Terahertz Vibrational Dynamics and DFT Calculations for the Quantum Spin Chain Linarite, PbCuSO4(OH)2

The low-dimensional quantum-magnet, linarite, PbCuS4(OH)2, has been investigated using terahertz (THz) spectroscopy coupled with detailed density functional theory (DFT) calculations in order to explore the effects of the temperature on its lattice vibrations. Linarite is characterized by largely isolated CuO chains propagating along the crystallographic b-axis, which at very low temperatures are responsible for exotic, quasi-1D magnetism in this material. To better understand the synergy between the structural bonds and lattice oscillations that contribute to these chains, polarized THz spectroscopic measurements were performed. Consolidating these results with detailed DFT calculations has revealed that the anisotropic vibrational motion for the THz modes is correlated with extreme motion associated with the crystallographic b-axis. An unexpected feature observed in the infrared spectrum is attributed to subtle lattice distortions which break the centro-symmetry in linarite at high temperatures. This phenomenon has not previously been observed in linarite and likely results from anharmonicity in lattice oscillations.

Theoretical modeling of the terahertz spectrum of l-tyrosine leads to experimental verification of previously unobserved vibrational mode

We have calculated the theoretical terahertz spectrum of the amino acid l-tyrosine using density functional theory (DFT). We tried two electron density functionals, Perdew-Burke-Ernzerhof (PBE) and PBE-d3. PBE-d3 includes dispersion corrections to build in van der Waals interactions, which play a role in intermolecular bonding. Both DFT models predicted a low-frequency mode that has not been previously reported. We designed an experiment to search for this mode. Using a deliberately thick sample, intense synchrotron radiation, low temperatures, and temperature variation has enabled us to observe a new resonance at 1.79 ±0.01 THz. While the PBE and PBE-d3 spectra are similar and both match the low-energy experimental data, overall the PBE-d3 appears to be slightly superior. Further refinement still of the functional may lead to even better agreement with experiment above 2.4 THz.

Quantifying production losses associated with foot and mouth disease outbreaks on large-scale dairy farms in Rift valley, Kenya

Foot and Mouth Disease (FMD) is a contagious viral disease to which dairy cattle are highly susceptible. An outbreak of FMD in a dairy herds can cause a drop in milk yield, increase mastitis infections, and force culling. These production losses can be substantial, but farmers undervalue the magnitude of the loss that they incur. The study quantified the association of FMD outbreaks with milk yield, mastitis incidences, and culling rates. The data was from three large-scale dairy farms with a recent history (2008 to 2018) of FMD outbreaks in a region endemic for the prevalence of serotype C of the FMD virus since the mid-1980s in the Rift valley of Kenya. A total of 507 cows were monitored for three consecutive periods of six weeks before, during, and after FMD outbreaks. Relative to the period before and after the disease outbreak, production losses were marked during the outbreak. A disease outbreak was associated with up to 4.7% of the cows drying off (n = 24) and milk production dropped by 16.1%. The incidence of mastitis increased from 5.4% to 21.5% (OR = 3.31, CI = 2.27, 4.83) and culling rates increased from 0.59% to 3.8% (OR = 6.71, CI = 1.99, 22.58).

Determination of Vibrational Modes of l-Alanine Single Crystals by a Combination of Terahertz Spectroscopy Measurements and Density Functional Calculations

Density-functional theory may be used to predict both the frequency and the dipole moment of the fundamental oscillations of molecular crystals. Suitably polarized photons at those frequencies excite such oscillations. Thus, in principle, terahertz spectroscopy may confirm the calculated fundamental modes of amino acids. However, reports to date have multiple shortcomings: (a) material of uncertain purity and morphology and diluted in a binder material is employed; (b) consequently, vibrations along all crystal axes are excited simultaneously; (c) data are restricted to room temperature, where resonances are broad and the background dominant; and (d) comparison with theory has been unsatisfactory (in part because the theory assumes zero temperature). Here, we overcome all four obstacles, in reporting detailed low-temperature polarized THz spectra of single-crystal l-alanine, assigning vibrational modes using density-functional theory, and comparing the calculated dipole moment vector direction to the electric field polarization of the measured spectra. Our direct and detailed comparison of theory with experiment corrects previous mode assignments for l-alanine, and reveals unreported modes, previously obscured by closely spaced spectral absorptions. The fundamental modes are thereby determined.

