Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library

BACKGROUND: The identification of endogenous cis-regulatory DNA elements (CREs) responsive to endogenous and environmental cues is important for studying gene regulation and for biotechnological applications but is labor and time intensive. Alternatively, by taking a synthetic biology approach small specific DNA binding sites tailored to the needs of the scientist can be generated and rapidly identified. RESULTS: Here we report a novel approach to identify stimulus-responsive synthetic CREs (SynCREs) from an unbiased random synthetic element (SynE) library. Functional SynCREs were isolated by screening the SynE libray for elements mediating transcriptional activity in plant protoplasts. Responsive elements were chromatin immunoprecipitated by targeting the active Ser-5 phosphorylated RNA polymerase II CTD (Pol II ChIP). Using sequential enrichment, deep sequencing and a bioinformatics pipeline, candidate responsive SynCREs were identified within a pool of constitutively active DNA elements and further validated. These included bonafide biotic/abiotic stress-responsive motifs along with novel SynCREs. We tested several SynCREs in Arabidopsis and confirmed their response to biotic stimuli. CONCLUSIONS: Successful isolation of synthetic stress-responsive elements from our screen illustrates the power of the described methodology. This approach can be applied to any transfectable eukaryotic system since it exploits a universal feature of the eukaryotic Pol II

The study of harmful and beneficial drug interactions in intensive care, Kerman, Iran

Since multidrug therapy is common in the intensive care unit (ICU), the risk of drug interactions is high. This study aimed to examine the prevalence of drug interactions and risk factors in patients who were admitted to ICUs. In a crosssectional study, the medication flow sheet of 101 patients was investigated in terms of the number and the type of drug interactions. The Drug Interaction Facts reference text book (2010 edition) was used to determine the type and the number of drug interactions. In total, 609 potential drug interactions were found. The mean number of drug interactions per patient was 6.1 (SD=5.6). Of all observed drug interactions, 66.9 were classified as harmful and 33.1 beneficial. In terms of the nature of interactions, delayed, moderate, and possible were the most common types. The most frequent harmful interaction was between phenytoin and omeprazole (63 occasions). Critically ill patients are at a higher risk of drug interactions. Although 33.1 of the drug interactions were considered beneficial, medical teams should be awarethat even beneficial interactions can have undesirable side-effects in the critically ill. © The Intensive Care Society 2013

A Polynomial Time Algorithm for Spatio-Temporal Security Games

An ever-important issue is protecting infrastructure and other valuable targets from a range of threats from vandalism to theft to piracy to terrorism. The "defender" can rarely afford the needed resources for a 100% protection. Thus, the key question is, how to provide the best protection using the limited available resources. We study a practically important class of security games that is played out in space and time, with targets and "patrols" moving on a real line. A central open question here is whether the Nash equilibrium (i.e., the minimax strategy of the defender) can be computed in polynomial time. We resolve this question in the affirmative. Our algorithm runs in time polynomial in the input size, and only polylogarithmic in the number of possible patrol locations (M). Further, we provide a continuous extension in which patrol locations can take arbitrary real values. Prior work obtained polynomial-time algorithms only under a substantial assumption, e.g., a constant number of rounds. Further, all these algorithms have running times polynomial in M, which can be very large

Sport injuries of karate during training: An epidemiologic study in Iran

Background: Karate is a public sport that has athletes in various age ranges and abundant active sport clubs in Iran. The pattern of injury in this sport in Iranian athletes seems diferent from other countries. Objectives: This study was performed with the purpose of considering the incidence and type of injury of karate athletes aged below 30 years from Tehran, Iran clubs. Materials and Methods: In a cross-sectional study, 10 karate clubs were selected in Tehran. Clubs were selected based on a cluster method from 5 diferent geographical regions of Tehran. All injuries were collected based on athletes� or clubs� weekly report with a designed questionnaire. The injuries were classifed according to: low, medium and severe injury. Collected data was analyzed with SPSS software version 17. Results: 620 athletes were studied totally and incidence rate of injury per athletes was 16.1 and 20.2 per 100 athletes. Ninety percent of than 70 kg and lower sport experience (P � 0.05). The commonest locations for injury were head and neck followed by trunk, lower and injuries were during bout practice, 6 during ftness and 4 during kata. The rate of injury was more common in athletes with weight less upper limb, respectively. Just 2 cases needed surgical intervention and no one led to decreased level of consciousness. The most common type of injury was contusion, bruise and superfcial scratch (64). Conclusions: Severe injury was uncommon in this study and similar to other Iranian studies head and neck had the most injuries. Athletes with lower experience and lower weight were associated with higher injuries. © 2015, Sports Medicine Research Center

