Complete nucleotide sequence and experimental host range of <Emphasis Type="Italic">Okra mosaic virus</Emphasis>

Okra mosaic virus (OkMV) is a tymovirus infecting members of the family Malvaceae. Early infections in okra (Abelmoschus esculentus) lead to yield losses of 12–19.5%. Besides intensive biological characterizations of OkMV only minor molecular data were available. Therefore, we determined the complete nucleotide sequence of a Nigerian isolate of OkMV. The complete genomic RNA (gRNA) comprises 6,223 nt and its genome organization showed three major ORFs coding for a putative movement protein (MP) of M_r 73.1 kDa, a large replication-associated protein (RP) of M_r 202.4 kDa and a coat protein (CP) of M_r 19.6 kDa. Prediction of secondary RNA structures showed three hairpin structures with internal loops in the 5′-untranslated region (UTR) and a 3′-terminal tRNA-like structure (TLS) which comprises the anticodon for valine, typical for a member of the genus Tymovirus. Phylogenetic comparisons based on the RP, MP and CP amino acid sequences showed the close relationship of OkMV not only to other completely sequenced tymoviruses like Kennedya yellow mosaic virus (KYMV), Turnip yellow mosaic virus (TYMV) and Erysimum latent virus (ErLV), but also to Calopogonium yellow vein virus (CalYVV), Clitoria yellow vein virus (CYVV) and Desmodium yellow mottle virus (DYMoV). This is the first report of a complete OkMV genome sequence from one of the various OkMV isolates originating from West Africa described so far. Additionally, the experimental host range of OkMV including several Nicotiana species was determined. The nucleotide sequence data reported in this article have been submitted to the Genbank nucleotide sequence database and have been assigned the accession number EF554577.     

Does the transition into daylight saving time really cause partial sleep deprivation?

Aim: To identify possible changes in the sleep patterns according to chronotype in undergraduate students during the daylight saving time (DST) transition.

Methods: A total of 378 students answered the Morningness-Eveningness Questionnaire (MEQ) to determine their chronotype and kept a diary about sleep–wake schedules 1 week before and after the DST transition. Oral mucosal cell samples were collected for genetic analysis.

Results: After the DST transition, intermediate types (I-types) delayed bedtime and increased their time in bed and all groups delayed their wake-up time. All groups presented a shorter phase angle between sunset and the bedtime after the DST transition. On the other hand, only E-types showed a tendency to reduce the phase angle between sunrise and wake-up time, while I-types and M-types kept the same phase angles between sunrise and wake-up time after the DST transition. The polymorphisms in the human genes CLOCK and PER3 were not associated with individual differences in sleep patterns, nor were they associated with an adjustment to the DST transition.

Conclusion: Under the new set of social times determined by DST, the adjustment was only partial. I-types delayed bedtime and all groups delayed their wake-up times after the beginning of DST. Consequently, the time in bed after the DST transition was not reduced; Morning (M-types) and Evening-types (E-types) kept the same time in bed and I-types showed an increase on it.     

AID mutant analyses indicate requirement for class-switch-specific cofactors

Activation-induced cytidine deaminase (AID) is the essential and sole B cell-specific factor required for class-switch recombination (CSR) and somatic hypermutation (SHM). However, it is not known how AID differentially regulates these two independent events. Involvement of several cofactors interacting with AID has been indicated by scattered distribution of loss-of-function point mutations and evolutionary conservation of the entire 198-amino-acid protein. Here, we report that human AID mutant proteins with insertions, replacements or truncations in the C-terminal region retained strong SHM activity but almost completely lost CSR activity. These results indicate that AID requires interaction with a cofactor(s) specific to CSR.     

Invasive Candida infections in children: the clinical characteristics and species distribution and antifungal susceptibility of Candida spp

The aims of the study were to examine the distribution of Candida spp. isolated from sterile body sites, the antifungal susceptibility of the isolates to amphotericin B, fluconazole, voriconazole, and caspofungin, and factors affecting mortality with invasive Candida infections in children. Thirty-five children with invasive candidiasis between January 2004 and January 2008 were evaluated retrospectively. The antifungal susceptibility of isolated Candida species was studied by Etest. Of the invasive Candida infections, 65.7% were due to C. albicans. The second most common isolated species was C. parapsilosis (11.4%). The rates of resistance to fluconazole, amphotericin B and voriconazole were 8.5%, 2.8% and 5.7%, respectively. Caspofungin was the most effective antifungal agent. 22.8% of the patients died in the first 30 days. In univariate analyses, increased mortality was associated with stay in the intensive care unit, the presence of central venous catheter (CVC), failure to remove CVC, and mechanical ventilation.     

