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A correction to the article "Room-temperature continuous-wave operation of long wavelength (λ=9.5 μm) MOVPE-grown quantum cascade lasers" that was published in the previous issue is presented.

Abstract Background Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (FST), Informativeness for Assignment Measure (In), and the Absolute Allele Frequency Differences (delta, δ). The objectives are to compare these measures of informativeness to select SNP markers for ancestry inference, and to determine the accuracy of AIM panels selected by each measure in estimating the contributions of the ancestors to the admixed population. Results FST and In had the highest Spearman correlation and the best agreement as measured by Kappa statistics based on deciles. Although the different measures of marker informativeness performed comparably well, analyses based on the top 1 to 10% ranked informative markers of simulated data showed that In was better in estimating ancestry for an admixed population. Conclusions Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error.

Abstract Background New technologies make it possible for the first time to genotype hundreds of thousands of SNPs simultaneously. A wealth of genomic information in the form of publicly available databases is underutilized as a potential resource for uncovering functionally relevant markers underlying complex human traits. Given the huge amount of SNP data available from the annotation of human genetic variation, data mining is a reasonable approach to investigating the number of SNPs that are informative for ancestry information. Methods The distribution and density of SNPs across the genome of African and European populations were extensively investigated by using the HapMap, Affymetrix, and Illumina SNP databases. We exploited these resources by mining the data available from each of these databases to prioritize potential candidate SNPs useful for admixture mapping in complex human diseases and traits. Over 4 million SNPs were compared between Africans and Europeans on the basis of a pre-specified recommended allele frequency difference (delta) value of ≥ 0.3. Results The method identified 15% of HapMap, 11% of Affymetrix, and 14% of Illumina SNP sets as candidate SNPs, termed ancestry informative markers (AIMs). These AIM panels with assigned rs numbers, allele frequencies in each ethnic group, delta value, and map positions are all posted on our website http://www.ssg.uab.edu/downloads/admixture_mapping/SNPAIMs.txt. All marker information in this data set is freely and publicly available without restriction. Conclusion The selected SNP sets represent valuable resources for admixture mapping studies. The overlap between selected AIMs by this single measure of marker informativeness in the different platforms is discussed.

Abstract To examine the relationship between mitochondrial DNA (mtDNA) alterations and colorectal tumorigenesis, we used high-resolution restriction endonucleases and sequencing to assess the mitochondrial genome from three histologic subtypes of colorectal adenomas (tubular = 8; tubulovillous = 9; and villous = 8), colorectal cancer (CRC) tissues = 27, and their matched surrounding normal tissue (MSNT) = 52. The mitochondrial genomes were amplified using 9 pairs of overlapping primers and systematically analyzed by means of high-resolution analysis. DNA fragments showing a shift in banding patterns between the three adenomas, CRC, in comparison to the MSNT were sequenced to identify the mtDNA alterations. A total of thirty-eight germ-line mtDNA variants were observed in this study. Twenty-two of the thirty-eight were identified as mutations and 59% (13 of 22) were silent mutations and one was a 1-bp insertion. Sixteen of thirty-eight were distinct SNPs in flanking regions of the restriction sites and, 6 of the 16 (37%) SNPs were not previously reported. Most of these mutations/SNPs were homoplasmic and distributed in various regions of mitochondrial genes including the 16S and 12S rRNA. Based on our results, mtDNA germline variants increased in prevalence with adenoma CRC progression. To the best of our knowledge, this is the first report to show an increased prevalence of mitochondrial gene variants in CRC tumorigenesis.

