A study on climatological features of the Asian summer monsoon: dynamics, energetics and variability

A continuing goal in the diagnostic studies of the atmospheric general circulation is to estimate various quantities that cannot be directly observed. Evaluation of all the dynamical terms in the budget equations for kinetic energy, vorticity, heat and moisture provide estimates of kinetic energy and vorticity generation, diabatic heating and source/sinks of moisture. All these are important forcing factors to the climate system. In this paper, diagnostic aspects of the dynamics and energetics of the Asian summer monsoon and its spatial variability in terms of contrasting features of surplus and deficient summer monsoon seasons over India are studied with reanalysis data sets. The daily reanalysis data sets from the National Centre for Environmental Prediction/National Centre for Atmospheric Research (NCEP/NCAR) are used for a fifty-two year (1948-1999) period to investigate the large-scale budget of kinetic energy, vorticity, heat and moisture. The primary objectives of the study are to comprehend the climate diagnostics of the Asian summer monsoon and the role of equatorial convection of the summer monsoon activity over India.It is observed that the entrance/exit regions of the Tropical Easterly Jet (TEJ) are characterized by the production/destruction of the kinetic energy, which is essential to maintain outflow/inflow prevailing at the respective location of the TEJ. Both zonal and meridional components contribute to the production of kinetic energy over the monsoon domain, though the significant contribution to the adiabatic generation of kinetic energy originates from the meridional component over the Bay of Bengal in the upper level and over the Somali Coast in the low level. The results indicate that the entire Indian peninsula including the Bay of Bengal is quite unstable during the summer monsoon associated with the production of vorticity within the domain itself and maintain the circulation. The summer monsoon evinces strong convergence of heat and moisture over the monsoon domain. Also, considerable heat energy is generated through the action of the adiabatic process. The combined effect of these processes leads to the formation of a strong diabatic heat source in the region to maintain the monsoon circulation. The interesting aspect noted in this study is that the large-scale budgets of heat and moisture indicate excess magnitudes over the Arabian Sea and the western equatorial Indian Ocean during surplus monsoon. On the other hand, the east equatorial Indian Ocean and the Bay of Bengal region show stronger activity during deficient monsoon. This is reflected in various budget terms considered in this study

Interannual variability of onset of the summer monsoon over India and its prediction

In this article, the interannual variability of certain dynamic and thermodynamic characteristics of various sectors in the Asian summer monsoon domain was examined during the onset phase over the south Indian peninsula (Kerala Coast). Daily average (0000 and 1200 UTC) reanalysis data sets of the National Centre for Environmental Prediction/National Centre for Atmospheric Research (NCEP/NCAR) for the period 1948-1999 were used. Based on 52 years onset date of the Indian summer monsoon, we categorized the pre-onset, onset, and post-onset periods (each an average of 5 days) to investigate the interannual variability of significant budget terms over the Arabian Sea, Bay of Bengal, and the Indian peninsula. A higher difference was noticed in low-level kinetic energy (850 hPa) and the vertically integrated generation of kinetic energy over the Arabian Sea from the pre-onset, onset, and post-onset periods. Also, significant changes were noticed in the net tropospheric moisture and diabatic heating over the Arabian Sea and Indian peninsula from the pre-onset to the post-onset period. It appears that attaining the magnitude of 40 m2 s-2 and then a sharp rise in kinetic energy at 850 hPa is an appropriate time to declare the onset of the summer monsoon over India. In addition to a sufficient level of net tropospheric moisture (40 mm), a minimum strength of low-level flow is needed to trigger convective activity over the Arabian Sea and the Bay of Bengal. An attempt was also made to develop a location-specific prediction of onset dates of the summer monsoon over India based on energetics and basic meteorological parameters using multivariate statistical techniques. The regression technique was developed with the data of May and June for 42 years (1948-1989) and validated with 10 years NCEP reanalysis from 1990 to 1999. It was found that the predicted onset dates from the regression model are fairly in agreement with the observed onset dates obtained from the Indian Meteorology Department

Onset characteristics of the southwest monsoon over India

Dynamic and thermodynamic characteristics of the Asian summer monsoon during the onset phase over the Indian Peninsula (Kerala coast) and its variability are examined with reanalysis data sets. For this study, daily averaged (0000 and 1200 UTC) reanalysis data sets of National Centre for Environmental Prediction-National Centre for Atmospheric Research for the period 1948-99 are used. Based on 52 years of onset dates of the Indian summer monsoon, we categorized pre-onset, onset and post-onset periods (each averaged 5 days) to investigate the mean circulation characteristics and the large-scale energetics of the Asian summer monsoon. It is found that the strength of the low-level Somali jet and upper tropospheric tropical easterly jet increase rapidly during the time of evolution of the summer monsoon over India. Over the Bay of Bengal and the Arabian Sea, predominant changes are noticed in the large-scale balances of kinetic energy, heat and moisture from the pre-onset to the post-onset periods. Prior to the onset of the summer monsoon over India, a zone of flux convergence of heat and moisture is noticed over the eastern sector of the Bay of Bengal and this intensifies in the onset and post-onset periods. During onset of the monsoon over India, the horizontal flux convergence of heat and moisture, as well as diabatic heating, are enhanced over the Arabian Sea. These subsequently increase with the evolution and advancement of the monsoon over India. Further, the dynamics of the evolution processes (15 days before and 30 days after the onset date of the monsoon over Kerala for each annual cycle) are studied over various sectors, such as the Arabian Sea, Bay of Bengal and Indian Peninsula region. The study reveals that the low-level kinetic energy, vertically integrated generation of kinetic energy and net tropospheric moisture over Arabian Sea can be used as potential predictors for the prediction of the possible onset date of the summer monsoon over the Indian Peninsula