Propagation of hepatitis E virus in an endemic and nonendemic regions

The role of hepatitis E (HE) in sporadic morbidity at an endemic territory (Southern Uzbekistan) and the incidence of anti-HEV in different populations of a nonendemic region (Russia) were evaluated. Antibodies to HEV were detected in 22.1% of patients with acute HE, including mixed infections (+ HA or HB), in the Dekhkanabad district of Kashkadarya region in 1993. The estimated incidence of acute HE was 51.7 per 100,000 population. Analysis of monthly incidence of acute HE demonstrated a seasonal pattern of the morbidity: more than 80% of total recorded cases occurred in August-September. These data indicate the presence of group HEV infections and an important role of this infection in the structure of acute viral hepatitis at the endemic territory. Anti-HEV were found in some population groups at a nonendemic territory: in free-of-charge blood donors in Surgut (4%), in patients with HIV infection (1.6%), and in medical workers in Moscow (1.1%).     

Infection with high‐risk HPV types among female sex workers in northern Vietnam

Vaccines against two high‐risk human papillomavirus (HPV) types, HPV‐16, and HPV‐18, are in use currently, with high efficacy for preventing infections with these HPV types and consequent cervical cancers. However, circulating HPV types can vary with geography and ethnicity. The aim of this study was to investigate the prevalence of HPV types and the association between HPV types and abnormal cervical cytology among female sex workers in Northern Vietnam. Cervical swabs and plasma samples were collected from 281 female sex workers at two health centers in Hanoi and Hai Phong in 2009. The HPV L1 gene was amplified by PCR using original and modified GP5⁺/6⁺ primers. Amplified PCR products were genotyped by the microarray system GeneSquare (KURABO) and/or clonal sequencing. Of the 281 women, 139 (49.5%) were positive for HPV DNA. Among the HPV‐positive samples, 339 strains and 29 different types were identified. Multiple‐type and high risk‐type HPV infections were found in 85 (61.2%) and 124 (89.2%) women, respectively. The most common genotype was HPV‐52, followed by HPV‐16, HPV‐18, and HPV‐58. Abnormal cervical cytology was detected in 3.2% (9/281) of the women, and all of these samples were positive for HPV‐DNA. Age ≤25 years and infection with human immunodeficiency virus were associated positively with HPV infection among the women while ever smoking was associated negatively. These results show that HPV‐52 is most prevalent among female sex workers in Northern Vietnam, most of whom had normal cervical cytology. This information may be important for designing vaccination strategies in Vietnam. J. Med. Virol. 85:288–294, 2013. © 2012 Wiley Periodicals, Inc.     

An exact approach to direct aperture optimization in IMRT treatment planning

We consider the problem of intensity-modulated radiation therapy (IMRT) treatment planning using direct aperture optimization. While this problem has been relatively well studied in recent years, most approaches employ a heuristic approach to the generation of apertures. In contrast, we use an exact approach that explicitly formulates the fluence map optimization (FMO) problem as a convex optimization problem in terms of all multileaf collimator (MLC) deliverable apertures and their associated intensities. However, the number of deliverable apertures, and therefore the number of decision variables and constraints in the new problem formulation, is typically enormous. To overcome this, we use an iterative approach that employs a subproblem whose optimal solution either provides a suitable aperture to add to a given pool of allowable apertures or concludes that the current solution is optimal. We are able to handle standard consecutiveness, interdigitation and connectedness constraints that may be imposed by the particular MLC system used, as well as jaws-only delivery. Our approach has the additional advantage that it can explicitly account for transmission of dose through the part of an aperture that is blocked by the MLC system, yielding a more precise assessment of the treatment plan than what is possible using a traditional beamlet-based FMO problem. Finally, we develop and test two stopping rules that can be used to identify treatment plans of high clinical quality that are deliverable very efficiently. Tests on clinical head-and-neck cancer cases showed the efficacy of our approach, yielding treatment plans comparable in quality to plans obtained by the traditional method with a reduction of more than 75% in the number of apertures and a reduction of more than 50% in beam-on time, with only a modest increase in computational effort. The results also show that delivery efficiency is very insensitive to the addition of traditional MLC constraints; however, jaws-only treatment requires about a doubling in beam-on time and number of apertures used. Finally, we showed the importance of accounting for transmission effects when assessing or, preferably, optimizing treatment plan quality.     

Functional impairments at school age of children with necrotizing enterocolitis or spontaneous intestinal perforation

We aimed to determine motor, cognitive, and behavioral outcome at school age of children who had either necrotizing enterocolitis (NEC) or spontaneous intestinal perforation (SIP). This case-control study included infants with NEC Bell's stage IIA onward, infants with SIP, and matched controls (1996-2002). At school age, we assessed motor skills, intelligence, visual perception, visuomotor integration, verbal memory, attention, behavior, and executive functions. Of 93 infants with NEC or SIP, 28 (30%) died. We included 52 of 65 survivors for follow-up. At mean age of 9 y, we found that 68% of the children had borderline or abnormal scores on the Movement Assessment Battery for Children (versus 45% of controls). Their mean total intelligence quotient (IQ) was 86 ± 14 compared with 97 ± 9 in the controls. In addition, attention and visual perception were affected (p < 0.01 and p = 0.02). In comparison to controls, surgically treated children were at highest risk for adverse outcome. In conclusion, at school age, the motor functions and intelligence of many children with NEC or SIP were borderline or abnormal and, specifically, attention and visual perception were impaired. Children with NEC or SIP form a specific risk group for functional impairments at school age even though the majority does not have overt brain pathology.