Inelastic light, neutron, and X-ray scatterings related to the heterogeneous elasticity of glasses

The effects of plasticization of poly(methyl methacrylate) glass on the boson peaks observed by Raman and neutron scattering are compared. In plasticized glass the cohesion heterogeneities are responsible for the neutron boson peak and partially for the Raman one, which is enhanced by the composition heterogeneities. Because the composition heterogeneities have a size similar to that of the cohesion ones and form quasiperiodic clusters, as observed by small angle X-ray scattering, it is inferred that the cohesion heterogeneities in a normal glass form nearly periodic arrangements too. Such structure at the nanometric scale explains the linear dispersion of the vibrational frequency versus the transfer momentum observed by inelastic X-ray scattering.Comment: 9 pages, 2 figures, to be published in J. Non-Cryst. Solids (Proceedings of the 4th IDMRCS

Force distributions near the jamming and glass transitions

We calculate the distribution of interparticle normal forces $P(F)$ near the glass and jamming transitions in model supercooled liquids and foams, respectively. $P(F)$ develops a peak that appears near the glass or jamming transitions, whose height increases with decreasing temperature, decreasing shear stress and increasing packing density. A similar shape of $P(F)$ was observed in experiments on static granular packings. We propose that the appearance of this peak signals the development of a yield stress. The sensitivity of the peak to temperature, shear stress and density lends credence to the recently proposed generalized jamming phase diagram.Comment: 4 pages, 3 postscript figures;Version 3 replaces figure 1 and removes figure 2 from version 1. Significant rewording of version 1 to emphasize the formation of peak in P(F) when these systems jam along five different routes of the recently proposed jamming phase diagram. Version 2 displayed the incorrect abstrac

Voronoi-Delaunay analysis of normal modes in a simple model glass

We combine a conventional harmonic analysis of vibrations in a one-atomic model glass of soft spheres with a Voronoi-Delaunay geometrical analysis of the structure. ``Structure potentials'' (tetragonality, sphericity or perfectness) are introduced to describe the shape of the local atomic configurations (Delaunay simplices) as function of the atomic coordinates. Apart from the highest and lowest frequencies the amplitude weighted ``structure potential'' varies only little with frequency. The movement of atoms in soft modes causes transitions between different ``perfect'' realizations of local structure. As for the potential energy a dynamic matrix can be defined for the ``structure potential''. Its expectation value with respect to the vibrational modes increases nearly linearly with frequency and shows a clear indication of the boson peak. The structure eigenvectors of this dynamical matrix are strongly correlated to the vibrational ones. Four subgroups of modes can be distinguished

A genome-wide scan for common alleles affecting risk for autism

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C

РИСК РАННЕЙ ДИСФУНКЦИИ ТРАНСПЛАНТАТА ПЕЧЕНИ АССОЦИИРОВАН С ГЕНОТИПОМ ГЕНА TLR-4 В ПОСЛЕДОВАТЕЛЬНОСТИ RS913930 И РЕАЛИЗУЕТСЯ ЧЕРЕЗ АКТИВАЦИЮ ЯДЕРНОГО БЕЛКА HMGB1, КЛЕТОК КУПФЕРА И IL-23

