Fluorescent In-Situ Hybridization is the Hand Mirror of Cytogenetics: A Rare Case of Near Tetraploidy in Pediatric Acute Lymphoblastic Leukemia

Identification of specific chromosomal changes has important prognostic and biological implications in childhood Acute Lymphoblastic Leukemia (ALL). ALL cases with 90 chromosomes are rare. Here, we report a case of near-tetraploidy in a 4 year old boy diagnosed with B-cell ALL, where the ploidy was identified by Fluorescent In- Situ Hybridization (FISH) and confirmed by Conventional Cytogenetics. Our aim was to enumerate multiple signals observed by FISH, and to confirm the same by cytogenetics. FISH on cytogenetically fixed air-dried slides was performed by using BCR/ABL and MLL probe .Two hundred cells were scored. BMA was cultured and G-banded metaphases were analyzed in accordance with ISCN 2013. The results of the FISH test showed more than two signals and cytogenetics revealed clones of near-tetraploidy with mn 90, karyotype: 90-92, 4nXXY,-Y,-10,-10,-13, +14, +17, along with normal clones. The tetraploidy condition compared to hyperdiploid ALL has a poorer prognosis and the rarity of these cases makes accounting on treatment decisions a supposition. Presently, the patient is on standard treatment for ALL (UK ALL regime A). The numerical abnormality detected by FISH was confirmed by cytogenetics, which facilitated in reporting the results of this case earlier than the defined turnaround time. Therefore author opines that FISH reports should also contain observed additional information along with positive or negative status of the requested test

Novel precoded relay-assisted algorithm for cellular systems

Cooperative schemes are promising solutions for cellular wireless systems to improve system fairness, extend coverage and increase capacity. The use of relays is of significant interest to allow radio access in situations where a direct path is not available or has poor quality. A data precoded relay-assisted scheme is proposed for a system cooperating with 2 relays, each equipped with either a single antenna or 2-antenna array. However, because of the half-duplex constraint at the relays, relaying-assisted transmission would require the use of a higher order constellation than in the case when a continuous link is available from the BS to the UT. This would imply a penalty in the power efficiency. The simple precoding scheme proposed exploits the relation between QPSK and 16-QAM, by alternately transmitting through the 2 relays, achieving full diversity, while significantly reducing power penalty. Analysis of the pairwise error probability of the proposed algorithm with a single antenna in each relay is derived and confirmed with numerical results. We show the performance improvements of the precoded scheme, relatively to equivalent distributed SFBC scheme employing 16-QAM, for several channel quality scenarios. Copyright © 2010 Sara Teodoro, et al.European project CODIVPortuguese project CADWINPortuguese project AGILEFC

Novel precoded relay-assisted algorithm for cellular systems

Cooperative schemes are promising solutions for cellular wireless systems to improve system fairness, extend coverage and increase capacity. The use of relays is of significant interest to allow radio access in situations where a direct path is not available or has poor quality. A data precoded relay-assisted scheme is proposed for a system cooperating with 2 relays, each equipped with either a single antenna or 2-antenna array. However, because of the half-duplex constraint at the relays, relaying-assisted transmission would require the use of a higher order constellation than in the case when a continuous link is available from the BS to the UT. This would imply a penalty in the power efficiency. The simple precoding scheme proposed exploits the relation between QPSK and 16-QAM, by alternately transmitting through the 2 relays, achieving full diversity, while significantly reducing power penalty. Analysis of the pairwise error probability of the proposed algorithm with a single antenna in each relay is derived and confirmed with numerical results. We show the performance improvements of the precoded scheme, relatively to equivalent distributed SFBC scheme employing 16-QAM, for several channel quality scenarios. Copyright © 2010 Sara Teodoro, et al.European project CODIVPortuguese project CADWINPortuguese project AGILEFC

Novel precoded relay-assisted algorithm for cellular systems

Cooperative schemes are promising solutions for cellular wireless systems to improve system fairness, extend coverage and increase capacity. The use of relays is of significant interest to allow radio access in situations where a direct path is not available or has poor quality. A data precoded relay-assisted scheme is proposed for a system cooperating with 2 relays, each equipped with either a single antenna or 2-antenna array. However, because of the half-duplex constraint at the relays, relaying-assisted transmission would require the use of a higher order constellation than in the case when a continuous link is available from the BS to the UT. This would imply a penalty in the power efficiency. The simple precoding scheme proposed exploits the relation between QPSK and 16-QAM, by alternately transmitting through the 2 relays, achieving full diversity, while significantly reducing power penalty. Analysis of the pairwise error probability of the proposed algorithm with a single antenna in each relay is derived and confirmed with numerical results. We show the performance improvements of the precoded scheme, relatively to equivalent distributed SFBC scheme employing 16-QAM, for several channel quality scenarios. Copyright © 2010 Sara Teodoro, et al.European project CODIVPortuguese project CADWINPortuguese project AGILEFC

