A Multilevel Model for Continuous Time Population Estimation

Summary .  Statistical methods have been developed and applied to estimating populations that are difficult or too costly to enumerate. Known as multilist methods in epidemiological settings, individuals are matched across lists and estimation of population size proceeds by modeling counts in incomplete multidimensional contingency tables (based on patterns of presence/absence on lists). As multilist methods typically assume that lists are compiled instantaneously, there are few options available for estimating the unknown size of a closed population based on continuously (longitudinally) compiled lists. However, in epidemiological settings, continuous time lists are a routine byproduct of administrative functions. Existing methods are based on time-to-event analyses with a second step of estimating population size. We propose an alternative approach to address the twofold epidemiological problem of estimating population size and of identifying patient factors related to duration (in days) between visits to a health care facility. A Bayesian framework is proposed to model interval lengths because, for many patients, the data are sparse; many patients were observed only once or twice. The proposed method is applied to the motivating data to illustrate the methods' applicability. Then, a small simulation study explores the performance of the estimator under a variety of conditions. Finally, a small discussion section suggests opportunities for continued methodological development for continuous time population estimation.     

Activated packed bed bioreactor for rapid nitrification in brackish water hatchery systems

A packed bed bioreactor (PBBR) was developed for rapid establishment of nitrification in brackish water hatchery systems in the tropics. The reactors were activated by immobilizing ammonia-oxidizing (AMONPCU-1) and nitrite-oxidizing (NIONPCU-1) bacterial consortia on polystyrene and low-density polyethylene beads, respectively. Fluorescence in situ hybridization demonstrated the presence of autotrophic nitrifiers belong to Nitrosococcus mobilis, lineage of β ammonia oxidizers and nitrite oxidizer Nitrobacter sp. in the consortia. The activated reactors upon integration to the hatchery system resulted in significant ammonia removal (P < 0.01) culminating to its undetectable levels. Consequently, a significantly higher percent survival of larvae was observed in the larval production systems. With spent water the reactors could establish nitrification with high percentage removal of ammonia (78%), nitrite (79%) and BOD (56%) within 7 days of initiation of the process. PBBR is configured in such a way to minimize the energy requirements for continuous operation by limiting the energy inputs to a single stage pumping of water and aeration to the aeration cells. The PBBR shall enable hatchery systems to operate under closed recirculating mode and pave the way for better water management in the aquaculture industry.     

Protein Modules Conserved Since LUCA

Universal scale of the sequence conservation has been recently introduced based on omnipresence of the protein sequence motifs across species. A large spectrum of short sequences, up to eight residues has been found to reside in all or almost all prokaryotic organisms. By this discovery a principally novel quantitative approach is introduced to the problem of reconstruction of the last universal common ancestor (LUCA). The most conserved elements (protein modules) with defined structures and sequences harboring the omnipresent motifs are outlined in this work, by combining the sequence and protein crystal structure data. The structurally conserved modules involve 25–30 amino acid residues and have appearance of closed loops, loop-n-lock structures. This confirms earlier conclusions on the loop-fold structure of globular proteins. Many of the topmost conserved modules represent the primary closed loop prototypes, that have been derived by whole genome sequence searches. The data presented, thus, make a basis for further developments toward the earliest stages of protein evolution. [Reviewing Editor: Dr. Martin Kreitman]     

胰岛素对离体大鼠胸主动脉血管张力的影响

制备离体大鼠胸主动脉环,分有内皮组和去内皮组,采用离体血管灌流技术,观察胰岛素对去氧肾上腺素（PE）和氯化钾（KCl）预收缩的胸主动脉环收缩张力的影响。结果表明胰岛素对PE预收缩的胸主动脉环产生浓度依赖性的舒张作用,且有内皮组和去内皮组间无显著差异。胰岛素对KCl预收缩的胸主动脉环没有显著影响。胰岛素对PE预收缩的胸主动脉环有非内皮依赖性舒张作用。     

Network-based analysis reveals novel gene signatures in the peripheral blood of patients with sporadic nonsyndromic thoracic aortic aneurysm

Thoracic aortic aneurysm (TAA), a serious cardiovascular disease that causes morbidity and mortality worldwide. At present, few biomarkers can accurately diagnose the appearance of TAA before dissection or rupture. Our research has the intention to investigate the developing applicable biomarkers for TAA promising clinically diagnostic biomarkers or probable regulatory targets for TAA. In our research, we built correlation networks utilizing the expression profile of peripheral blood mononuclear cell obtained from a public microarray data set (GSE9106). Furthermore, we chose the turquoise module, which has the strongest significance with TAA and was further analyzed. Fourteen genes that overlapped with differentially expressed proteins in the medial aortic layer were obtained. Subsequently, we verified the results applying quantitative polymerase chain reaction (Q-PCR) to our clinical specimen. In general, the Q-PCR results coincide with the majority of the expression profile. Fascinatingly, a notable change occurred in CLU, DES, MYH10, and FBLN5. In summary, using weighted gene coexpression analysis, our study indicates that CLU, DES, MYH10, and FBLN5 were identified and validated to be related to TAA and might be candidate biomarkers or therapeutic targets for TAA.     

