There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Recent advances in sequencing technology make it possible to comprehensively catalogue genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (1) initial read mapping; (2) local realignment around indels; (3) base quality score recalibration; (4) SNP discovery and genotyping to find all potential variants; and (5) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We discuss the application of these tools, instantiated in the Genome Analysis Toolkit (GATK), to deep whole-genome, whole-exome capture, and multi-sample low-pass (~4×) 1000 Genomes Project datasets.

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A framework for variation discovery and genotyping using next-generation DNA sequencing data

CA : A Cancer Journal for Clinicians

I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

■ Abstract Apoptosis is a genetically programmed, morphologically distinct form of cell death that can be triggered by a variety of physiological and pathological stimuli. Studies performed over the past 10 years have demonstrated that proteases play critical roles in initiation and execution of this process. The caspases, a family of cysteine-dependent aspartate-directed proteases, are prominent among the death proteases. Caspases are synthesized as relatively inactive zymogens that become activated by scaffold-mediated transactivation or by cleavage via upstream proteases in an intracellular cascade. Regulation of caspase activation and activity occurs at several different levels: ( a) Zymogen gene transcription is regulated; ( b) antiapoptotic members of the Bcl-2 family and other cellular polypeptides block proximity-induced activation of certain procaspases; and ( c) certain cellular inhibitor of apoptosis proteins (cIAPs) can bind to and inhibit active caspases. Once activated, caspases cleave a variety of intracellular polypeptides, including major structural elements of the cytoplasm and nucleus, components of the DNA repair machinery, and a number of protein kinases. Collectively, these scissions disrupt survival pathways and disassemble important architectural components of the cell, contributing to the stereotypic morphological and biochemical changes that characterize apoptotic cell death.

Mammalian caspases: structure ,a ctivation ,s ubstrates, and functions during apoptosis

Objective: The present study was conducted to evaluate the antibacterial activity of Miswak extracts on periodontal pathogenic bacteria Materials and Methods: Miswak sticks were grounded to fine powder and then ethanol and aqueous extraction were formulated Chlorhexidine (Oradex) mouth wash used as positive control and sterilized distal water used as negative control Dental biofilm bacteria investigated including Eikenella corrodens, Streptococcus constellatus, Streptococcus sanguis, and Streptococcus salivariu All bacteria cultured in Brain Heart Infusion (BHI) agar Single pure colonies of bacteria were transferred into fresh BHI broth and incubated overnight Bacterial counting was done by using Colony Forming Unit (CFU) Antibacterial activities were determined using bacteria grown on Mueller Hinton II agar by Minimum Inhibition Concentration (MIC) test and Minimum Bactericidal Concentration (MBC) test Bacterial morphological alterations following treatment with Miswak extracts, Oradex and distilled water investigated under Scanning Electron Microscope (SEM) at 3500x, 10000x and 20000x magnifications Results: MIC tests showed that Miswak ethanol extract mouthwash only require 25%w/v to inhibit growth of a fixed amount (02ml) of bacteria Sconstellatus, Ssalivarius and Ecorrodens while S mutans and Ssanguis only require 15% w/v Miswak ethanol extract to inhibit its growth, while aqueous extract at 50% w/v concentration did not inhibit any bacterial growth MBC results revealed that 50% w/v ethanol Miswak extract mouthwash inhibited 100% of bacteria growth However, 50% w/v aqueous Miswak extract mouthwash inhibited 20–60% of the bacterial growth Under SEM ethanolic extract of Miswak and Oradex produced obvious alterations to the bacterial morphology while no changes were observed after treatment with aqueous Miswak extract Conclusion: Miswak ethanol extract has stronger antibacterial action against periodontal pathogenic bacteria, it can be proposed as a good alternative mouthwash to control and inhibit periodontal pathogenic bacteria

Effect of mouthwash extracted from Miswak (Salvadora Persica) on periodontal pathogenic bacteria an in-vitro study

Quinazoline is an aromatic bicyclic compound exhibiting several pharmaceutical and biological activities This study was conducted to investigate the potential wound healing properties of Synthetic Quinazoline Compound (SQC) on experimental rats The toxicity of SQC was determined by MTT cell proliferation assay The healing effect of SQC was assessed by in vitro wound healing scratch assay on the skin fibroblast cells (BJ-5ta) and in vivo wound healing experiment of low and high dose of SQC on adult Sprague-Dawley rats compared with negative (gum acacia) and positive control (Intrasite-gel) Hematoxylin and Eosin (H&E), Masson's Trichrome (MT) staining and immunohistochemistry analysis were performed to evaluate the histopathological alterations and proteins expression of Bax and Hsp70 on the wound tissue after 10 days In addition, levels of antioxidant enzymes (catalase, glutathione peroxidase and superoxide dismutase), and malondialdehyde (MDA) were measured in wound tissue homogenates The SQC significantly enhanced BJ-5ta cell proliferation and accelerated the percentage of wound closure, with less scarring, increased fibroblast and collagen fibers and less inflammatory cells compared with the negative control The compound also increases endogenous enzymes and decline lipid peroxidation in wound homogenate

Synthesis of Novel Derivatives of Quinazoline Schiff base Compound Promotes Epithelial Wound Healing.

The leaves of Polygonum minus were fractionated using an eluting solvent to evaluate the pharmacological mechanisms underlying the anti-ulcerogenic activity of P. minus. Different P. minus fractions were obtained and evaluated for their ulcer preventing capabilities using the ethanol induction method. In this study, Sprague Dawley rats weighing 150-200 g were used. Different parameters were estimated to identify the active fraction underlying the mechanism of the gastroprotective action of P. minus: the gastric mucus barrier, as well as superoxide dismutase, total hexosamine, and prostaglandin synthesis. Amongst the five fractions from the ethanolic extract of P. minus, the ethyl acetate:methanol 1:1 v/v fraction (F2) significantly (p < 0.005) exhibited better inhibition of ulcer lesions in a dose-dependent manner. In addition, rats pre-treated with F2 showed a significant elevation in superoxide dismutase (SOD), hexosamine and PGE2 levels in the stomach wall mucosa in a dose-dependent matter. Based on these results, the ethyl acetate:methanol 1:1 v/v fraction was considered to be the best fraction for mucous

Pharmacological Mechanisms Underlying Gastroprotective Activities of the Fractions Obtained from Polygonum minus in

[This corrects the article DOI: 10.1155/2013/739850.].

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Corrigendum to "Hepatoprotective Role of Ethanolic Extract of Vitex negundo in Thioacetamide-Induced Liver Fibrosis in Male Rats".

The composition of the oil and protein contents of eight Lagenaria siceraria varieties was characterized in order to evaluate their suitability as a source of edible oil and protein. The physicochemical properties and fatty acids of seed oils were determined. The oil yield ranged from 24.11 to 26.32 %. The refractive indices and relative densities of the oils fell within the narrow ranges of 1.464–1.468 and 0.857–0.907 g/cm3, respectively. The saponification value ranged from 158.48 to 179.52 mg KOH/g, unsaponifiable matter was between 0.749 and 0.937 %, and the peroxide values were lower than Codex values for vegetable oils. The principal fatty acids were linoleic (62.1–67.9 %), oleic (11.54–15.46 %), palmitic (12.13–14.03 %), and stearic (6.71–7.71 %) acids. Low linolenic acid levels were also observed (<1 %) within the range of 0.32–0.44 %. The major essential amino acids were arginine (2.04–3.77 g/100 g), leucine (1.245–1.726 g/100 g), phenylalanine (0.803–1.396 g/100 g), and lysine (0.921–1.383 g/100 g). The non-essential amino acids were glutamic acid (2.5–4.37 g/100 g), aspartic acid (1.39–2.36 g/100 g), serine (0.69–1.19 g/100 g), glycine (0.79–1.37 g/100 g), alanine (0.72–1.37 g/100 g), and proline (0.63–1.02 g/100 g). Nine minerals (Na, Ca, Mg, K, Cu, Fe, Mn, Zn, and P) were determined with significant (p < 0.05) differences. The studied oils showed promising results and can be used in the food, cosmetics, and pharmaceutical industries. This is the first study on the eight L. siceraria seed varieties grown in Sudan, opening the way for further studies on these seeds.

Mahmood Ameen Abdulla

Papers

Effect of mouthwash extracted from Miswak (Salvadora Persica) on periodontal pathogenic bacteria an in-vitro study

Synthesis of Novel Derivatives of Quinazoline Schiff base Compound Promotes Epithelial Wound Healing.

Pharmacological Mechanisms Underlying Gastroprotective Activities of the Fractions Obtained from Polygonum minus in

Corrigendum to "Hepatoprotective Role of Ethanolic Extract of Vitex negundo in Thioacetamide-Induced Liver Fibrosis in Male Rats".

Investigation of Oil and Protein Contents of Eight Sudanese Lagenaria siceraria Varieties