Finite-Length Scaling of Polar Codes

Consider a binary-input memoryless output-symmetric channel $W$. Such a channel has a capacity, call it $I(W)$, and for any $R<I(W)$ and strictly positive constant $P_{\rm e}$ we know that we can construct a coding scheme that allows transmission at rate $R$ with an error probability not exceeding $P_{\rm e}$. Assume now that we let the rate $R$ tend to $I(W)$ and we ask how we have to "scale" the blocklength $N$ in order to keep the error probability fixed to $P_{\rm e}$. We refer to this as the "finite-length scaling" behavior. This question was addressed by Strassen as well as Polyanskiy, Poor and Verdu, and the result is that $N$ must grow at least as the square of the reciprocal of $I(W)-R$. Polar codes are optimal in the sense that they achieve capacity. In this paper, we are asking to what degree they are also optimal in terms of their finite-length behavior. Our approach is based on analyzing the dynamics of the un-polarized channels. The main results of this paper can be summarized as follows. Consider the sum of Bhattacharyya parameters of sub-channels chosen (by the polar coding scheme) to transmit information. If we require this sum to be smaller than a given value $P_{\rm e}>0$, then the required block-length $N$ scales in terms of the rate $R < I(W)$ as $N \geq \frac{\alpha}{(I(W)-R)^{\underline{\mu}}}$, where $\alpha$ is a positive constant that depends on $P_{\rm e}$ and $I(W)$, and $\underline{\mu} = 3.579$. Also, we show that with the same requirement on the sum of Bhattacharyya parameters, the block-length scales in terms of the rate like $N \leq \frac{\beta}{(I(W)-R)^{\overline{\mu}}}$, where $\beta$ is a constant that depends on $P_{\rm e}$ and $I(W)$, and $\overline{\mu}=6$.Comment: In IEEE Transactions on Information Theory, 201

The effect of black and green-tea extracts on dental-plaque forming Streptococci

زمینه و هدف: چای از پرمصرف‌ترین نوشیدنی‌ها در ایران است. اثرات ضد میکربی چای روی میکروارگانیسم‌های متعددی به اثبات رسیده است و یافتن فرآورده های طبیعی مانند مشتقات چای، که فاقد مخاطرات بر سلامت انسان باشند جهت کاهش ارگانیسم های پاتوژن ضروری بنظر می رسد. لذا این پژوهش با هدف بررسی اثر عصاره چای سیاه و سبز ایرانی بر استرپتوکوک‌های دهانی (استرپتوکوکوس موتانس، استرپتوکوکوس میتیس و استرپتوکوکوس سنگوییس) و اثر بازدارندگی آنها از تشکیل بیوفیلم، روی عوامل ایجاد کنندۀ پلاک‌های دندانی و پوسیدگی دندان انجام شد. روش بررسی: در این مطالعه تجربی پس از عصاره گیری نمونه ها با حلال متانول50 و جدا نمودن مجدد در فاز اتیل استـــات، عصاره ها توسط فیلتر 44/0 میکرون استریل شده و در 4 درجۀ سانتیگراد نگهداری شدند. از روش تهیۀ رقت های متوالی در محیط مایع برای محاسبۀ حداقل غلظت بازدارندگی و با تلقیح باکتری‌ها به درون ارلن های حاوی لام‌های شیشه‌ای برای سنجش تشکیل بیوفیلم استفاده شد. تشکیل بیوفیلم با کشت نمونه از روی لام ها و شمارش کلنی‌ها و همچنین مقایسۀ آنها در زیر میکروسکوپ فاز کنتراست با نمونۀ شاهد (محیط های تیمار نشده) مقایسه گردید. میانگین اندازه گیری‌ها در سه بار تکرار بیان و خطاها در هر نمونه با استفاده از آزمون آماری استاندارد (ANOVA) تعیین گردید. یافته ها: میکروسکوپ فاز کنتراست کاهش فوق العاده ای را در چسبیدن میکروارگانیسم های تیمار شده به یکدیگر در مقایسه با نمونۀ شاهد نشان داد. در غلظت 1 میلی گرم در میلی لیتر از عصارۀ چای سیاه بیوفیلم تشکیل نشد و غلظت 5/1 میلی گرم در میلی لیتر از عصارۀ چای سبز نیز بازدارندۀ کامل تشکیل بیوفیلم بود. عصاره های چای سیاه و سبز، به ترتیب در غلظت 5/2 و 3 میلی گرم در میلی لیتر اثر باکتریسایدی روی استرپتوکوکوس موتانس، استرپتوکوکوس میتیس و استرپتوکوکوس سنگوییس داشتند. نتیجه گیری: عصاره های چای به هر دو صورت چای سیاه و سبز خاصیت باکتریسایدی داشتند و اثر ضد میکربی چای سیاه بر روی استرپتوکوک های دهانی و ممانعت از تشکیل بیوفیلم توسط آنها بیشتر از چای سبز است

Host Cell Signalling and Leishmania Mechanisms of Evasion

Leishmania parasites are able to secure their survival and propagation within their host by altering signalling pathways involved in the ability of macrophages to kill pathogens or to engage adaptive immune system. An important step in this immune evasion process is the activation of host protein tyrosine phosphatase SHP-1 by Leishmania. SHP-1 has been shown to directly inactivate JAK2 and Erk1/2 and to play a role in the negative regulation of several transcription factors involved in macrophage activation. These signalling alterations contribute to the inactivation of critical macrophage functions (e.g., Nitric oxide, IL-12, and TNF-α). Additionally, to interfere with IFN-γ receptor signalling, Leishmania also alters several LPS-mediated responses. Recent findings from our laboratory revealed a pivotal role for SHP-1 in the inhibition of TLR-induced macrophage activation through binding to and inactivating IL-1-receptor-associated kinase 1 (IRAK-1). Furthermore, we identified the binding site as an evolutionarily conserved ITIM-like motif, which we named kinase tyrosine-based inhibitory motif (KTIM). Collectively, a better understanding of the evasion mechanisms utilized by Leishmania parasite could help to develop more efficient antileishmanial therapies in the near future