Charcot–Marie–Tooth disease: Genetics, epidemiology and complications

Background and aims: Charcot Marie Tooth disease (CMT) is the most prevalent hereditary neuropathy and its frequency is 1 in 2500. CMT is a heterogeneous disease and has different clinical symptoms. The prevalence of CMT and involved genes differ in different countries. CMT patients experience considerable sleep problems and a higher risk of decreased quality of life. In this work it was aimed to provide a review on the genetic and epidemiologic aspects of this disease. Methods: In the current review article, we performed a literature search on the epidemiology of Charcot–Marie–Tooth disease” and provided a brief review on epidemiology, genetic, and complications of CMT. Databases Web of Science and PubMed were searched using the Endnote software for the publications on CMT during 2000 to 2016. Results: Charcot Marie Tooth disease has different prevalence around the world and is the most common neuropathy. Epidemiological studies have estimated the prevalence of CMT in Japan 1/9200, in Iceland 1/8300, in Spain 1/3500 and in Italy 1/5700.The patients have different phenotype and the age of onset. There is a variety of inherited patterns of disease and many genes have been identified responsible whose mutations are main cause of the disease. Conclusion: Due to the impact of this kind of disabilities on the national health, further studies seem to be necessary to gain better knowledge of the disease particularly in the regions with higher prevalence. Moreover molecular biology services offered by genetic laboratories can reduce the incidence of disorder

Caring experiences and challenges of families with patients in vegetative state

زمینه و هدف: داشتن یک بیمار نباتی در خانواده تجربه پیچیده و استرس زایی است و مراقبت از چنین بیمارانی با ناتوانی کامل در منزل بسیار چالش زا می باشد. مطالعه حاضر با هدف تبیین تجارب و چالش های مراقبتی خانواده های دارای بیمار در وضعیت نباتی صورت گرفته است. روش بررسی: در مطالعه کیفی حاضر که به صورت مقطعی از مرداد ماه سال 1392 تا شهریور ماه سال 1393 در برخی استان های ایران (خوزستان، تهران و لرستان) صورت گرفت، 17 مشارکت کننده شامل 14 مراقب خانگی و 3 مراقب حرفه ای به مطالعه وارد شدند. جهت جمع آوری داده ها از مصاحبه های بدون ساختار و مشاهده استفاده شد. جمع آوری داده ها تا رسیدن به اشباع داده ها و پدیدار شدن الگوهای اصلی ادامه یافت. تحلیل داده ها با استفاده از روش تحلیل محتوایی صورت گرفت. یافته ها: چالش های مراقبتی که خانواده های دارای بیمار نباتی با آن مواجه بودند در قالب پنج الگوی اصلی شامل ولع آموزش، عهده داری مراقبتی دشوار، هزینه های فرساینده، برزخ حرف و حدیث ها و پسرفت روحی پدیدار گردید. نتیجه گیری: یافته های مطالعه حاضر نشان داد که خانواده های دارای بیماران نباتی طی دوره مراقبت از بیمار خود با چالش های متعددی روبرو هستند که بخش عمده ی این چالش ها مرتبط با سیاست های سیستم سلامت و برخی نیز مرتبط با سطح آگاهی عموم جامعه می باشد، لذا توجه بیشتر به این چالش ها از سوی مسئولان مرتبط پیشنهاد می گردد

Singular Value Approximation and Sparsifying Random Walks on Directed Graphs

In this paper, we introduce a new, spectral notion of approximation between directed graphs, which we call singular value (SV) approximation. SV-approximation is stronger than previous notions of spectral approximation considered in the literature, including spectral approximation of Laplacians for undirected graphs (Spielman Teng STOC 2004), standard approximation for directed graphs (Cohen et. al. STOC 2017), and unit-circle approximation for directed graphs (Ahmadinejad et. al. FOCS 2020). Further, SV approximation enjoys several useful properties not possessed by previous notions of approximation, e.g., it is preserved under products of random-walk matrices and bounded matrices. We provide a nearly linear-time algorithm for SV-sparsifying (and hence UC-sparsifying) Eulerian directed graphs, as well as $\ell$-step random walks on such graphs, for any $\ell\leq \text{poly}(n)$. Combined with the Eulerian scaling algorithms of (Cohen et. al. FOCS 2018), given an arbitrary (not necessarily Eulerian) directed graph and a set $S$ of vertices, we can approximate the stationary probability mass of the $(S,S^c)$ cut in an $\ell$-step random walk to within a multiplicative error of $1/\text{polylog}(n)$ and an additive error of $1/\text{poly}(n)$ in nearly linear time. As a starting point for these results, we provide a simple black-box reduction from SV-sparsifying Eulerian directed graphs to SV-sparsifying undirected graphs; such a directed-to-undirected reduction was not known for previous notions of spectral approximation.Comment: FOCS 202

Analyzing the Influence of Personal Construction of Mahmoud Ahmadinejad on the Formation and Modeling of the Nuclear Case Decision Making in George Kelly's Theory

recognition his behavior, action and decision making. In fact, although many factors influence a leader's understanding and decision-making process, personal construction undoubtedly have a unique role in the process of understanding, value, and beliefs. Therefore, understanding the representation of the Iranian nuclear case and the decision-making model of this representation would be incomplete without recognizing the personality structure of the leaders in foreign policy. Based on this same issue, the main focus of this article is to identify the influence of Ahmadinejad's personality construction on the path of nuclear confrontation with the West as the opposite. According to this, the question of this article is that, how did Ahmadinejad's personal construction influences the formation and then influences the modeling of the nuclear case? Qualitative research findings in the framework of George Kelly's theory and then applying these findings to the quantitative test, shows that the role of Ahmadinejad's personal construction, while substantially influencing the nuclear case, represents it as a security-identity issue and, accordingly, forms the psychological-value decision based on five principles of construction, dichotomy, choice, modulation, and sociality served as the model of choice. The research method is qualitative and statistical, descriptive and survey (questionnaire)