Specification of coordination behaviors in software architecture using the Reo coordination language

One of the key goals of a software architecture is to help application designers analyze a software system at a higher level of abstraction than implementation. Software architects often use architecture description languages (ADLs) and their supporting tools to specify software architectures. Existing ADLs often lack formal foundations for design, analysis and reconfiguration of software architectures. The Reo language has a strong formal basis and promotes loose coupling, distribution, mobility, exogenous coordination, and dynamic reconfigurability. This thesis focus on assessing the Reo coordination language as an ADL by doing the following work: a) specify a distributed meeting scheduling system using the Reo coordination language; b) assess the Reo coordination language as an ADL using an existing metho

A genome-wide association study identifies FSHR rs2300441 associated with follicle-stimulating hormone levels

Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) play critical roles in female reproduction, while the underlying genetic basis is poorly understood. Genome-wide association studies (GWASs) of FSH and LH levels were conducted in 2590 Chinese females including 1882 polycystic ovary syndrome (PCOS) cases and 708 controls. GWAS for FSH level identified multiple variants at FSHR showing genome-wide significance with the top variant (rs2300441) located in the intron of FSHR. The A allele of rs2300441 led to a reduced level of FSH in the PCOS group (β = −.43, P = 6.70 × 10−14) as well as in the control group (β = −.35, P = 6.52 × 10−4). In the combined sample, this association was enhanced after adjusting for the PCOS status (before: β = −.38, P = 1.77 × 10−13; after: β = −.42, P = 3.33 × 10−16), suggesting the genetic effect is independent of the PCOS status. The rs2300441 explained sevenfold higher proportion of the FSH variance than the total variance explained by the two previously reported FSHR missense variants (rs2300441 R2 = 1.40% vs rs6166 R2 = 0.17%, rs6165 R2 = 0.03%). GWAS for LH did not identify any genome-wide significant associations. In conclusion, we identified genome-wide significant association between variants in FSHR and circulating FSH first, with the top associated variant rs2300441 might be a primary contributor at the population level

SN 2022vqz: A Peculiar SN 2002es-like Type Ia Supernova with Prominent Early Excess Emission

We present extensive photometric and spectroscopic observations of a peculiar type Ia supernova (SN Ia) 2022vqz. It shares many similarities with the SN 2002es-like SNe Ia, such as low luminosity (i.e., $M_{B,\rm max}=-18.11\pm0.16$ mag) and moderate post-peak decline rate (i.e., $\Delta m_{15,B}=1.33\pm0.11$ mag). The nickel mass synthesized in the explosion is estimated as $0.20\pm0.04~{\rm M}_\odot$ from the bolometric light curve, which is obviously lower than normal SNe Ia. SN 2022vqz is also characterized by a slow expanding ejecta, with Si II velocities persisting around 7000 km s$^{-1}$ since 16 days before the peak, which is unique among all known SNe Ia. While all these properties imply a less energetic thermonuclear explosion that should leave considerable amount of unburnt materials, however, absent signature of unburnt carbon in the spectra of SN 2022vqz is puzzling. A prominent early peak is clearly detected in the $c$- and $o$-band light curves of ATLAS and in the $gr$-band data of ZTF within days after the explosion. Possible mechanisms for the early peak are discussed, including sub-Chandrasekhar mass double detonation model and interaction of SN ejecta with circumstellar material (CSM). We found both models face some difficulties in replicating all aspects of the observed data. As an alternative, we propose a hybrid CONe white dwarf as progenitor of SN 2022vqz which can simultaneously reconcile the tension between low ejecta velocity and absence of carbon. We further discuss the diversity of 02es-like objects and possible origins of different scenarios.Comment: 24 pages, 12 figures, submitted to MNRA

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample