Evolution and diversity of copy number variation in the great ape lineage

Copy number variation (CNV) contributes to disease and has restructured the genomes of great apes. The diversity and rate of this process, however, have not been extensively explored among great ape lineages. We analyzed 97 deeply sequenced great ape and human genomes and estimate 16% (469 Mb) of the hominid genome has been affected by recent CNV. We identify a comprehensive set of fixed gene deletions (n = 340) and duplications (n = 405) as well as >13.5 Mb of sequence that has been specifically lost on the human lineage. We compared the diversity and rates of copy number and single nucleotide variation across the hominid phylogeny. We find that CNV diversity partially correlates with single nucleotide diversity (r² = 0.5) and recapitulates the phylogeny of apes with few exceptions. Duplications significantly outpace deletions (2.8-fold). The load of segregating duplications remains significantly higher in bonobos, Western chimpanzees, and Sumatran orangutans—populations that have experienced recent genetic bottlenecks (P = 0.0014, 0.02, and 0.0088, respectively). The rate of fixed deletion has been more clocklike with the exception of the chimpanzee lineage, where we observe a twofold increase in the chimpanzee–bonobo ancestor (P = 4.79 × 10⁻⁹) and increased deletion load among Western chimpanzees (P = 0.002). The latter includes the first genomic disorder in a chimpanzee with features resembling Smith-Magenis syndrome mediated by a chimpanzee-specific increase in segmental duplication complexity. We hypothesize that demographic effects, such as bottlenecks, have contributed to larger and more gene-rich segments being deleted in the chimpanzee lineage and that this effect, more generally, may account for episodic bursts in CNV during hominid evolution.Sequence and assembly of great ape reference genomes have consistently revealed that copy number variation (CNV) affects more base pairs than single nucleotide variation (SNV) (Cheng et al. 2005; The Chimpanzee Sequencing and Analysis Consortium 2005; Locke et al. 2011). Segmental duplications, in particular, have disproportionately affected the African great ape (human, chimpanzee, and gorilla) lineages, where they appear to have accumulated at an accelerated rate (Cheng et al. 2005; Marques-Bonet et al. 2009). This has led to speculation that differences in fixation and copy number polymorphism may have contributed to the phenotypic “plasticity” and species-specific differences between humans and great apes (Olson 1999; Varki et al. 2008). While there is some evidence that fixed deletions and duplications contribute to morphological differences between humans and great apes (McLean et al. 2011; Charrier et al. 2012; Dennis et al. 2012), a comprehensive assessment of these differences at the level of the genome has not yet been performed. Previous studies of CNV have been predominated by array comparative genomic hybridization (CGH) experiments (Fortna et al. 2004; Perry et al. 2006; Dumas et al. 2007; Gazave et al. 2011; Locke et al. 2011), which provide limited size resolution, are imprecise in absolute copy number differences, and are biased by probes derived from the human reference genome. Comparisons of reference genomes have been complicated by assessments of a single individual and distinguishing CNVs from assembly errors (The Chimpanzee Sequencing and Analysis Consortium 2005; Locke et al. 2011; Ventura et al. 2011; Prüfer et al. 2012). Here, we compare the evolution and diversity of deletions, duplications, and SNVs in 97 great ape individuals sequenced to high coverage (median ∼25×) (Prado-Martinez et al. 2013). The set includes multiple individuals from the four great ape genera, including Bornean and Sumatran orangutans, each of the four recognized chimpanzee subspecies, bonobos, and both Eastern and Western gorillas, in addition to 10 diverse humans and a high-coverage archaic Denisovan individual. This data set provides unprecedented genome-wide resolution to interrogate multiple forms of genetic variation and a unique opportunity to directly compare mutational processes and patterns of diversity in great apes.     