Aim. To evaluate the associations of genotypes of clinically relevant nucleotides rs11536865, rs913930 and rs5030717 of the TLR-4 gene with the risk of development and severity of early allograft dysfunction after liver transplantation. Materials and methods. A case-control study enrolling 71 patients was organized. Inclusion criteria: DBD liver transplantation. Exclusion criteria: living related liver transplantation, reduced graft transplantation, recipient’s age fewer than 18. Results. Within rs5030717 there were identifi ed three genotypes: AA (81.6%) and two genotypes with the minor G-allele: AG (12.6%) and GG (5.6%). Within rs913930 there identi- fi ed three genotypes: TT (59.1%) and two genotypes with the minor C-allele: C/T (29.5%) and CC (11.2%). The rs11536865 studying revealed no polymorphism (GG genotype). The early allograft liver dysfunction (EAD) developed in 19.7% of patients, the severe EAD in 11.2% of patients, septic complications in 14%, acute cellular rejection in 23.9% of cases. The C/T genotype of the TLR-4 gene in the SNP rs913930 sequence was closely associated with the EAD development (OR 4.8 to 1; p = 0.047; 95% CI 1–23.4). Рatients with the donor’s liver C/T genotype had a reliably higher proportion (%) of the HMGB1 positive hepatocytes in the donor’s bioptate, 21 (17–29%) vs the СС+TT genotypes, 16 (10–19%) (Mann–Whitney test, p = 0.01). The CD68 expression in the liver bioptate at the donor’s stage was reliably higher in the carriers of heterozygotes in the SNP rs913930 (C/T genotype) and in the SNP rs5030717 (AG genotype), (Mann–Whitney test, p = 0.03). Signifi cant positive correlation between the CD68 expression in the donor’s liver bioptates and the IL-23 level in the hepatic vein has been determined in an hour after the portal reperfusion (ρ = 0.62; p = 0.04) as well as between the HMGB1 expression in the donor’s liver bioptates and the АSТ level in 24 hours after the reperfusion (r = 0.4; p = 0.02). The HMGB1 staining in the donor’s liver bioptates was higher in the EAD patients, 21 (20; 29) cells/mm2 in comparison with the patients without EAD, 16 (12; 18) (Mann–Whitney test, p = 0.0036). Conclusion. The early allograft liver dysfunction is associated with the genetic predisposition caused by the TLR-4 gene polymorphism and is implemented via the HMGB1, Kupffer cells and IL-23 activation. Цель исследования. Оценить ассоциации генотипов клинически значимых последовательностей нуклеотидов rs11536865, rs913930 и rs5030717 гена TLR-4 с риском возникновения и выраженностью ранней дисфункции трансплантатов печени. Материалы и методы. Для достижения поставленной цели было организованно исследование «случай–контроль», включавшее 71 пациента. Критерии включения: трансплантация печени от умершего донора. Критерии исключения: трансплантация от родственного донора, редуцированный графт, возраст реципиента менее 18 лет. Результаты. В пределах rs5030717 были выявлены три генотипа: AA (81,6%) и два генотипа с минорной аллелью G – AG (12,6%) и GG (5,6%). В пределах rs913930 были выявлены 3 генотипа: TT (59,1%) и два генотипа с минорной аллелью С – TC (29,5%), CC (11,2%). Изучение rs11536865 не выявило полиморфизма (генотип – GG). Ранняя дисфункция трансплантата печени развилась у 19,7% пациентов, тяжелая ранняя дисфункция трансплантата – 11,2%, септические осложнения – 14%, острое клеточное отторжение – 23,9%. Генотип C/T гена TLR-4 в последовательности SNP rs913930 имеет сильную связь с развитием ранней дисфункции трансплантата (Отношение шансов 4,8:1; p = 0,047; 95% ДИ 1–23,4). Пациенты с генотипом донорской печени С/T имели достоверно большую пропорцию HMGB1 (%) положительных гепатоцитов в донорском биоптате, 21 (17–29)%, по сравнению с генотипами СС+TT, 16 (10–19)% (Mann–Whitney p = 0,01). Экспрессии CD68 в биоптате печени на этапе донорского забора достоверно выше у носителей гетерозигот по SNP rs913930 (генотип C/T) и SNP rs5030717 (генотип AG), (Mann–Whitney test, p = 0,03). Получена достоверная корреляция между экспрессией CD68 в биоптатах печени доноров и уровнем IL-23 в печеночных венах трансплантата через 1 час после реперфузии (ρ = 0,62; p = 0,04) и между экспрессией HMGB1 в биоптатах печени доноров и уровнем АСТ через 24 часа после реперфузии (r = 0,4; p = 0,02). Экспрессия HMGB1 в биоптатах печени доноров была больше у пациентов с РДТ, 21 (20; 29) кл/мм2 , по сравнению с пациента- ми без РДТ 16 (12; 18) (Mann–Whitney test, p = 0,0036). Заключение. Ранняя дисфункция трансплантата имеет генетические предпосылки, обусловленные полиморфизмом гена TLR-4 и реализующиеся через активацию HMGB1, клеток Купфера и IL-23.

Connecting Peptide Physicochemical and Antimicrobial Properties by a Rational Prediction Model

The increasing rate in antibiotic-resistant bacterial strains has become an imperative health issue. Thus, pharmaceutical industries have focussed their efforts to find new potent, non-toxic compounds to treat bacterial infections. Antimicrobial peptides (AMPs) are promising candidates in the fight against antibiotic-resistant pathogens due to their low toxicity, broad range of activity and unspecific mechanism of action. In this context, bioinformatics' strategies can inspire the design of new peptide leads with enhanced activity. Here, we describe an artificial neural network approach, based on the AMP's physicochemical characteristics, that is able not only to identify active peptides but also to assess its antimicrobial potency. The physicochemical properties considered are directly derived from the peptide sequence and comprise a complete set of parameters that accurately describe AMPs. Most interesting, the results obtained dovetail with a model for the AMP's mechanism of action that takes into account new concepts such as peptide aggregation. Moreover, this classification system displays high accuracy and is well correlated with the experimentally reported data. All together, these results suggest that the physicochemical properties of AMPs determine its action. In addition, we conclude that sequence derived parameters are enough to characterize antimicrobial peptides