The contrasting features of Asian summer monsoon during surplus and deficient rainfall over India

An endeavour is made to distinguish the mean summer monsoon features during surplus and deficient monsoon seasons. Based on all-India summer monsoon rainfall, over 42 years (1958-99), seven surplus and ten deficient monsoon seasons are identified. Making use of daily averaged (00 Z and 12 Z) reanalysis data sets from the National Center for Environmental Prediction-National Center for Atmospheric Research for the corresponding surplus and deficient monsoon seasons, the mean circulation characteristics and large-scale energetics are examined. The circulation features denote that the cross equatorial flow, low-level jet and tropical easterly jet are stronger during a surplus monsoon. Further, strong Tibetan anticyclonic flow characterizes a surplus monsoon. The large-scale balances of kinetic energy, heat and moisture show a significantly large quantity of diabatic heating, adiabatic generation of kinetic energy, and horizontal convergence of heat and moisture during the surplus monsoon season compared with the deficient state. The regions with statistically significant difference between surplus and deficient monsoon seasons are delineated by a Student's t-test at the 95% confidence level. The remarkable aspect noticed in this study is that the Arabian Sea branch of the monsoon circulation is more vigorous during a surplus monsoon season, whereas the eastern Bay of Bengal branch is stronger during a deficient monsoon. The various large-scale budget terms of kinetic energy, heat and moisture are found to be consistent and in agreement with the seasonal monsoon activity over India

A study on dynamic and thermodynamic aspects of breaks in the summer monsoon over India

The rainfall associated with the Indian summer monsoon shows large intraseasonal and interannual variability. Break-monsoon conditions are one of the important epochs of the monsoon, and they contribute significantly to the intraseasonal variability of the monsoon. The National Centers for Environmental Prediction-National Center for Atmospheric Research reanalysis data sets are used to investigate the significant energy budget terms during the pre-break (5 days prior to the commencement of the break), break and post-break (5 days after the cessation of the break) periods. In the present study, certain dynamic and thermodynamic characteristics of the monsoon circulation during break-monsoon conditions are investigated. The important terms in the various energy budget equations are analysed between the surface and 100 hPa for the break and its departures from pre- and post-break for the period 1968-96. The statistical significance of these departures is also examined by Student's t-test at the 95% confidence level. The volume integral of the budget terms is also examined in four sectors, i.e. the Arabian Sea, Bay of Bengal, northern India and central India. Significant changes in the wind field and vorticity at 850 hPa take place in the monsoon trough zone, coastal regions of the western coast of India and the southwestern Bay of Bengal off the southern Indian coast. The vertically upward rising arm of the Hadley cell weakens during the break phase. The strong flux convergence of kinetic energy in the central Arabian Sea and flux divergence in the northeastern Bay of Bengal weakens during pre- and post-break periods. Significant changes in the diabatic heating horizontal flux of heat and moisture are observed in the monsoon trough zone, central and northwestern Bay of Bengal. The Bay of Bengal and central India sectors show higher magnitudes and changes in respect of dynamic and thermodynamic parameters compared with the Arabian Sea and northern India

Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study

BACKGROUND: Mutations altering BLM function are associated with highly elevated cancer susceptibility (Bloom syndrome). Thus, genetic variants of BLM and proteins that form complexes with BLM, such as TOP3A and RMI1, might affect cancer risk as well. METHODS: In this study we have studied 26 tagged single nucleotide polymorphisms (tagSNPs) in RMI1, TOP3A, and BLM and their associations with cancer risk in acute myeloid leukemia/myelodysplatic syndromes (AML/MDS; N = 152), malignant melanoma (N = 170), and bladder cancer (N = 61). Two population-based control groups were used (N = 119 and N = 156). RESULTS: Based on consistency in effect estimates for the three cancer forms and similar allelic frequencies of the variant alleles in the control groups, two SNPs in TOP3A (rs1563634 and rs12945597) and two SNPs in BLM (rs401549 and rs2532105) were selected for analysis in breast cancer cases (N = 200) and a control group recruited from spouses of cancer patients (N = 131). The rs12945597 in TOP3A and rs2532105 in BLM showed increased risk for breast cancer. We then combined all cases (N = 584) and controls (N = 406) respectively and found significantly increased risk for variant carriers of rs1563634 A/G (AG carriers OR = 1.7 [95%CI 1.1-2.6], AA carriers OR = 1.8 [1.2-2.8]), rs12945597 G/A (GA carriers OR = 1.5 [1.1-1.9], AA carriers OR = 1.6 [1.0-2.5]), and rs2532105 C/T (CT+TT carriers OR = 1.8 [1.4-2.5]). Gene-gene interaction analysis suggested an additive effect of carrying more than one risk allele. For the variants of TOP3A, the risk increment was more pronounced for older carriers. CONCLUSION: These results further support a role of low-penetrance genes involved in BLM-associated homologous recombination for cancer risk