Autophagy-mediated degradation is necessary for regression of cardiac hypertrophy during ventricular unloading

Cardiac hypertrophy occurs in response to a variety of stresses as a compensatory mechanism to maintain cardiac output and normalize wall stress. Prevention or regression of cardiac hypertrophy can be a major therapeutic target. Although regression of cardiac hypertrophy occurs after control of etiological factors, the molecular mechanisms remain to be clarified. In the present study, we investigated the role of autophagy in regression of cardiac hypertrophy. Wild-type mice showed cardiac hypertrophy after continuous infusion of angiotensin II for 14 days using osmotic minipumps, and regression of cardiac hypertrophy was observed 7 days after removal of the minipumps. Autophagy was induced during regression of cardiac hypertrophy, as evidenced by an increase in microtubule-associated protein 1 light chain 3 (LC3)-II protein level. Then, we subjected cardiac-specific Atg5-deficient (CKO) and control mice (CTL) to angiotensin II infusion for 14 days. CKO and CTL developed cardiac hypertrophy to a similar degree without contractile dysfunction. Seven days after removal of the minipumps, CKO showed significantly less regression of cardiac hypertrophy compared with CTL. Regression of pressure overload-induced cardiac hypertrophy after unloading was also attenuated in CKO. These results suggest that autophagy is necessary for regression of cardiac hypertrophy during unloading of neurohumoral and hemodynamic stress.     

Closed Loops of TIM Barrel Protein Fold

Abstract

The closed loops within the proteins of the TIM-barrel fold family are analyzed and compared sequence- and structure-wise. The size distribution of the closed loops of the TIM-barrels confirms universal preference to the standard size of 25–30 residues. 3D structural RMSD comparisons of the closed loops and presentation of their sequences in binary form suggest that the TIM-barrel proteins are built from descendants of several types of basic closed loop prototypes. Comparison of these prototypes points to a likely common ancestor—the alpha helix containing closed loops of 28 amino acids. The presumed ancestor is characterized by specific binary consensus sequence.     

Effect of intercostal muscle and costovertebral joint material properties on human ribcage stiffness and kinematics

Current finite element (FE) models of the human thorax are limited by the lack of local-level validation, especially in the ribcage. This study exercised an existing FE ribcage model for a 50th percentile male under quasi-static point loading and dynamic sternal loading. Both force-displacement and kinematic responses of the ribcage were compared against experimental data. The sensitivity of the model response to changes in the material properties of the costovertebral (CV) joints and intercostal muscles was assessed. The simulations found that adjustments to the CV joints tended to change the amount of rib rotation in the sagittal plane, while changes to the elastic modulus and thickness of the intercostal muscles tended to alter both the stiffness and the direction and magnitude of rib motions. This study can lend insight into the role that the material properties of these two thoracic structures play in the dynamics of the ribcage during a frontal loading condition.     

Divergent enhancer haplotype of ebony on inversion In(3R)Payne associated with pigmentation variation in a tropical population of Drosophila melanogaster

The pattern and intensity of pigmentation have direct impact on individual fitness through various ecological factors. In a Drosophila melanogaster population from southern Japan, thoracic trident pigmentation intensity of most of the strains could be classified into Dark or Light‐type. The expression level variation of the ebony gene correlated well with this phenotype and the allelic differences in expression indicated that the variation is partly due to cis‐regulatory changes. In the ～13 kb gene region, we identified 17 nucleotide sites and 2 indels that were in complete association with the thoracic trident pigmentation intensity. Interestingly, 11 out of 19 sites located within ～0.5 kb of the core epidermis enhancer. These sites had no obvious association with the abdominal pigmentation intensity in the previously analysed African populations from Uganda and Kenya, which suggested that multiple potential mutational pathways in the cis‐regulatory control region of a single gene could lead to similar phenotypic variation within this species. We also found that the Light‐type enhancer haplotype is strongly linked to a cosmopolitan inversion, In(3R)Payne, which is predominant in warmer climatic regions in both hemispheres. The sequence pattern suggested that the strong linkage may be due to selective forces related to thermal adaptation. The inferred selection for lighter pigmentation in the Japanese population is in the opposite direction of the previously reported case of selection for darker individuals in African populations. Nevertheless, both adaptive changes involved cis‐regulatory changes of ebony, which shows that this gene is likely to be a common target of natural selection.