Terahertz tyrosine modes

We have measured the terahertz spectrum of pure l-tyrosine at nineteen temperatures in the range 6K to 300K using a synchrotron as the source of radiation. By fitting the temperature dependence of the observed modes with a Bose-Einstein model, we determine unequivocal low-frequency modes of l-tyrosine at absolute zero temperature occur at 1.02 ± 0.01, 1.61 ± 0.01, 1.97 ± 0.01, and 2.19 ± 0.01THz. This determination is consistent with the more reliable of the earlier measurements. We conclude that many of the recently reported features in the terahertz spectrum of l-tyrosine are experimental artefacts.

Temperature-dependent terahertz spectroscopy of l-phenylalanine

Undiluted l-phenylalanine has been cooled to 6K and its transmission spectrum obtained under terahertz radiation from a synchrotron source. Three distinct absorption bands are evident: at 1.37, 2.14, and 2.32THz. Each of these tracks to lower frequency ("redshifts") as the temperature is increased from 6 to 250K. The observed shifts are in the range of 0.1-0.2THz. The form of the temperature dependence is well accounted for by a Bose-Einstein model, from which the zero-temperature frequency of each mode and the characteristic temperature of the associated phonon bath may be estimated. At 6K a fourth band is evident, at 2.65THz. However, the depth of this, touching the noise floor, coupled with the increasing opacity of the sample with temperature for frequencies beyond 2.5THz, makes it difficult to track. The frequencies of all four modes are in good accord with and thus confirm a previous calculation.

High-quality, temperature-dependent terahertz spectroscopy of single crystalline L-alanine: Experiment and density-functional theory

For the first time, the terahertz transmittance spectra of l-alanine have been measured using a single crystal. Measurements were obtained over a large temperature range (12-300 K) and revealed 18 absorptions between 20 and 250 cm^-1. These modes were sharp and symmetric, a feature of single crystals and low temperatures. The spectra were directly compared to those of a powdered pellet sample. Raman spectroscopy and x-ray diffraction were used to confirm the sample's structure and purity. With increasing temperature, all modes exhibit spectral redshift, well described by a Bose-Einstein model, indicating the phonon origin of the absorptions. The exceptions are the 91 and 128 cm^-1 modes. The former blueshifts. The latter initially blueshifts but transitions to redshifting. Both behaviors are anomalous. Density-functional theory modeling helped assign all the observed modes.

The 3, 5, 6, and 7 THz resonances of α-glycine

Using an optically thin single crystal sample, mounted in a cryostat permitting cooling to 6 K, and a synchrotron as a bright light source, exceptionally well defined absorption spectra of well-characterised α-glycine have been obtained in the spectral range 2.5-7.5 THz (approximately 80-240 cm^-1). Four separate resonances have been observed, respectively at 93, 152, 188, and 223 cm^-1 at the lowest temperature. Each reduces in frequency (redshifts) as temperature increases. The origin of this observed behaviour is attributed to a phonon-mediated anharmonicity in the crystal potential.

Terahertz response of DL-alanine: experiment and theory

The terahertz (THz) spectrum of dl-alanine has been measured for the first time at cryogenic temperatures and with a pure sample. Several sharp absorptions are observed, over a wide frequency range (0.8-4.8 THz), at 8 K. The sample structure and purity were confirmed with both Raman spectroscopy and X-ray diffraction. Temperature dependent spectra revealed redshifting, with increasing temperature, for all modes except one at 2.70 THz. This mode exhibits blueshifting until ≈120 K, where it starts to redshift. A Bose-Einstein distribution has been used to model the frequency shift with temperature for the four lowest energy modes. Strong correlations between the fits and data indicate that these modes are caused by phonon excitation in an anharmonic potential. Density functional theory has also been used to identify the origin of these low frequency modes. They are attributed to large scale molecular vibrations.

Anharmonicity-driven redshift and broadening of sharp terahertz features of α-glycine single crystal from 20 K to 300 K: Theory and experiment

For the first time, large single crystals of the simplest amino acid, glycine, have been used to determine the temperature dependence of its terahertz spectrum. High-quality spectra with very sharp absorption features are observed at cryogenic temperatures. The α-glycine structure and the purity of the crystals were verified via Raman spectroscopy and X-ray diffraction. Spectral redshift with increasing temperature was observed for all absorption bands in the terahertz region (10-250 cm^-1, or 1-8 THz) over the temperature range of 20-300 K. X-ray diffraction revealed expansion in all planes of the crystal lattice over the same temperature range. A Bose-Einstein distribution was used to model the frequency position shift of the two lowest-energy fundamental modes at 50 cm^-1 and 69 cm^-1. On this basis, we attribute the observed redshift and broadening with increasing temperature to the anharmonic potential associated with the phonon bath.

