Statistical Methods for Identifying Wolf Kill Sites Using Global Positioning System Locations

Abstract: Accurate estimates of kill rates remain a key limitation to addressing many predator—prey questions. Past approaches for identifying kill sites of large predators, such as wolves (Canis lupus), have been limited primarily to areas with abundant winter snowfall and have required intensive ground-tracking or aerial monitoring. More recently, attempts have been made to identify clusters of locations obtained using Global Positioning System (GPS) collars on predators to identify kill sites. However, because decision rules used in determining clusters have not been consistent across studies, results are not necessarily comparable. We illustrate a space—time clustering approach to statistically define clusters of wolf GPS locations that might be wolf kill sites, and we then use binary and multinomial logistic regression to model the probability of a cluster being a non—kill site, kill site of small-bodied prey species, or kill site of a large-bodied prey species. We evaluated our approach using field visits of kills and assessed the accuracy of the models using an independent dataset. The cluster-scan approach identified 42–100% of wolf-killed prey, and top logistic regression models correctly classified 100% of kills of large-bodied prey species, but 40% of small-bodied prey species were classified as nonkills. Although knowledge of prey distribution and vulnerability may help refine this approach, identifying small-bodied prey species will likely remain problematic without intensive field efforts. We recommend that our approach be utilized with the understanding that variation in prey body size and handling time by wolves will likely have implications for the success of both the cluster scan and logistic regression components of the technique. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):798–807; 2008)     

Selecting near-native protein structures from ab initio models using ensemble clustering

Background: Ab initio protein structure prediction is to predict the tertiary structure of a protein from its amino acid sequence alone. As an important topic in bioinformatics, considerable efforts have been made on designing the ab initio methods. Unfortunately, lacking of a perfect energy function, it is a difficult task to select a good near-native structure from the predicted decoy structures in the last step. Methods: Here we propose an ensemble clustering method based on k-medoids to deal with this problem. The k-medoids method is run many times to generate clustering ensembles, and then a voting method is used to combine the clustering results. A confidence score is defined to select the final near-native model, considering both the cluster size and the cluster similarity. Results: We have applied the method to 54 single-domain targets in CASP-11. For about 70.4% of these targets, the proposed method can select better near-native structures compared to the SPICKER method used by the I-TASSER server. Conclusions: The experiments show that, the proposed method is effective in selecting the near-native structure from decoy sets for different targets in terms of the similarity between the selected structure and the native structure.     

Synergic Interface and Optical Engineering for High‐Performance Semitransparent Polymer Solar Cells

In this study the thickness of the PTB7‐Th:PC₇₁BM bulk heterojunction (BHJ) film and the PF3N‐2TNDI electron transport layer (ETL) is systematically tuned to achieve polymer solar cells (PSCs) with optimized power conversion efficiency (PCE) of over 9% when an ultrathin BHJ of 50 nm is used. Optical modeling suggests that the high PCE is attributed to the optical spacer effect from the ETL, which not only maximizes the optical field within the BHJ film but also facilitates the formation of a more homogeneously distributed charge generation profile across the BHJ film. Experimentally it is further proved that the extra photocurrent produced at the PTB7‐Th/PF3N‐2TNDI interface also contributes to the improved performance. Taking advantage of this high performance thin film device structure, one step further is taken to fabricate semitransparent PSCs (ST‐PSCs) by using an ultrathin transparent Ag cathode to replace the thick Ag mirror cathode, yielding a series of high performance ST‐PSCs with PCEs over 6% and average visible transmittance between 20% and 30%. These ST‐PSCs also possess remarkable transparency color perception and rendering properties, which are state‐of‐the‐art and fulfill the performance criteria for potential use as power‐generating windows in near future.     

Improving the production,activity, and stability of CLEAs with diepoxides

Among enzyme immobilization techniques, the preparation of cross‐linked enzyme aggregates has shown promising results in biocatalysis, because they are easy to prepare, versatile, and cheap. The method involves the precipitation of enzymes with ammonium sulfate or an organic solvent and subsequent cross‐linking with glutaraldehyde. However, the Schiff base produced with glutaraldehyde is reversible and can be broken with acids or bases, releasing proteins to the reaction medium. To solve this problem, we propose replacing glutaraldehyde with diepoxide compounds to obtain an irreversible secondary amine bond. Such a substitution avoids protein leakage during the biocatalytic process, contamination of the final products, and loss of enzyme. It also improves the synthesis of the biocatalyst, because, while the Schiff base is favored at mildly acidic pH, the epoxide reaction can be made at the optimal enzyme pH, assuring its structural stability and catalytic performance. The proposed method has been successfully used in the production and optimization of aldolase epoxy‐cross‐linked aggregates, which retain 98% activity. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1425–1429, 2017     

A study on interaspecific biodiversity of eight groups of silkworm （Bombyx mori） by biochemical markers

The recognition of biodiversity in different races and lines of silkworm (Bombyx mori) is very useful for breeding programs and production of high efficiency hybrids. In this study eight groups of silkworm were selected including 103, 107, Xihang 1 and 2 of Japanese origin and 104, 110, Koming 1 and 2 of Chinese origin. The activity levels of three enzymes including alkaline phosphatase, alanine aminotransferase and aspartate aminotransferase in haemolymph of fifth instar larva were measured. Moreover, the quantitative amount of total protein, cholesterol and glucose of haemolymph was evaluated.The data reveal that the activity level of measured macromolecules except for alkaline phosphatase were significantly different in all the groups. Hierarchical agglomerative clustering under UPGMA model separated line 104 from other groups. Two groups of Koming 1 and Xihang 1 had the most intergroup similarities.     