Translocation t(1;11)(p32;q23) with MLL-EPS15 fusion gene formation in acute leukemias: a review and 6 new case reports. Approaches to minimal residual disease monitoring

We performed clinical and laboratory characterization of patients with rare translocation t(1;11)(p32;q23) leading to MLL-EPS15 fusion gene formation. Study cohort consisted of 33 primary acute leukemia (AL) cases including 6 newly diagnosed and 27 patients previously described in literature. Among study group patients t(1;11)(p32;q23) was found most frequently in infant AL cases (median age 8 months). In acute lymphoblastic leukemia (ALL) male/female ratio was 1:3, in acute myeloid leukemia (AML) it was 1:1. Additional cytogenetic aberrations in 38 % of patients were revealed. The most frequent breakpoint position in EPS15 gene was intron 1. Four different types of MLLEPS15 fusion gene transcripts were detected. Primers-probe-plasmid combination for MLL-EPS15 fusion gene transcript monitoring by realtime quantitative polymerase chain reaction (RQ-PCR) was developed and successfully applied. In 3 patients RQ-PCR was done on genomic DNA for absolute quantification of MLL-EPS15 fusion gene. High qualitative concordance rate (92 %) was noted between minimal residual disease data obtained in cDNA and genomic DNA for MLL-EPS15 fusion detection.</p

Intramolecular Cohesion of Coils Mediated by Phenylalanine–Glycine Motifs in the Natively Unfolded Domain of a Nucleoporin

The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine–glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin–cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion

Genetic influences on attention deficit hyperactivity disorder symptoms from age 2 to 3: A quantitative and molecular genetic investigation

<p>Abstract</p> <p>Background</p> <p>A twin study design was used to assess the degree to which additive genetic variance influences ADHD symptom scores across two ages during infancy. A further objective in the study was to observe whether genetic association with a number of candidate markers reflects results from the quantitative genetic analysis.</p> <p>Method</p> <p>We have studied 312 twin pairs at two time-points, age 2 and age 3. A composite measure of ADHD symptoms from two parent-rating scales: The Child Behavior Checklist/1.5 - 5 years (CBCL) hyperactivity scale and the Revised Rutter Parent Scale for Preschool Children (RRPSPC) was used for both quantitative and molecular genetic analyses.</p> <p>Results</p> <p>At ages 2 and 3 ADHD symptoms are highly heritable (<it>h</it>^{<it>2 </it>}<it>= </it>0.79 and 0.78, respectively) with a high level of genetic stability across these ages. However, we also observe a significant level of genetic change from age 2 to age 3. There are modest influences of non-shared environment at each age independently (<it>e</it>^{<it>2 </it>}= 0.22 and 0.21, respectively), with these influences being largely age-specific. In addition, we find modest association signals in <it>DAT1 </it>and <it>NET1 </it>at both ages, along with suggestive specific effects of <it>5-HTT </it>and <it>DRD4 </it>at age 3.</p> <p>Conclusions</p> <p>ADHD symptoms are heritable at ages 2 and 3. Additive genetic variance is largely shared across these ages, although there are significant new effects emerging at age 3. Results from our genetic association analysis reflect these levels of stability and change and, more generally, suggest a requirement for consideration of age-specific genotypic effects in future molecular studies.</p

No evidence for the association of DRD4 with ADHD in a Taiwanese population within-family study

BACKGROUND: Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent and highly heritable childhood disorder. The dopamine D4 receptor (DRD4) gene has shown a genetic association with ADHD in Caucasian populations with meta-analysis indicating a small but significant effect across datasets. It remains uncertain whether this association can be generalised to non-Caucasian ethnic groups. Here we investigate two markers within the DRD4 gene in a Taiwanese population, the exon 3 variable number tandem repeat (VNTR) and a 5' 120 base-pair duplication. METHODS: Within-family transmission disequilibrium tests of association of the 5' 120 base-pair duplication, and exon 3 VNTR in a Taiwanese population. RESULTS: No evidence of association of ADHD with either polymorphism in this population was observed. CONCLUSION: The DRD4 gene markers investigated were not found to be associated with ADHD in this Taiwanese sample. Further work in Taiwanese and other Asian populations will therefore be required to establish whether the reports of association of DRD4 genetic variants in Caucasian samples can be generalised to Asian populations