Data-precoded algorithm for multiple-relay-assisted systems

A data-precoded relay-assisted (RA) scheme is proposed for a system cooperating with multiple relay nodes (RNs), each equipped with either a single-antenna or a two-antenna array. The classical RA systems using distributed space-time/frequency coding algorithms, because of the half-duplex constraint at the relays, require the use of a higher order constellation than in the case of a continuous link transmission from the base station to the user terminal. This implies a penalty in the power efficiency. The proposed precoding algorithm exploits the relation between QPSK and 4 L -QAM, by alternately transmitting through L relays, achieving full diversity, while significantly reducing power penalty. This algorithm explores the situations where a direct path (DP) is not available or has poor quality, and it is a promising solution to extend coverage or increase system capacity. We present the analytical derivation of the gain obtained with the data-precoded algorithm in comparison with distributed space-frequency block code (SFBC) ones. Furthermore, analysis of the pairwise error probability of the proposed algorithm is derived and confirmed with numerical results. We evaluate the performance of the proposed scheme and compare it relatively to the equivalent distributed SFBC scheme employing 16-QAM and non-cooperative schemes, for several link quality scenarios and scheme configurations, highlighting the advantages of the proposed scheme

Making new genetic diagnoses with old data:iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders

Purpose Given the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge. Methods We tested this hypothesis in the United Kingdom–wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes. Results We are now able to diagnose an additional 182 individuals, taking our overall diagnostic yield to 454/1,133 (40%), and another 43 (4%) have a finding of uncertain clinical significance. The majority of these new diagnoses are due to novel developmental disorder–associated genes discovered since our original publication. Conclusion This study highlights the importance of coupling large-scale research with clinical practice, and of discussing the possibility of iterative reanalysis and recontact with patients and health professionals at an early stage. We estimate that implementing parent–offspring whole-exome sequencing as a first-line diagnostic test for developmental disorders would diagnose >50% of patients.</p

Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential

Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism

Is there a space–time continuum in olfaction?

The coding of olfactory stimuli across a wide range of organisms may rely on fundamentally similar mechanisms in which a complement of specific odorant receptors on olfactory sensory neurons respond differentially to airborne chemicals to initiate the process by which specific odors are perceived. The question that we address in this review is the role of specific neurons in mediating this sensory system—an identity code—relative to the role that temporally specific responses across many neurons play in producing an olfactory perception—a temporal code. While information coded in specific neurons may be converted into a temporal code, it is also possible that temporal codes exist in the absence of response specificity for any particular neuron or subset of neurons. We review the data supporting these ideas, and we discuss the research perspectives that could help to reveal the mechanisms by which odorants become perceptions

High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

Genomic islands (GIs), frequently associated with the pathogenicity of bacteria and having a substantial influence on bacterial evolution, are groups of “alien” elements which probably undergo special temporal–spatial regulation in the host genome. Are there particular hallmark transcriptional signals for these “exotic” regions? We here explore the potential transcriptional signals that underline the GIs beyond the conventional views on basic sequence composition, such as codon usage and GC property bias. It showed that there is a significant enrichment of the transcription start positions (TSPs) in the GI regions compared to the whole genome of Salmonella enterica and Escherichia coli. There was up to a four-fold increase for the 70% GIs, implying high-density TSPs profile can potentially differentiate the GI regions. Based on this feature, we developed a new sliding window method GIST, Genomic-island Identification by Signals of Transcription, to identify these regions. Subsequently, we compared the known GI-associated features of the GIs detected by GIST and by the existing method Islandviewer to those of the whole genome. Our method demonstrates high sensitivity in detecting GIs harboring genes with biased GI-like function, preferred subcellular localization, skewed GC property, shorter gene length and biased “non-optimal” codon usage. The special transcriptional signals discovered here may contribute to the coordinate expression regulation of foreign genes. Finally, by using GIST, we detected many interesting GIs in the 2011 German E. coli O104:H4 outbreak strain TY-2482, including the microcin H47 system and gene cluster ycgXEFZ-ymgABC that activates the production of biofilm matrix. The aforesaid findings highlight the power of GIST to predict GIs with distinct intrinsic features to the genome. The heterogeneity of cumulative TSPs profiles may not only be a better identity for “alien” regions, but also provide hints to the special evolutionary course and transcriptional regulation of GI regions