Heteropolymer Sequence Design and Preferential Solvation of Hydrophilic Monomers: One More Application of Random Energy Model

In this paper, we study the role of surface of the globule and the role of interactions with the solvent for designed sequence heteropolymers using random energy model (REM). We investigate the ground state energy and surface monomer composition distribution. By comparing the freezing transition in random and designed sequence heteropolymers, we discuss the effects of design. Based on our results, we are able to show under which conditions solvation effect improves the quality of sequence design. Finally, we study sequence space entropy and discuss the number of available sequences as a function of imposed requirements for the design quality

Broadening the ecological mindset

Over the past three decades, the Harvard Forest Summer Research Program in Ecology (HF-SRPE) has been at the forefront of expanding the ecological tent for minoritized or otherwise marginalized students. By broadening the definition of ecology to include fields such as data science, software engineering, and remote sensing, we attract a broader range of students, including those who may not prioritize field experiences or who may feel unsafe working in rural or urban field sites. We also work towards a more resilient society in which minoritized or marginalized students can work safely, in part by building teams of students and mentors. Teams collaborate on projects that require a diversity of approaches and create opportunities for students and mentors alike to support one another and share leadership. Finally, HF-SRPE promotes an expanded view of what it means to become an ecologist. We value and support diverse career paths for ecologists to work in all parts of society, to diversify the face of ecology, and to bring different perspectives together to ensure innovations in environmental problem solving for our planet

Protein folding rates correlate with heterogeneity of folding mechanism

By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of native contacts. Statistically significant correlations are observed between folding rates and measures of heterogeneity inherent in the native topology, as well as between rates and the variance in the distribution of either experimentally measured or simulated phi-values.Comment: 11 pages, 3 figures, 1 tabl

On the Number of Iterations for Dantzig-Wolfe Optimization and Packing-Covering Approximation Algorithms

We give a lower bound on the iteration complexity of a natural class of Lagrangean-relaxation algorithms for approximately solving packing/covering linear programs. We show that, given an input with $m$ random 0/1-constraints on $n$ variables, with high probability, any such algorithm requires $\Omega(\rho \log(m)/\epsilon^2)$ iterations to compute a $(1+\epsilon)$-approximate solution, where $\rho$ is the width of the input. The bound is tight for a range of the parameters $(m,n,\rho,\epsilon)$. The algorithms in the class include Dantzig-Wolfe decomposition, Benders' decomposition, Lagrangean relaxation as developed by Held and Karp [1971] for lower-bounding TSP, and many others (e.g. by Plotkin, Shmoys, and Tardos [1988] and Grigoriadis and Khachiyan [1996]). To prove the bound, we use a discrepancy argument to show an analogous lower bound on the support size of $(1+\epsilon)$-approximate mixed strategies for random two-player zero-sum 0/1-matrix games

Optically Selected BL Lacertae Candidates from the Sloan Digital Sky Survey Data Release Seven

We present a sample of 723 optically selected BL Lac candidates from the SDSS DR7 spectroscopic database encompassing 8250 deg^2 of sky; our sample constitutes one of the largest uniform BL Lac samples yet derived. Each BL Lac candidate has a high-quality SDSS spectrum from which we determine spectroscopic redshifts for ~60% of the objects. Redshift lower limits are estimated for the remaining objects utilizing the lack of host galaxy flux contamination in their optical spectra; we find that objects lacking spectroscopic redshifts are likely at systematically higher redshifts. Approximately 80% of our BL Lac candidates match to a radio source in FIRST/NVSS, and ~40% match to a ROSAT X-ray source. The homogeneous multiwavelength coverage allows subdivision of the sample into 637 radio-loud BL Lac candidates and 86 weak-featured radio-quiet objects. The radio-loud objects broadly support the standard paradigm unifying BL Lac objects with beamed radio galaxies. We propose that the majority of the radio-quiet objects may be lower-redshift (z<2.2) analogs to high-redshift weak line quasars (i.e., AGN with unusually anemic broad emission line regions). These would constitute the largest sample of such objects, being of similar size and complementary in redshift to the samples of high-redshift weak line quasars previously discovered by the SDSS. However, some fraction of the weak-featured radio-quiet objects may instead populate a rare and extreme radio-weak tail of the much larger radio-loud BL Lac population. Serendipitous discoveries of unusual white dwarfs, high-redshift weak line quasars, and broad absorption line quasars with extreme continuum dropoffs blueward of rest-frame 2800 Angstroms are also briefly described.Comment: 24 pages, 14 figures, 8 tables. Accepted for publication in A