Estimating my equilibrium energy intake during lockdown: very introspective study

OBJECTIVE

To estimate the daily dietary energy intake for me to maintain a constant body weight. How hard can it be?

DESIGN

Very introspective study.

SETTING

At home. In lockdown. (Except every Tuesday afternoon and Saturday morning, when I went for a run.) PARTICIPANTS: Me. n=1.

MAIN OUTCOME MEASURES

My weight, measured each day.

RESULTS

Sleeping, I shed about a kilogram each night (1.07 (SD 0.25) kg). Running 5 km, I shed about half a kilogram (0.57 (SD 0.15) kg). My daily equilibrium energy intake is about 10 000 kJ (10 286 (SD 201) kJ). Every kJ above (or below) 10 000 kJ adds (or subtracts) about 40 mg (35.4 (SD 3.2) mg).

CONCLUSIONS

Body weight data show persistent variability, even when the screws of control are tightened and tightened.

Identifying and explaining vibrational modes of quinacridones via temperature-resolved terahertz spectroscopy: absorption experiments and solid-state density functional theory simulations

Quinacridone and its substituted analogs are pigments widely used in art and industry. The temperature dependence of the crystal structures of two quinacridone polymorphs (β and γ), along with the common variant 2,9-dimethylquinacridone, were investigated using powder X-ray diffraction and terahertz spectroscopy. These were then compared with solid-state density functional theory simulations of both structures and vibrations. X-ray patterns were collected at eight temperatures in the range 13-298 K and terahertz spectra at fifteen temperatures in the range 20-300 K. Simulations were at absolute zero and at appropriate expansions to model room temperature. It was found that some of the powder X-ray diffraction features in only β-quinacridone (15.7°, 19.7° and 31.2° at 13 K) underwent anomalous shifting with temperature change. We attribute this to the unique coplanar hydrogen bonding pattern of β-quinacridone compared to the other solids, with the unusual diffraction peaks originating from crystallographic planes perpendicular to the a axis intermolecular hydrogen bonds. This observation coincides with a contraction of the a axis with heating and results from its relatively weak N-HO hydrogen bonds and significant C-HH-C repulsions. Associated with this anomalous contraction, for β-quinacridone only spectral peaks are seen to increase in energy with temperature.

Superficial and Fundamental Correspondences in the Terahertz/IR (6-15 THz) Absorption Spectra of Aspirin and Benzoic Acid

The terahertz absorption spectra of aspirin and benzoic acid have been measured in the range 200-500 cm^-1 (6-15 THz). Density-functional theory (DFT) modeling has assigned fundamental vibrational modes to the observed absorption bands. Hydrogen bonds between the crystalline planes of aspirin resulted in better agreement between the experimental and modeled spectra than for benzoic acid. The similar structure of these two molecules suggests a similar absorption spectrum, which indeed was obtained experimentally. However, the detailed crystal structure and molecular differences result in some of the apparently common absorption bands being assigned to different vibrational modes through the DFT modeling. Thus, our study importantly reveals that even though crystalline forms of two similar molecules may have similar experimental terahertz spectra, the resemblance may be superficial rather than fundamental.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Mechanism of periodic height variations along self-aligned VLS-grown planar nanostructures

In this study we report in-plane nanotracks produced by molecular-beam-epitaxy (MBE) exhibiting lateral self-assembly and unusual periodic and out-of-phase height variations across their growth axes. The nanotracks are synthesized using bismuth segregation on the GaAsBi epitaxial surface, which results in metallic liquid droplets capable of catalyzing GaAsBi nanotrack growth via the vapor-liquid-solid (VLS) mechanism. A detailed examination of the nanotrack morphologies is carried out employing a combination of scanning electron and atomic force microscopy and, based on the findings, a geometric model of nanotrack growth during MBE is developed. Our results indicate diffusion and shadowing effects play significant roles in defining the interesting nanotrack shape. The unique periodicity of our lateral nanotracks originates from a rotating nucleation "hot spot" at the edge of the liquid-solid interface, a feature caused by the relative periodic circling of the non-normal ion beam flux incident on the sample surface, inside the MBE chamber. We point out that such a concept is divergent from current models of crawling mode growth kinetics and conclude that these effects may be utilized in the design and assembly of planar nanostructures with controlled non-monotonous structure.