Obesity and Cardiovascular Disease Risk Factors in Firefighters: A Prospective Cohort Study

Objective: Obesity, despite being a significant determinant of fitness for duty, is reaching epidemic levels in the workplace. Firefighters’ fitness is important to their health and to public safety. Research Methods and Procedures: We examined the distribution of BMI and its association with major cardiovascular disease (CVD) risk factors in Massachusetts firefighters who underwent baseline (1996) and annual medical examinations through a statewide medical surveillance program over 5 years of follow‐up. We also evaluated firefighters’ weight change over time. Results: The mean BMI among 332 firefighters increased from 29 at baseline to 30 at the follow‐up examination (2001), and the prevalence of obesity increased from 35% to 40%, respectively (p < 0.0001). In addition, the proportion of firefighters with extreme obesity increased 4‐fold at follow‐up (from 0.6% to 2.4%, p < 0.0001). Obese firefighters were more likely to have hypertension (p = 0.03) and low high‐density lipoprotein‐cholesterol (p = 0.01) at follow‐up. Firefighters with extreme obesity had an average of 2.1 CVD risk factors (excluding obesity) in contrast to 1.5 CVD risk factors for normal‐weight firefighters (p = 0.02). Finally, on average, normal‐weight firefighters gained 1.1 pounds, whereas firefighters with BMI ≥ 35 gained 1.9 pounds per year of active duty over 5 years of follow‐up. Discussion: Obesity is a major concern among firefighters and shows worsening trends over time. Periodic medical evaluations coupled with exercise and dietary guidelines are needed to address this problem, which threatens firefighters’ health and may jeopardize public safety.     

Increased poly-β-hydroxybutyrate (PHB) chain length by the modulation of PHA synthase activity in recombinant Escherichia coli

A second promoter (P1) was inserted to the PHA (poly--hydroxyalkanoate) operon (pSP2) of Esherichia coli DH5 with an optimal E. coli ribosome binding site and a trc strong promoter (pSJS1) to obtain poly--hydroxybutyrate (PHB) with long chain length. When the inducer, IPTG was added to the culture at 0.4 mM, the average molecular weight was 1.1 × 10⁶ Da. However, an even greater increase of the PHB average molecular weight to 2.5 × 10⁷ Da was observed without IPTG being added.     

Bayesian detection and modeling of spatial disease clustering

Many current statistical methods for disease clustering studies are based on a hypothesis testing paradigm. These methods typically do not produce useful estimates of disease rates or cluster risks. In this paper, we develop a Bayesian procedure for drawing inferences about specific models for spatial clustering. The proposed methodology incorporates ideas from image analysis, from Bayesian model averaging, and from model selection. With our approach, we obtain estimates for disease rates and allow for greater flexibility in both the type of clusters and the number of clusters that may be considered. We illustrate the proposed procedure through simulation studies and an analysis of the well-known New York leukemia data.     

Evidence for a Conformational Change in Subunit III of Bovine Heart Mitochondrial Cytochrome c Oxidase1

The role of subunit III in the function of mitochondrial cytochrome c oxidase is not clearly understood. Previous work has shown that chemical modification of subunit III with N,N-dicyclohexylcarbodiimide (DCCD) reduced the proton-pumping efficiency of the enzyme by an unknown mechanism. In the current work, we have employed biochemical approaches to determine if a conformational change is occurring within subunit III after DCCD modification. Control and DCCD modified beef heart enzyme were subjected to limited proteolysis in nondenaturing detergent solution. Subunit III in DCCD treated enzyme was more susceptible to chymotrypsin digestion than subunit III in the control enzyme. We also labeled control and DCCD-modified enzyme with iodoacetyl—biotin, a sulfhydryl reagent, and found that subunit III of the DCCD-modified enzyme was more reactive when compared to subunit III of the control enzyme, indicating an increase in reactivity of subunit III upon DCCD binding. The cross linking of subunit III of the enzyme induced by the heterobifunctional reagent, N-succinimidyl(4-azidophenyl -1,3-dithio)-propionate (SADP), was inhibited by DCCD modification, suggesting that DCCD binding prevents the intersubunit cross linking of subunit III. Our results suggest that DCCD modification of subunit III causes a conformational change, which most likely disrupts critical hydrogen bonds within the subunit and also those at the interface between subunits III and I in the enzyme. The conformational change induced in subunit III by covalent DCCD binding is the most likely mechanism for the previously observed inhibition of proton-pumping activity.