Abstract Background We sought to evaluate the hypothesis that the high incidence of cutaneous melanoma in white persons in central Alabama is associated with a predominance of Irish and Scots descent. Methods Frequencies of country of ancestry reports were tabulated. The reports were also converted to scores that reflect proportional countries of ancestry in individuals. Using the scores, we computed aggregate country of ancestry indices as estimates of group ancestry composition. HLA-DRB1*04 allele frequencies and relationships to countries of ancestry were compared in probands and controls. Results were compared to those of European populations with HLA-DRB1*04 frequencies. Results Ninety evaluable adult white cutaneous melanoma probands and 324 adult white controls reported countries of ancestry of their grandparents. The respective frequencies of Ireland, and Scotland and "British Isles" reported countries of ancestry were significantly greater in probands than in controls. The respective frequencies of Wales, France, Italy and Poland were significantly greater in controls. 16.7% of melanoma probands and 23.8% of controls reported "Native American" ancestry; the corresponding "Native American" country of ancestry index was not significantly different in probands and controls. The frequency of HLA-DRB1*04 was significantly greater in probands, but was not significantly associated with individual or aggregate countries of ancestry. The frequency of DRB1*04 observed in Alabama was compared to DRB1*04 frequencies reported from England, Wales, Ireland, Orkney Island, France, Germany, and Australia. Conclusion White adults with cutaneous melanoma in central Alabama have a predominance of Irish, Scots, and "British Isles" ancestry and HLA-DRB1*04 that likely contributes to their high incidence of cutaneous melanoma.

A letter to the editor is presented in response to an article on myeloproliferative disorders in the previous issue.

Background: Jelebu is one of Negeri Sembilan districts of Malaysia, famous for its wide variety of D. zibethinus. It is also recognized as the top hotspot area for consumers looking for genuine Durian Kampung. This study aimed at discovering and recording significant morphological data in identification and classification of D. zibethinus fruit in Jelebu. Methods: Fifty-three accessions of durian were observed from January 2020 to September 2020 in accordance with Malaysia's Department of Agriculture guidelines. Result: Forty-one parameters were compiled and divided into two primary morphological data sets: external and internal structures. Size, shape, color and aril characteristics of fruits were several engrossing parameters for identifying and classifying D. zibethinus varieties. Fruit weight varies between 665 g and 2.7 kg, depending on size. The results also revealed six different variants in the fruit shape and color. Aril characteristics included a variety of aril color and thickness ranging from 0.23 cm to 1.17 cm. Therefore, this research revealed that external and internal morphological data from durian fruits were valuable for recognizing and categorizing D. zibethinus Jelebu variants. [ABSTRACT FROM AUTHOR]

5.6 µm quantum cascade lasers based on the Al0.78In0.22As/In0.69Ga0.31As active region composition with the measured pulsed room temperature wall plug efficiency of 28.3% are reported. Injection efficiency for the upper laser level of 75% was measured for the design by testing devices with variable cavity lengths. A threshold current density of 1.7 kA/cm² and a slope efficiency of 4.9W/A were measured for uncoated 3.15mm x 9 µm lasers. Threshold current density and slope efficiency dependence on temperature in the range from 288K to 348K for the structure can be described by characteristic temperatures T0 ~ 140K and T1 ~ 710 K, respectively. [ABSTRACT FROM AUTHOR]

Herbaria play important roles in providing information for plant research. However, the data in a herbarium are often hard to obtain unless visits are made to the particular herbarium. Digitalizing the herbaria data becomes a vital move to enable efficient work especially when targeted plant materials could not be easily accessed. There is a lack of efficiency in field data collections due to different constraints limiting the assessment of conservation status of orchids, especially the epiphytic ones. With digital data available from various herbaria abroad and herbarium specimens in local herbaria, a database of orchids in Aeridinae was constructed and used to estimate the Extent of Occurrence of endemic vandaceous orchids in Peninsular Malaysia and their extinction risks were assessed. There are 48 endemic vandaceous orchids in Peninsular Malaysia and most of the species are currently categorized as threatened species. Conservation status and extinction risks of these orchids which were not assessed previously could be used as guidelines in decision making and for effective conservation plans to protect them from risk of extinction as these orchids are highly depending on the forest for survival. [ABSTRACT FROM AUTHOR]