Terahertz (6-15 THz) Spectroscopy and Numerical Modeling of Intermolecular Vibrations in Benzoic Acid and Its Derivatives

Terahertz spectroscopy of benzoic acid (BA) and two of its derivatives, 2-hydroxybenzoic acid (2OH-BA) and 3-hydroxybenzoic acid (3OH-BA), has been investigated in the spectral region 200 to 500 cm(-1) (6.06 to 15.15 THz). The spectra show distinct absorption features. There is agreement between some of the absorption lines observed for these compounds, despite a shift in energy, which is attributed to the differences in the molecular structures. Numerical modeling gave corresponding absorption lines, and this helped in the assignment. Temperature dependence studies revealed that most of the absorption lines are composite lines in this frequency region.

Terahertz spectroscopy of 2,4-dinitrotoluene over a wide temperature range (7-245 K)

Previous THz spectroscopy of the TNT explosive precursor, 2,4-dinitrotoluene (DNT), has been restricted to room temperature (apart from one set of data at 11 K). Here, for the first time, we investigate the spectrum as the temperature is systematically varied, from 7 to 245 K. Many new features appear in the spectrum on cooling below room temperature. As well as the five absorption lines observed previously, we observe five additional lines. In addition, a new room-temperature line at 8.52 THz (281 cm(-1)) is observed. Six of the lines red-shift with temperature and four of them blue-shift. The blue shift is explained by interplay between intramolecular and intermolecular hydrogen bonds. The variation in line width and line intensity with temperature is not systematic, although a conspicuous decrease in line intensity with temperature is observed in all cases. Modeling with hybrid PBE0 and TPSSh functionals helps identify absorption modes.

7th International Immunoglobulin Conference: Neurology

Data presented demonstrate the versatility of immunoglobulin (Ig) therapy for a variety of neurological disorders with different pathogenesis and presentations. In indications where the efficacy of Ig is well established, the neurology community is striving to improve the use of this valuable and limited resource by perfecting best practice guidelines, individualizing dosing schemes and investigating combination therapies to enhance treatment benefit. The data showing the efficacy of Ig therapy in conditions such as chronic pain and autoimmune encephalitis are promising. Future challenges for Ig use in neurological disorders were also outlined. Ongoing and upcoming randomized controlled trials will be pivotal to the use of Ig in the future, by identifying responder groups and elucidating the most effective administration practices. As our understanding and use of the therapy increases, it is essential that we collect data on the effects of long-term Ig treatment in neurological conditions, of which very little currently exists.

Laser-induced oxidation kinetics of bismuth surface microdroplets on GaAsBi studied in situ by Raman microprobe analysis

We report the cw-laser-induced oxidation of molecular-beam-epitaxy grown GaAsBi bismuth surface microdroplets investigated in situ by micro-Raman spectroscopy under ambient conditions as a function of irradiation power and time. Our results reveal the surface droplets are high-purity crystalline bismuth and the resultant Bi₂O₃ transformation to be β-phase and stable at room temperature. A detailed Raman study of Bi microdroplet oxidation kinetics yields insights into the laser-induced oxidation process and offers useful real-time diagnostics. The temporal evolution of new β-Bi₂O₃ Raman modes is shown to be well described by Johnson-Mehl-Avrami-Kolmogorov kinetic transformation theory and while this study limits itself to the laser-induced oxidation of GaAsBi bismuth surface droplets, the results will find application within the wider context of bismuth laser-induced oxidation and direct Raman laser processing.

7th International Immunoglobulin Conference: Neurology

Immunoglobulin (Ig) therapy has been used and studied as a treatment for a variety of neurological conditions for decades. In some of these disorders Ig therapy has a significant role as a first-line treatment. This session explores the use of Ig therapy in immune-mediated peripheral neuropathies and various central nervous system (CNS) diseases. Informative practice points relating to the management and treatment of these diseases are discussed. Potential future neurological indications for Ig therapy, as well as data on efficacy and possible mechanisms of action, are also presented. In peripheral immune-mediated neuropathies, data show good response rates to Ig therapy and it is often used as a first-line treatment. Intravenous immunoglobulin (IVIg) and subcutaneous immunoglobulin (SCIg) are both well tolerated, but dose and dosing frequency should be based on individual clinical responses. In Alzheimer's disease, although clinical data show no significant differences between IVIg and placebo, biomarker studies indicate that plasma-derived antibodies may be involved in clearance of amyloid aggregates from the brain. Data suggest that the use of high IVIg doses in early-stage Alzheimer's treatment may warrant further investigation. Ig therapy is considered a valuable option for autoimmune encephalitis, an antibody-mediated CNS disease. Combination treatment with IVIg and corticosteroids shows promising results and is proposed as a first-line treatment in these disorders. Until recently, very little was understood about the pathogenesis of chronic pain disorders. Data now indicate that perpetuation of the pain response may be underpinned by central immune activation. Some data suggest that Ig therapy may mitigate this effect, with good response rates in a number of studies, but these data need confirmation.