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Анализ эффективности применения аскорбиновой кислоты, гидрокортизона и тиамина в комплексе адъювантной терапии сепсиса и септического шока

The objective: to analyze efficacy of ascorbic acid or its combination with glucocorticoids and thiamine on clinical outcomes in patients with sepsis and septic shock.Subjects and Methods. The literature search was carried out in the database of MEDLINE, Embase, and the Cochrane Library systems. It is limited to published articles from January 1, 2008 to March 1, 2022. The selection criteria were observational studies in patients over 18 years of age with septic shock, if they provide data on the use of ascorbic acid in the form of monotherapy or in combination with hydrocortisone and thiamine.Conclusion. The review includes 18 publications, including 3 meta-analyses on the use of ascorbic acid or its combination with hydrocortisone and thiamine in patients in the adjuvant therapy program for sepsis and septic shock. Clinical efficacy has been proven in 11 studies. However, 7 publications did not show global changes in the outcomes of sepsis and septic shock therapy compared to basic therapy. Currently, there is a need for further research.Цель обзора: анализ влияния аскорбиновой кислоты или ее комбинации с глюкокортикоидами и тиамином на клинические исходы у пациентов с сепсисом и септическим шоком.Материалы и методы. Поиск литературы проведен в базе данных систем MEDLINE, Embase, Кокрановской библиотеки и ограничен опубликованными статьями с 1 января 2008 г. по 1 марта 2022 г. Критериями выбора были обсервационные исследования у пациентов старше 18 лет с септическим шоком, если в них представлены данные о применении аскорбиновой кислоты в виде монотерапии или в сочетании с гидрокортизоном и тиамином.Заключение. В обзор включены 18 публикаций, из них 3 метаанализа, посвященных применению аскорбиновой кислоты или ее сочетанию с гидрокортизоном и тиамином у пациентов в программе адъювантной терапии сепсиса и септического шока. В 11 исследованиях доказана клиническая эффективность. Однако 7 публикаций не показало глобальных изменений в исходах терапии сепсиса и септического шока по сравнению с базовой терапией. В настоящее время существует необходимость дальнейших исследований

ПЛОТКИН СЕМЁН ЯКОВЛЕВИЧ (К 110-ЛЕТИЮ СО ДНЯ РОЖДЕНИЯ)

The article tells about life and fate of S.Ya. Plotkin, whose 110-th anniversary of birth was marked on March 2016. He was born in 1906 in Melitopole town (Ukraine). Having graduated at the Moscow Institute of Fine Chemical Technology in 1931, he was asked for administration works firstly as the director of the Institute and then as the member of the All-Union Committee for High School problems. During all his life S.Ya. Plotkin successfully combine administrative, scientific, pedagogical and journalistic activities. He was the expert in the problems of hard alloys and powder metallurgy, professor, editor in chief of the journal «History of Natural Sciences and Technique». He was the member of the Journalist’s Union of the USSR, Honorary member of the International Institute for the Sciences of Sintering and Honorary worker of Culture of Russian Federation.В статье рассказано о жизни и судьбе, научной, общественной и журналистской работе Плоткина Семена Яковлевича (1906-2000). С момента образования МИТХТ как самостоятельного института он был назначен его директором и успешно руководил им в течение шести лет, когда был переведён на должность начальника главка Всесоюзного комитета по делам высшей школы, преобразованного впоследствии в Минвуз СССР. В годы войны он был уполномоченным Правительства по эвакуации ВУЗов на Восток и последующей их реэвакуации. В разные годы С.Я. Плоткин был корреспондентом, автором статей, сотрудником редакций во многих газетах и журналах. Он член Союза журналистов СССР, Заслуженный работник культуры РСФСР, Почетный член Международного Института науки о спекании

Radio non-detection during nearly-simultaneous Swift/XRT observations of MAXI J0911-635/Swift J0911.9-6452 in NGC 2808

We report nearly-simultaneous radio and X-ray observations of the newly discovered X-ray transient MAXI J0911-635/Swift J0911.9-6452 in the globular cluster NGC 2808 (ATel #8872, #8884)