Background: Data on the effect of systemic immunoglobulin light chain amyloidosis (AL amyloidosis) on thyroid function are limited.Objective: To assess the prevalence of hypothyroidism in AL amyloidosis patients and determine its predictors.Methods: 1142 newly diagnosed AL amyloidosis patients were grouped based on the thyroid-stimulating hormone (TSH) measurement at diagnosis: hypothyroid group (TSH above upper normal reference; >5 mIU L-1 ; n = 217, 19% of study participants) and euthyroid group (n = 925, 81%). Predictors for hypothyroidism were assessed in a binary multivariate model. Survival between groups was compared using the log-rank test and a multivariate analysis.Results: Patients with hypothyroidism were older, more likely to present with renal and hepatic involvement and had a higher light chain burden compared to patients in the euthyroid group. Higher proteinuria in patients with renal involvement and lower albumin in patients with hepatic involvement were associated with hypothyroidism. In a binary logistic regression model, age ≥65 years, female sex, renal involvement, hepatic involvement, kappa light chain restriction and amiodarone use were independently associated with hypothyroidism. Ninety-three per cent of patients in the hypothyroid group with free thyroxine measurement had normal values, consistent with subclinical hypothyroidism. Patients in the hypothyroid group had a shorter survival compared to patients in the euthyroid group (4-year survival 36% vs 43%; P = 0.008), a difference that was maintained in a multivariate analysis.Conclusion: A significant proportion of patients with AL amyloidosis present with hypothyroidism, predominantly subclinical, which carries a survival disadvantage. Routine assessment of TSH in these patients is warranted. [ABSTRACT FROM AUTHOR]

Aims: Traditionally, crustacean wastes have been managed by using acid and alkali which leads to major environmental issue. However, over the recent years microbial fermentation has gained its way whereby producing similar effects as chemical treatment and a higher quality product can be obtained. Extracellular protease from Bacillus subtilis was used further by optimizing its culture medium to enhance protease production. Methodology and Results: The culture media was optimized with 4 various sources; Shrimp Crab Shell Powder (SCSP), nitrogen sources, inorganic salts, and carbon sources. It was found that culture media supplemented with 9% SCSP, 3% yeast extract, 1% sodium chloride and 9% glucose augmented protease activity up to 565.80 ± 19.41 U/mL compared to the un-optimized media (170.57 ± 6.75 U/mL). By using this optimized media, the ability and efficiency of B. subtilis in a period of 6 days was investigated whereby acid treated shrimp shells (ATSS) and raw shrimp shell powder (RSSP) were used in substitution of SCSP. In a period of 6 days, the protein content in both ATSS and RSSP was found to have been removed up to 60% and 42% respectively. However deproteinization was found to be more efficient in RSSP with the ratio of tyrosine to protein remained constantly high throughout the 6 days period. Conclusion, significance and impact of study: A better, more efficient and environmental friendly method iscontinuously being improvised to manage shrimp wastes with the use of microbes.

Operation of continuous wave quantum cascade lasers with a frequency-shifted feedback provided by an acousto-optic modulator is reported. Measured linewidth of 1.7 cm-1 for these devices, under CW operating conditions, was in a good agreement with predictions of a model based on frequency-shifted feedback seeded by spontaneous emission. Linewidth broadening was observed for short sweep times, consistent with sound wave grating period variation across the illuminated area on the acousto-optic modulator. Standoff detection capability of the AOM-based QCL setup was demonstrated for several solid materials. [ABSTRACT FROM AUTHOR]

We report operation of tunable external cavity quantum cascade lasers with emission wavelength controlled by an acousto-optic modulator (AOM). A long-wave infrared quantum cascade laser wavelength tuned from ~8.5 µm to ~9.8 µm when the AOM frequency was changed from ~41MHz to ~49 MHz. The laser delivered over 350 mW of average power at the center of the tuning curve in a linewidth of ~4.7 cm-1. Measured wavelength switching time between any two wavelengths within the tuning range of the QCL was less than 1 µs. Spectral measurements of infrared absorption features of Freon demonstrated a capability of obtaining complete spectral data in less than 20 µs. [ABSTRACT FROM AUTHOR]