Raman scattering reveals strong LO-phonon-hole-plasmon coupling in nominally undoped GaAsBi: optical determination of carrier concentration

We report room-temperature Raman scattering studies of nominally undoped (100) GaAs1−xBix epitaxial layers exhibiting Bi-induced (p-type) longitudinal-optical-plasmon-coupled (LOPC) modes for 0.018 ≤ x ≤ 0.048. Redshifts in the GaAs-like optical modes due to alloying are evaluated and are paralleled by strong damping of the LOPC. The relative integrated Raman intensities of LO(Γ) and LOPC ALO/ALOPC are characteristic of heavily doped p-GaAs, with a remarkable near total screening of the LO(Γ) phonon (ALO/ALOPC → 0) for larger Bi concentrations. A method of spectral analysis is set out which yields estimates of hole concentrations in excess of 5×1017cm−3 and correlates with the Bi molar fraction. These findings are in general agreement with recent electrical transport measurements performed on the alloy, and while the absolute size of the hole concentrations differ, likely origins for the discrepancy are discussed. We conclude that the damped LO-phonon-hole-plasmon coupling phenomena plays a dominant role in Raman scattering from unpassivated nominally undoped GaAsBi.

Collective librations of water molecules in the crystal lattice of rubidium bromide: experiment and simulation

Terahertz spectroscopy of RbBr reveals four prominent absorption lines at room temperature and a further 15 lines at 10 K. Via density-functional-theory (DFT) numerical modelling using the PBE0 hybrid GGA functional, all the absorptions are identified as correlated librations of water molecules in the RbBr lattice. Each libration mode is a combination of rocking, wagging and twisting motions of the water molecules. The number of libration lines and numerical modelling show that the C2v symmetry of water in RbBr is broken. Our modelling shows that the distribution of libration amplitudes and phases for different water molecules in the RbBr unit cell varies greatly between the different modes. All librational lines red-shift with increasing temperature. The rate of change for most lines is in the range 60-90 MHz K(-1) (or (2-3) × 10(-3) cm(-1) K(-1)). Two lines shift more rapidly with temperature, at rates of 240 and 300 MHz K(-1) (or (8 and 10) × 10(-3) cm(-1) K(-1)), respectively. Furthermore, the temperature dependence of the linewidth distinguishes two groups of lines. For one group, with weak linear temperature dependence of linewidth, cubic anharmonic terms in the RbBr crystal field are significant. This group is mainly associated with fully symmetric correlated librations. For the second group, with strong non-linear temperature dependence of the linewidth, quartic anharmonic terms in the RbBr crystal field are significant. However, the distribution of libration amplitudes, as well as the type of libration modes, influence the temperature dependence of the red shift, the linewidth, and the intensity, as well. Our combined experimental and theoretical investigation confirms the necessity of obtaining low-temperature data to observe all the calculated modes; moreover, the richness of detail in the temperature dependence of the data invites further modelling spanning a range of temperatures.

Spherical, cylindrical and tetrahedral symmetries; hydrogenic states at high magnetic field in Si:P

Phosphorous donors in silicon have an electronic structure that mimics the hydrogen atom, albeit on a larger length, smaller energy and smaller magnetic field scale. While the hydrogen atom is spherically symmetric, an applied magnetic field imposes cylindrical symmetry, and the solid-state analogue involves, in addition, the symmetry of the Si crystal. For one magnetic field direction, all six conduction-band valleys of Si:P become equivalent. New experimental data to high laboratory fields (30 T), supported by new calculations, demonstrate that this high symmetry field orientation allows the most direct comparison with free hydrogen.