Capacity building and mentorship among pan-Canadian early career researchers in community-based primary health care

Aim: To describe activities and outcomes of a cross-team capacity building strategy that took place over a five-year funding period within the broader context of 12 community-based primary health care (CBPHC) teams. Background: In 2013, the Canadian Institutes of Health Research funded 12 CBPHC Teams (12-Teams) to conduct innovative cross-jurisdictional research to improve the delivery of high-quality CBPHC to Canadians. This signature initiative also aimed to enhance CBPHC research capacity among an interdisciplinary group of trainees, facilitated by a collaboration between a capacity building committee led by senior researchers and a trainee-led working group. Methods: After the committee and working group were established, capacity building activities were organized based on needs and interests identified by trainees of the CBPHC Teams. This paper presents a summary of the activities accomplished, as well as the outcomes reported through an online semistructured survey completed by the trainees toward the end of the five-year funding period. This survey was designed to capture the capacity building and mentorship activities that trainees either had experienced or would like to experience in the future. Descriptive and thematic analyses were conducted based on survey responses, and these findings were compared with the existing core competencies in the literature. Findings: Since 2013, nine webinars and three online workshops were hosted by trainees and senior researchers, respectively. Many of the CBPHC Teams provided exposure for trainees to innovative methods, CBPHC content, and showcased trainee research. A total of 27 trainees from 10 of the 12-Teams responded to the survey (41.5%). Trainees identified key areas of benefit from their involvement in this initiative: skills training, networking opportunities, and academic productivity. Trainees identified gaps in research and professional skill development, indicating areas for further improvement in capacity building programs, particularly for trainees to play a more active role in their education and preparation

Immunomodulatory Impact of <i>Leishmania</i>-Induced Macrophage Exosomes: A Comparative Proteomic and Functional Analysis

<div><p>Released by many eukaryotic cells, the exosomes are 40–100 nm vesicles shown to operate over the complex processes of cell-cell communication. Among the metazoan cell lineages known to generate exosomes is the mononuclear phagocyte lineage, a lineage that parasites such as <i>Leishmania</i> are known to subvert as host cells. We previously reported that mouse macrophage signaling and functions are modified once co-incubated with exoproteome of <i>Leishmania</i> promastigotes. Using mass spectrometry analysis, we were curious to further compare the content of purified exosomes released by the J774 mouse macrophage cell line exposed or not to either LPS or to stationary phase <i>Leishmania mexicana</i> promastigotes. Collectively, our analyses resulted in detection of 248 proteins, ∼50–80% of which were shared among the three sources studied. Using exponentially modified protein abundance index (emPAI) and network analyses, we found that the macrophage exosomes display unique signatures with respect to composition and abundance of many functional groups of proteins, such as plasma membrane-associated proteins, chaperones and metabolic enzymes. Moreover, for the first time, <i>L. mexicana</i> surface protease GP63 is shown to be present in exosomes released from J774 macrophages exposed to stationary phase promastigotes. We observed that macrophage exosomes are able to induce signaling molecules and transcription factors in naive macrophages. Finally, using qRT-PCR, we monitored modulation of expression of multiple immune-related genes within macrophages exposed to exosomes. We found all three groups of exosomes to induce expression of immune-related genes, the ones collected from macrophages exposed to <i>L. mexicana</i> sharing properties with exosomes collected from macrophage left unexposed to any agonist. Overall, our results allowed depicting that protein sorting into macrophage-derived exosomes depends upon the cell status and how such distinct protein sorting can in turn impact the functions of naive J774 cells.</p></div

Distribution of LEISHX/LPSX emPAI ratios.

<p>A. The ratio of LEISHX/LPSX emPAI values. The ratios are sorted from highest to lowest for LEISHX/LPSX. B shows the frequency distribution of different ranges of the emPAI ratios.</p

Exosomes induce translocation of NF-κB and AP-1 to the nucleus in naive macrophages.

<p>EMSAs show induction of nuclear translocation of NF-κB (A) and AP-1 (B) after 1 h stimulation with NILX, LPSX and LEISHX exosomes, although LEISHX exosomes appear to induce less activation of NF- κB compared to the other two. Infection with <i>L. mexicana</i> (<i>L. mex</i>) results in degradation AP-1 and cleavage of NF-κB. Stimulation with 100 ng/ml of LPS was used as a positive control. CS: Specific Control (100× cold oligo), CN: Nonspecific Control (100× cold consensus oligo for SP-1), N.S.: Non-specific band. Results are representative of 3 separate experiments.</p

Exosome induced upregulation and downregulation of immune-related genes in naive macrophages measured by qRT-PCR.

<p>Macrophages were stimulated for 8 h with 5 µg of exosomes and modulation of gene expression was measured by qRT-PCR array. Venn diagrams show genes that were at least 2 fold upregulated (A) or downregulated (B) following stimulations. Results are average of duplicates.</p

List of genes upregulated by at least one set of macrophage exosomes.

<p>Fold regulation against non-treated samples, calculated using ΔΔCt method, normalized against a panel of 3 house-keeping genes.</p><p>Results are average of 2 replicates. Numbers in bold are indicative of at least 2-fold upregulation.</p><p>Genes that are at least 2-fold up-regulated by one of the exosomes are listed.</p