Background High levels of cyclin E (CCNE) are accompanied by shorter survival in cyclophosphamide, hydroxydaunorubicin, oncovin and prednisone (CHOP)- treated diffuse large B-cell lymphomas (DLBCL), independent of the international prognostic index (IPI). Data on the prognostic role of CCNE in the 'rituximab (R)-era' are lacking. Methods To test reproducibility and applicability of observations from the 'pre-R era' to the 'R era', we examined the prognostic role of CCNE expression by immunohistochemistry in 1579 DLBCL on tissue microarrays (TMA); 339 patients were treated by CHOP and 635 by R-CHOP. Results 1209 samples (77%) were evaluable; failures were due to missing TMA punches and fixation artefacts. Mean expression of CCNE was 13% (0-85%); applying a cut-off of >16%, 382 DLBCL (31%) were positive. CCNE did not correlate with any of the known variables (IPI, primary site, cell of origin, proliferation, and BCL2- or C-MYC rearrangements). We were able to reproduce data suggesting an IPI- and response to therapy independent, negative prognostic impact of CCNE in CHOP-treated DLBCL patients: CCNE-positive cases had a median survival of 16 months compared with 57 months in negative ones (p=0.012). In R-CHOP-treated patients the prognostic impact of CCNE was abrogated and only IPI, cell of origin and response to therapy had a prognostic significance. Conclusions Addition of R to CHOP overcomes the negative prognostic impact of CCNE in DLBCL. Thus, R not only prolongs survival in DLBCL but also serves a cautionary note that prognostic factors should not be transferred into the 'R era' without proper scientific studies. [ABSTRACT FROM AUTHOR]

Background. Herpes virus infections can cause cognitive impairment during and after acute encephalitis. Although chronic, latent/persistent infection is considered to be relatively benign, some studies have documented cognitive impairment in exposed persons that is untraceable to encephalitis. These studies were conducted among schizophrenia (SZ) patients or older community dwellers, among whom it is difficult to control for the effects of co-morbid illness and medications. To determine whether the associations can be generalized to other groups, we examined a large sample of younger control individuals, SZ patients and their non-psychotic relatives (n = 1852). Method. Using multivariate models, cognitive performance was evaluated in relation to exposures to herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2) and cytomegalovirus (CMV), controlling for familial and diagnostic status and sociodemographic variables, including occupation and educational status. Composite cognitive measures were derived from nine cognitive domains using principal components of heritability (PCH). Exposure was indexed by antibodies to viral antigens. Results. PCH1, the most heritable component of cognitive performance, declines with exposure to CMV or HSV-1 regardless of case/relative/control group status (p = 1.09 x 10-5 and 0.01 respectively), with stronger association with exposure to multiple herpes viruses (β=-0.25, p = 7.28 x 10-10). There were no significant interactions between exposure and group status. Conclusions. Latent/persistent herpes virus infections can be associated with cognitive impairments regardless of other health status. [ABSTRACT FROM AUTHOR]

Genes involved in cellular mechanisms to repair oxidative damage are strong candidates as etiologic factors for Alzheimer’s disease (AD). One important enzyme involved in this mechanism is superoxide dismutase 2 (SOD2). The gene for this enzyme lies within a single haplotype block at 6q25.3, a region showing evidence for linkage to AD in a genome scan. We genotyped four single nucleotide polymorphisms (SNPs) in SOD2 in families of the National Institute of Mental Health-AD Genetics Initiative (ADGI): rs2758346 in the 5′ untranslated region (UTR), rs4880 in exon 2, rs2855116 in intron 3 and rs5746136 in the 3′UTR. Under a dominant model, family-based association tests showed significant evidence for association of AD with the first three loci in a candidate gene set of families with individuals having age of onset of at least 50 years and two affected and one unaffected sibling, and in a late-onset subset of families (families with all affected individuals having age of onset of at least 65 years) from the full ADGI sample. The alleles transmitted more frequently to cases than expected under the null hypothesis were T, C, G, and G. Global tests of the transmission of haplotypes indicate that the first two loci have the most consistent association with risk of AD. Because of the high linkage disequilibrium in this small (14 kb) gene, and the presence of 100 SNPs in this gene, 26 of which may have functional significance, additional genotyping and sequencing are needed to identify the functionally relevant SNP. We discuss the importance of our findings and the relevance of SOD2 to AD risk. [ABSTRACT FROM AUTHOR]