Summary of the British Thoracic Society guidelines for advanced diagnostic and therapeutic flexible bronchoscopy in adults

This new guideline covers the rapidly advancing field of interventional bronchoscopy using flexible bronchoscopy. It includes the use of more complex diagnostic procedures such as endobronchial ultrasound, interventions for the relief of central airway obstruction due to malignancy and the recent development of endobronchial therapies for chronic obstructive pulmonary disease and asthma. The guideline aims to help all those who undertake flexible bronchoscopy to understand more about this important area. It also aims to inform respiratory physicians and other specialists dealing with lung cancer of the procedures possible in the management and palliation of central airway obstruction. The guideline covers transbronchial needle aspiration and endobronchial ultrasound-guided transbronchial needle aspiration, electrocautery/diathermy, argon plasma coagulation and thermal laser, cryotherapy, cryoextraction, photodynamic therapy, brachytherapy, tracheobronchial stenting, electromagnetic navigation bronchoscopy, endobronchial valves for emphysema and bronchial thermoplasty for asthma.

Mutations in SDCCAG8/NPHP10 Cause Bardet-Biedl Syndrome and Are Associated with Penetrant Renal Disease and Absent Polydactyly

The ciliopathies are an expanding group of disorders caused by mutations in genes implicated in the biogenesis and function of primary cilia. Bardet-Biedl syndrome (BBS) is a model ciliopathy characterized by progressive retinal degeneration, obesity, polydactyly, cognitive impairment, kidney anomalies and hypogonadism. Mutations in SDCCAG8(NPHP10) were described recently in patients with nephronophthisis and retinal degeneration (Senior-Loken syndrome; SLS). Given the phenotypic and genetic overlap between known ciliopathy genes, we hypothesized that mutations in SDCCAG8 might also contribute alleles to more severe, multisystemic ciliopathies. We performed genetic and phenotypic analyses of 2 independent BBS cohorts. Subsequent to mutation screening, we made a detailed phenotypic analysis of 5 families mutated for SDCCAG8 (3 homozygous and 2 compound heterozygous mutations) and conducted statistical analyses across both cohorts to examine possible phenotype-genotype correlations with mutations at this locus. All patients with mutations in SDCCAG8 fulfilled the diagnostic criteria for BBS (retinal degeneration, obesity, cognitive defects, renal failure, hypogonadism). Interestingly, none of the patients with primary SDCCAG8 mutations had polydactyly, a frequent but not obligatory BBS feature. In contrast, the same patients displayed early-onset renal failure, obesity, as well as recurrent pulmonary and ENT infections. Comparison of the phenotypes of these families with our entire BBS cohort indicated that renal impairment and absent polydactyly correlated significantly with causal SDCCAG8 mutations. Thus, SDCCAG8 mutations are sufficient to cause BBS in 1-2% of our combined cohorts, and define this gene as the sixteenth BBS locus (BBS16). The absence of polydactyly and the concomitant, apparently fully penetrant association with early kidney failure represents the first significant genotype-phenotype correlation in BBS that potentially represents an indicator for phenotype-driven priority screening and informs specific patient management.

Spontaneous periodic deformations in nonchiral planar-aligned bimesogens with a nematic-nematic transition and a negative elastic constant

Hydrocarbon linked mesogenic dimers are found to exhibit an additional nematic phase below the conventional uniaxial nematic phase as confirmed by x-ray diffraction. The phase produces unusual periodic stripe domains in planar cells. The stripes are found to be parallel to the rubbing direction (in rubbed cells) with a well-defined period equal to double the cell gap. The stripes appear without external electromagnetic field, temperature or thickness gradients, rubbing or hybrid alignment treatments. Simple modeling proposes a negative sign for at least one of the two elastic constants: splay and twist, as a necessary condition for the observed pattern.

Practice parameter: the evaluation of distal symmetric polyneuropathy: the role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Report of the American Academy of Neurology, the American Association of Neuromuscular and Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation

BACKGROUND

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy and skin biopsy for the assessment of polyneuropathy.

METHODS

A literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence.

RESULTS AND CONCLUSIONS

1. Autonomic testing may be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). 2. Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). 3. Skin biopsy is a validated technique for determining intraepidermal nerve fiber (IENF) density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.

Practice parameter: the evaluation of distal symmetric polyneuropathy: the role of laboratory and genetic testing (an evidence-based review). Report of the American Academy of Neurology, the American Association of Neuromuscular and Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation

BACKGROUND

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP.

METHODS

A literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence.

RESULTS AND CONCLUSIONS

1. Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B12 with metabolites (methylmalonic acid with or without homocysteine) and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). 2. Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).

Peeling adhesive tape emits electromagnetic radiation at terahertz frequencies

An unusual concept for a simple and inexpensive terahertz source is presented: unpeeling adhesive tape. The observed spectrum of this terahertz radiation exhibits a peak at 2 THz and a broader peak at 18 THz. The radiation is not polarized. The mechanism of terahertz radiation is tribocharging of the adhesive tape and subsequent discharge, possibly bremsstrahlung with absorption or energy density focusing during the dielectric breakdown of a gas. The accompanying optical emission is also a consequence of tribocharging.