Pooled Analysis of a Self-Sampling HPV DNA Test as a Cervical Cancer Primary Screening Method

BackgroundWorldwide, one-seventh of cervical cancers occur in China, which lacks a national screening program. By evaluating the diagnostic accuracy of self-collected cervicovaginal specimens tested for human papillomavirus (HPV) DNA (Self-HPV testing) in China, we sought to determine whether Self-HPV testing may serve as a primary cervical cancer screening method in low-resource settings.MethodsWe compiled individual patient data from five population-based cervical cancer–screening studies in China. Participants (n = 13 140) received Self-HPV testing, physician-collected cervical specimens for HPV testing (Physician-HPV testing), liquid-based cytology (LBC), and visual inspection with acetic acid (VIA). Screen-positive women underwent colposcopy and confirmatory biopsy. We analyzed the accuracies of pooled Self-HPV testing, Physician-HPV testing, VIA, and LBC to detect biopsy-confirmed cervical intraepithelial neoplasia grade 2 or more severe (CIN2+) and CIN3+. All statistical tests were two-sided.ResultsOf 13 004 women included in the analysis, 507 (3.9%) were diagnosed as CIN2+, 273 (2.1%) as CIN3+, and 37 (0.3%) with cervical cancer. Self-HPV testing had 86.2% sensitivity and 80.7% specificity for detecting CIN2+ and 86.1% sensitivity and 79.5% specificity for detecting CIN3+. VIA had statistically significantly lower sensitivity for detecting CIN2+ (50.3%) and CIN3+ (55.7%) and higher specificity for detecting CIN2+ (87.4%) and CIN3+ (86.9%) (all P values < .001) than Self-HPV testing, LBC had lower sensitivity for detecting CIN2+ (80.7%, P = .015), similar sensitivity for detecting CIN3+ (89.0%, P = .341), and higher specificity for detecting CIN2+ (94.0%, P < .001) and CIN3+ (92.8%, P < .001) than Self-HPV testing. Physician-HPV testing was more sensitive for detecting CIN2+ (97.0%) and CIN3+ (97.8%) but similarly specific for detecting CIN2+ (82.7%) and CIN3+ (81.3%) (all P values <.001) than Self-HPV testing.ConclusionsThe sensitivity of Self-HPV testing compared favorably with that of LBC and was superior to the sensitivity of VIA. Self-HPV testing may complement current screening programs by increasing population coverage in settings that do not have easy access to comprehensive cytology-based screening

A Cost-Effective ELP-Intein Coupling System for Recombinant Protein Purification from Plant Production Platform

BACKGROUND: Plant bioreactor offers an efficient and economical system for large-scale production of recombinant proteins. However, high cost and difficulty in scaling-up of downstream purification of the target protein, particularly the common involvement of affinity chromatography and protease in the purification process, has hampered its industrial scale application, therefore a cost-effective and easily scale-up purification method is highly desirable for further development of plant bioreactor. METHODOLOGY/PRINCIPAL FINDINGS: To tackle this problem, we investigated the ELP-intein coupling system for purification of recombinant proteins expressed in transgenic plants using a plant lectin (PAL) with anti-tumor bioactivity as example target protein and rice seeds as production platform. Results showed that ELP-intein-PAL (EiP) fusion protein formed novel irregular ER-derived protein bodies in endosperm cells by retention of endogenous prolamins. The fusion protein was partially self-cleaved in vivo, but only self-cleaved PAL protein was detected in total seed protein sample and deposited in protein storage vacuoles (PSV). The in vivo uncleaved EiP protein was accumulated up to 2-4.2% of the total seed protein. The target PAL protein could be purified by the ELP-intein system efficiently without using complicated instruments and expensive chemicals, and the yield of pure PAL protein by the current method was up to 1.1 mg/g total seed protein. CONCLUSION/SIGNIFICANCE: This study successfully demonstrated the purification of an example recombinant protein from rice seeds by the ELP-intein system. The whole purification procedure can be easily scaled up for industrial production, providing the first evidence on applying the ELP-intein coupling system to achieve cost-effective purification of recombinant proteins expressed in plant bioreactors and its possible application in industry