Projection optics design for tilted projection of fringe patterns

A challenge in the semiconductor industry is 3-D inspection of the miniaturized solder bumps grown on wafers for direct die-to-die bonding. An inspection mechanism proposed earlier requires the projection of a binary fringe grating to the inspected surface from an inclined angle. For high speed and accuracy of the mechanism, the projection optics has to meet these requirements: (1) it allows a tilt angle between the inspected surface and the projector's optical axis; (2) it has a high bandwidth to let high-spatial-frequency harmonics contained in the binary grating pass through the lens and be projected onto the inspected surface properly; (3) it has a high modulation transfer function; (4) it has a large field of view; and (5) it has an adequate depth of field that matches the depth range of the inspected surface. In this paper, we describe a projection optics design, consisting of a fringe grating and several pieces of spherical lens, that addresses the requirements. To reduce the lens aberrations, the grating is laid out with an angle chosen specifically to make the grating, the lens, and the average plane of the inspected surface intersect in the same line. Performance analysis and tolerance analysis are shown to demonstrate the feasibility of the design. © 2008 Society of Photo-Optical Instrumentation Engineers.published_or_final_versio

A chronological review of COVID-19 case fatality rate and its secular trend and investigation of all-cause mortality and hospitalization during the Delta and Omicron waves in the United States: a retrospective cohort study

IntroductionCoronavirus disease 2019 (COVID-19) has caused more than 690 million deaths worldwide. Different results concerning the death rates of the Delta and Omicron variants have been recorded. We aimed to assess the secular trend of case fatality rate (CFR), identify risk factors associated with mortality following COVID-19 diagnosis, and investigate the risks of mortality and hospitalization during Delta and Omicron waves in the United States.MethodsThis study assessed 2,857,925 individuals diagnosed with COVID-19 in the United States from January 2020, to June 2022. The inclusion criterion was the presence of COVID-19 diagnostic codes in electronic medical record or a positive laboratory test of the SARS-CoV-2. Statistical analysis was bifurcated into two components, longitudinal analysis and comparative analysis. To assess the discrepancies in hospitalization and mortality rates for COVID-19, we identified the prevailing periods for the Delta and Omicron variants.ResultsLongitudinal analysis demonstrated four sharp surges in the number of deaths and CFR. The CFR was persistently higher in males and older age. The CFR of Black and White remained higher than Asians since January 2022. In comparative analysis, the adjusted hazard ratios for all-cause mortality and hospitalization were higher in Delta wave compared to the Omicron wave. Risk of all-cause mortality was found to be greater 14–30 days after a COVID-19 diagnosis, while the likelihood of hospitalization was higher in the first 14 days following a COVID-19 diagnosis in Delta wave compared with Omicron wave. Kaplan–Meier analysis revealed the cumulative probability of mortality was approximately 2-fold on day 30 in Delta than in Omicron cases (log-rank p < 0.001). The mortality risk ratio between the Delta and Omicron variants was 1.671 (95% Cl 1.615–1.729, log-rank p < 0.001). Delta also had a significantly increased mortality risk over Omicron in all age groups. The CFR of people aged above 80 years was extremely high as 17.33%.ConclusionMale sex and age seemed to be strong and independent risk factors of mortality in COVID-19. The Delta variant appears to cause more hospitalization and death than the Omicron variant

Reconstruction of phyletic trees by global alignment of multiple metabolic networks

Background: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. Results: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis. Conclusions: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.National Institutes of Health (U.S.) (Grant GM081871

Type-Directed Weaving of Aspects for Polymorphically Typed Functional Languages

Incorporating aspect-oriented paradigm to a polymorphically typed functional language enables the declaration of type-scoped advice, in which the effect of an aspect can be harnessed by introducing possibly polymorphic type constraints to the aspect. The amalgamation of aspect orientation and functional programming enables quick behavioral adaption of functions, clear separation of concerns and expressive type-directed programming. However, proper static weaving of aspects in polymorphic languages with a type-erasure semantics remains a challenge. In this paper, we describe a type-directed static weaving strategy, as well as its implementation, that supports static type inference and static weaving of programs written in an aspect-oriented polymorphically typed functional language, AspectFun. We show examples of type-scoped advice, identify the challenges faced with compile-time weaving in the presence of type-scoped advice, and demonstrate how various advanced aspect features can be handled by our techniques. Lastly, we prove the correctness of the static weaving strategy with respect to the operational semantics of AspectFun

Intra- and Inter-Individual Variance of Gene Expression in Clinical Studies

BACKGROUND: Variance in microarray studies has been widely discussed as a critical topic on the identification of differentially expressed genes; however, few studies have addressed the influence of estimating variance. METHODOLOGY/PRINCIPAL FINDINGS: To break intra- and inter-individual variance in clinical studies down to three levels--technical, anatomic, and individual--we designed experiments and algorithms to investigate three forms of variances. As a case study, a group of "inter-individual variable genes" were identified to exemplify the influence of underestimated variance on the statistical and biological aspects in identification of differentially expressed genes. Our results showed that inadequate estimation of variance inevitably led to the inclusion of non-statistically significant genes into those listed as significant, thereby interfering with the correct prediction of biological functions. Applying a higher cutoff value of fold changes in the selection of significant genes reduces/eliminates the effects of underestimated variance. CONCLUSIONS/SIGNIFICANCE: Our data demonstrated that correct variance evaluation is critical in selecting significant genes. If the degree of variance is underestimated, "noisy" genes are falsely identified as differentially expressed genes. These genes are the noise associated with biological interpretation, reducing the biological significance of the gene set. Our results also indicate that applying a higher number of fold change as the selection criteria reduces/eliminates the differences between distinct estimations of variance