Pollen challenge study of a phototherapy device for reducing the symptoms of hay fever

OBJECTIVE

The objective was to investigate the effect of intranasal phototherapy delivered by a phototherapy device (allergy reliever SN-206) on symptoms of hay fever (seasonal rhinitis) due to grass pollen in adults. This registered class IIA medical device had been on sale for 15 months with no adverse effects reported but there had been no assessment of efficacy. Previous research had indicated that phototherapy could alleviate symptoms of allergic rhinitis but no double-blind, placebo-controlled trails had been done.

RESEARCH DESIGN AND METHODS

The trial is a double-blind, placebo-controlled grass pollen challenge conducted out of the pollen season, on 101 adult male and female hay fever sufferers. Subjects were assigned to placebo or active groups by stratified random sampling using responses to a baseline questionnaire. All subjects used active or placebo devices three times a day for 14 days before pollen challenge. Subjects were monitored for 2.5 h after challenge.

MAIN OUTCOME MEASURES

Primary outcome measures were observed severity scores for sneezing, running eyes, running nose, and the amount of eosinophil cationic proteins (ECP) in nasal secretions. Secondary outcome measures were symptom scores by subject report (itching eyes, itching nose, itching throat, itching mouth/palate), and nasal peak inspiratory flow (PIFn) and peak expiratory flow (PEFn).

RESULTS

Significant reductions in severity of symptom scores were found for sneezing, running nose, running eyes and itchy mouth/palate (p < or = 0.05). No significant differences were found in the results for itchy eyes, itchy nose, itchy throat, ECPs, PIFn and PEFn. No adverse events occurred.

CONCLUSIONS

The results show that the device significantly reduced some hay fever symptoms. The study would have been improved if compliance was monitored electronically and if nasal congestion was monitored by report. The mode of action is unclear. The study does not consider long-term implications of the therapy.

Evaluation of distal symmetric polyneuropathy: the role of laboratory and genetic testing (an evidence-based review)

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP. A literature review using MEDLINE, EMBASE, Science Citation Index, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based on the level of evidence. (1) Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B(12) with metabolites (methylmalonic acid with or without homocysteine), and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). (2) Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities, which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).

Evaluation of distal symmetric polyneuropathy: the role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review)

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy, and skin biopsy for the assessment of polyneuropathy. A literature review using MEDLINE, EMBASE, Science Citation Index, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based on the level of evidence. (1) Autonomic testing may be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). (2) Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). (3) Skin biopsy is a validated technique for determining intraepidermal nerve fiber (IENF) density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.

Practice Parameter: Evaluation of distal symmetric polyneuropathy: Role of laboratory and genetic testing (an evidence-based review)

Background: Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP.

Methods: A literature review using MEDLINE, EMBASE, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence.

Results and Recommendations: 1) Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B12 with metabolites (methylmalonic acid with or without homocysteine), and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). 2) Genetic testing should be conducted for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic features and should focus on the most common abnormalities which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).

AAN = American Academy of Neurology; AANEM = American Academy of Neuromuscular and Electrodiagnostic Medicine; AAPM&R = American Academy of Physical Medicine and Rehabilitation; CMT = Charcot-Marie-Tooth; DSP = distal symmetric polyneuropathy; EDX = electrodiagnostic; GTT = glucose tolerance testing; IFE = immunofixation electrophoresis; QSS = Quality Standards Subcommittee; SPEP = serum protein electrophoresis.

Practice Parameter: evaluation of distal symmetric polyneuropathy: role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Report of the American Academy of Neurology, American Association of Neuromuscular and Electrodiagnostic Medicine, and American Academy of Physical Medicine and Rehabilitation

BACKGROUND

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy, and skin biopsy for the assessment of polyneuropathy.

METHODS

A literature review using MEDLINE, EMBASE, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence.

RESULTS AND RECOMMENDATIONS

1) Autonomic testing should be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). 2) Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). 3) Skin biopsy is a validated technique for determining intraepidermal nerve fiber density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.

Neuropathy progression in Charcot-Marie-Tooth disease type 1A

OBJECTIVE

To determine the rate of disease progression in Charcot-Marie-Tooth disease type 1A (CMT1A).