Anesthetic Efficacy of Meperidine in Teeth With Symptomatic Irreversible Pulpitis

Achieving adequate pulpal anesthesia in mandibular teeth is always a challenge. Supplementary injections and using drugs in combination are some methods implemented to overcome this hurdle. In this randomized clinical trial, use of meperidine in conjunction with lidocaine in intraligamentary injection did not exhibit significant improvement in anesthesia.Key Words: Periodontal ligament, Meperidine, Irreversible pulpitis, Dental anesthesiaThe failure rate of the inferior alveolar nerve block (IANB) in some experimental studies has been reported up to 75%.^1–4 This lack of success has even increased to a maximum of 81% in some recent studies.^5–7 To overcome this shortcoming, dental clinicians have actively sought measures to improve the patients'' anesthesia during different dental procedures. Apart from the anatomical variations mentioned in the applied anatomy of injections,⁸ several authors have attempted to modify the anesthetic technique,^9–12 and others have compared different anesthetic agents¹³ or their concentrations¹⁴ to improve their efficacy.Activating the opioid receptors peripherally in inflammatory conditions has become a new trend in research to manage postoperative pain.¹⁵ Synergy between local anesthetics and opioids has become an interesting field of research recently.¹⁶ Opioids are frequently added to local anesthetics in a variety of surgical procedures, eg, intrathecal application for minor surgery.¹⁷ Meperidine or its derivatives, eg, pethidine (meperidine chloride) or norpethidine (Pethidine Intermediate B) are agonists of μ-opioid receptors, which block the pathway of pain signals to the trigeminal nucleus. They also activate peripheral opioid receptors and block sodium channels.^17–22 Despite controversy regarding the use of meperidine as an anesthetic,²² recent studies have demonstrated its benefits over prilocaine in arthroscopy with local anesthesia,¹⁶ nasal packing removal,²³ etc.However, only a few studies have investigated the dental anesthetic efficacy of such combinations.^24,25 The effect of the addition of meperidine to lidocaine in IANB for pain management in normal teeth²⁴ and also in teeth with irreversible pulpitis²⁵ has been studied. The aim of our study was to compare the efficacy of local anesthetics with and without meperidine for intraligamentary supplemental injection for teeth with irreversible pulpitis. Our null hypothesis stated that the addition of meperidine to standard lidocaine with epinephrine does not improve the efficacy of supplemental intraligamentary anesthesia in teeth with symptomatic irreversible pulpitis. The specific objectives were to randomly allocate volunteers with complete soft tissue anesthesia following an IANB, yet having positive pulp response, into 2 groups, and then compare the efficacy of lidocaine with epinephrine plus meperidine with that of lidocaine with epinephrine plus an equal volume of sterile water for supplemental periodontal ligament anesthesia.     

AIDS and heart disease: is cardiac surgery justified?

A compromised immune system, limited survival and increased risk to the anaesthetic and surgical team of acquiring HIV infection have been the major concerns in offering cardiac surgery to patients with AIDS. The current report presents a patient with AIDS who underwent successful, uncomplicated coronary artery surgery. He remains free of ischaemic and any infectioe symptoms 12 months postoperatively.     

Effects of Hybridized Synthetic Fibers on the Shear Properties of Cement Composites

The use of fibers in cementitious composites yields numerous benefits due to their fiber-bridging capabilities in resisting cracks. Therefore, this study aimed to improve the shear-resisting capabilities of conventional concrete through the hybridization of multiple synthetic fibers, specifically on reinforced concrete structures in seismic-prone regions. For this study, 16 hybrid fiber-reinforced concretes (HyFRC) were developed from the different combinations of Ferro macro-synthetic fibers with the Ultra-Net, Super-Net, Econo-Net, and Nylo-Mono microfibers. These hybrids were tested under direct shear, resulting in improved shear strength of controlled specimens by Ferro-Ultra (32%), Ferro-Super (24%), Ferro-Econo (44%), and Ferro-Nylo (24%). Shear energy was further assessed to comprehend the effectiveness of the fiber interactions according to the mechanical properties, dosage, bonding power, manufactured material, and form of fibers. Conclusively, all fiber combinations used in this study produced positive synergistic effects under direct shear at large crack deformations.     

Task-specific stability in muscle activation space during unintentional movements

We used robot-generated perturbations applied during position-holding tasks to explore stability of induced unintentional movements in a multidimensional space of muscle activations. Healthy subjects held the handle of a robot against a constant bias force and were instructed not to interfere with hand movements produced by changes in the external force. Transient force changes were applied leading to handle displacement away from the initial position and then back toward the initial position. Intertrial variance in the space of muscle modes (eigenvectors in the muscle activations space) was quantified within two subspaces, corresponding to unchanged handle coordinate and to changes in the handle coordinate. Most variance was confined to the former subspace in each of the three phases of movement, the initial steady state, the intermediate position, and the final steady state. The same result was found when the changes in muscle activation were analyzed between the initial and final steady states. Changes in the dwell time between the perturbation force application and removal led to different final hand locations undershooting the initial position. The magnitude of the undershot scaled with the dwell time, while the structure of variance in the muscle activation space did not depend on the dwell time. We conclude that stability of the hand coordinate is ensured during both intentional and unintentional actions via similar mechanisms. Relative equifinality in the external space after transient perturbations may be associated with varying states in the redundant space of muscle activations. The results fit a hierarchical scheme for the control of voluntary movements with referent configurations and redundant mapping between the levels of the hierarchy.     

Osseous reaction to implantation of two endodontic cements: Mineral trioxide aggregate (MTA) and calcium enriched mixture (CEM)

Aim: The aim of the present in vivo study was to determine bone tissue reaction to calcium enriched mixture (CEM) and mineral trioxide aggregate (MTA) using a rat femur model. Study Design: Sixty-three rats were selected and randomly divided into three groups of 21 each [experimental groups (n=15), control (n=6)]. Implantation cavities were prepared in each femoral bone and randomly filled with the biomaterials only in the experimental groups. The animals in three groups were sacrificed 1, 4, and 8 weeks postoperatively. Histologic evaluations comprising inflammation severity and new bone formation were blindly made on H&E-stained decalcified 6-μm sections. Results: At 1, 4, and 8 weeks after implantation number of inflammatory cells had decreased in the CEM, MTA and control groups, respectively, with no statistically significant differences. Conversely, new bone formation had increased in all the experimental and control groups, without statistically significant differences. Conclusion: The results suggest that biocompatibility of MTA, as gold standard, and CEM cement as a new endodontic biomaterial are comparable.     

Percutaneous vertebroplasty in symptomatic hemangioma versus osteoporotic compression fracture

Background:

Percutaneous vertebroplasty (PVP) is more commonly used for osteoporotic compression fractures (OCFs) and osteolytic vertebral body tumors. This study aimed to study the differences between OCFs and vertebral hemangiomas (VHs) treated with PVP.

Materials and Methods:

Between September 2007 and January 2010, we prospectively treated 28 consecutive patients of OCFs (43 recently symptomatic OCFs) and 24 cases of VHs (26 VHs). We used visual analogue scale (VAS) pain and Oswestry Disability Index (ODI) to evaluate the patients. The followup period in group 1 and 2 were 25.1 months (range 12 - 31 months) and 21.3 months (range 14 - 28 months), respectively. Comparison of means was carried out with the Chi Square Tests, t-test, and N Par-Test for multiple comparisons, whenever appropriate. The level of statistical significance was set at P < 0.05.

Results:

Following PVP the VAS score decreased to 4.57 and 4.17 in group 1 and 2, respectively. The ODI scores were 32.5% and 30%, respectively. This decrease in ODI scores lasted throughout the followup period.

Conclusions:

Although the preoperative scores were significantly different between group 1 and 2, there was no significant difference between two groups following the PVP.