД).Наиболее воспроизводимыми и ценными составляющими модели признаны ДВИ с автоматическим построением карт ИКД. Значение ИКД от зоны параметральной клетчатки значимо увеличивало вероятность рецидива, а при проведении ROC-анализа точка отсечения составила 1,1×10–3 мм2/с.ОБСУЖДЕНИЕ: Проведен анализ медицинских изображений УЗИ и МРТ в плане их ценности для радиомики. По результатам исследования МРТ является предпочтительным методом. Следующий важный шаг — стандартизация серий для извлечения дополнительной ценности из диагностических исследований и проведение многоцентровых ретроспективных исследований с использованием многокомпонентной модели.ЗАКЛЮЧЕНИЕ: Воспроизводимым и часто используемым методом с возможностью извлечения дополнительной ценности из изображений признана МРТ. Наиболее часто используемыми методиками признаны Т2 TSE в сагиттальной плоскости и ДВИ в аксиальной плоскости с автоматическим построением карт ИКД с последующей сегментацией зоны параметральной клетчатки, расположенной в непосредственной близости к опухоли. Постконтрастные изображения не являются воспроизводимой методикой и не имеют дополнительной ценности. Модель процедуры МРТ для определения дополнительных текстурных характеристик у пациенток с ЗНО ШМ состоит из Т2-взвешенных изображений в сагиттальной плоскости, ДВИ в аксиальной плоскости с автоматическим построением карт ИКД

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Measurement of the top quark pair cross section with ATLAS in pp collisions at √s=7 TeV using final states with an electron or a muon and a hadronically decaying τ lepton

A measurement of the cross section of top quark pair production in proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 7 TeV is reported. The data sample used corresponds to an integrated luminosity of 2.05 fb -1. Events with an isolated electron or muon and a τ lepton decaying hadronically are used. In addition, a large missing transverse momentum and two or more energetic jets are required. At least one of the jets must be identified as originating from a b quark. The measured cross section, σtt-=186±13(stat.)±20(syst.)±7(lumi.) pb, is in good agreement with the Standard Model prediction

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde

Measurement of the flavour composition of dijet events in pp collisions at root s=7 TeV with the ATLAS detector

This paper describes a measurement of the flavour composition of dijet events produced in pp collisions at √s=7 TeV using the ATLAS detector. The measurement uses the full 2010 data sample, corresponding to an integrated luminosity of 39 pb−1. Six possible combinations of light, charm and bottom jets are identified in the dijet events, where the jet flavour is defined by the presence of bottom, charm or solely light flavour hadrons in the jet. Kinematic variables, based on the properties of displaced decay vertices and optimised for jet flavour identification, are used in a multidimensional template fit to measure the fractions of these dijet flavour states as functions of the leading jet transverse momentum in the range 40 GeV to 500 GeV and jet rapidity |y|<2.1. The fit results agree with the predictions of leading- and next-to-leading-order calculations, with the exception of the dijet fraction composed of bottom and light flavour jets, which is underestimated by all models at large transverse jet momenta. The ability to identify jets containing two b-hadrons, originating from e.g. gluon splitting, is demonstrated. The difference between bottom jet production rates in leading and subleading jets is consistent with the next-to-leading-order predictions