BACKGROUND

CMT1A is the most common inherited peripheral neuropathy, affecting approximately 1:5,000 people irrespective of ethnic background or gender. There is no cure for CMT1A. Clinical trials are being initiated that use the CMT Neuropathy Score (CMTNS), a composite score based on patient symptoms, signs, and neurophysiologic abnormalities, as the primary outcome variable. The sensitivity of the CMTNS or any other score to change over time, as a measure of CMT1A progression, has yet to be determined.

METHODS

We determined the CMTNS as well as the Neuropathy Impairment Score (NIS) on 72 patients followed for up to 8 years. The rate of disease progression was evaluated for the CMTNS and NIS using mixed effects linear regression models, adjusting for age and gender.

RESULTS

Both CMTNS and NIS showed changes over time. The CMTNS increased an average of 0.686 points per year (95% CI 0.461 to 0.911, p <or= 0.0001). The NIS increased 1.368 points per year on average (95% CI 0.616 to 2.121, p = 0.0005). There was a suggestion that the rate of progression increased with age.

CONCLUSION

Progression of CMT1A can be detected by both the CMT Neuropathy Score (CMTNS) and the Neuropathy Impairment Score (NIS). This supports the feasibility of clinical trials to detect a slowing of disease progression using either or both of these scales as outcome measures. Since the CMTNS combines symptoms, signs, and electrophysiology and the NIS is based solely on the neurologic examination, the two scales may be complementary.

A double blind, placebo-controlled cross over trial of cellulose powder by nasal provocation with Der p1 and Der f1

OBJECTIVE

The purpose of this study was to assess whether inert cellulose powder would reduce the response to nasal challenge with house dust mite antigens. The study aimed to investigate the efficacy of inert cellulose powder applied to the nose for the control of persistent allergic rhinitis in adults due to house dust mite allergy. The powder has been registered as a medical device since 1994 and is available in many countries as a remedy for hay fever. Anecdotal evidence reported that it reduced symptoms of persistent rhinitis but no scientific evidence exists for this.

RESEARCH DESIGN AND METHODS

A double blind, placebo-controlled cross over trial was conducted on 15 adult persistent rhinitis sufferers (diagnosed positive to Der p1 and/or Der f1 by SPT) and who had symptoms over the previous 2 years. The placebo was lactose powder. Challenge was by measured dose of homogenised allergenic dust. The study took place in the spring of 2006 before the main pollen seasons.

MAIN OUTCOME MEASURES

The primary outcome measures were observed severity scores for 3 symptom categories and the amount of ECP in nasal secretions. The secondary outcome measures were symptom scores by subject report (nasal blockage, itching of nose, throat and eyes), nasal peak inspiratory (PIFn) and expiratory flow (PEFn).

RESULTS

The results show significant differences for sneezing, itchy nose, runny nose and ECPs in nasal secretions. Some results are also significantly different between placebo and active for PIFn and for PEFn (all at p = 0.05). There were no adverse reactions.

CONCLUSIONS

The inert cellulose powder can have significant effects in reducing some symptoms of persistent rhinitis due to house dust mite allergy.

Analyser-based phase contrast image reconstruction using geometrical optics

Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 microm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.

CMT1X phenotypes represent loss of GJB1 gene function

OBJECTIVE

To investigate possible genotype-phenotype correlations and to evaluate the natural history of patients with Charcot-Marie-Tooth disease type 1X (CMT1X).

BACKGROUND

CMT1X is caused by over 260 distinct mutations in the gap junction beta 1 (GJB1) gene, located on the X chromosome, which encodes the gap junction protein connexin 32 (Cx32). The natural history of CMT1X is poorly understood, and it remains unknown whether particular mutations cause more severe neuropathies through abnormal gain-of-function mechanisms.

METHODS

We evaluated 73 male patients with CMT1X, who each have 1 of 28 different GJB1 mutations predicted to affect nearly all domains of Cx32. Disability was evaluated quantitatively by the CMT Neuropathy Score (CMTNS) as well as by the CMT Symptom Score (CMTSS) and the CMT Examination Score (CMTES), which are both based on the CMTNS. Patients were also evaluated by neurophysiology.

RESULTS

In all patients, disability increased with age, and the degree of disability was comparable with that observed in patients with a documented GJB1 deletion. Disability correlated with a loss of motor units as assessed by motor unit number estimates.

CONCLUSIONS

Taken together, these data suggest that most GJB1 mutations cause neuropathy by a loss of normal connexin 32 function. Therefore, treatment of male patients with Charcot-Marie-Tooth disease type 1X may prove amenable to gene replacement strategies.