Impact of food availability on ranging behaviour of the Sumatran orangutans (Pongo abelii) at the Suaq Balimbing population

Orangutans are the largest arboreal mammals on Earth, one of human’s closest relatives, and a keystone species for biodiversity conservation, but they are threatened by extinction. Factors such as slow life history, large body size, frugivory, arboreal lifestyle, and low population density make them particularly vulnerable to population decline, especially when they face fragmentation and loss of habitat and wildlife trade. Therefore, scientists and conservationists alike are interested in their spatial and temporal ranging behavior and their ecological needs. Since they face different food availability in different tropical forests, orangutans likely adopt different strategies to ensure sufficient energy intake. Sumatran orangutans (Pongo abelii) in Suaq Balimbing spend most of their day searching for fruit. Further, they live in a habitat with higher fruit availability, in higher densities, and are more sociable than orangutans at other research sites. However, past studies found very little to no evidence that habitat fruit availability, represented as the percentage of fruit-bearing trees, has an effect on their ranging behavior. In contrast, several studies showed that the fluctuation of fruit availability in Bornean rain forests impacted the orangutans’ range behavior in Tuanan on Borneo. In the first part, this thesis aims to find an alternative way to represent food availability by looking at the actual feeding behavior of orangutans. I introduced a new food availability index called ‘experienced FAI’ (eFAI) and two sub-indices, which are based on this eFAI but split into a fruit (fruit eFAI) and non-fruit component (non-fruit eFAI). I analyzed and compared behavioral and GPS data from 2007 to 2021, collected in 1743 focal follow days and in accordance with standardized field methods by the Department of Anthropology of the University of Zurich and the Development and Evolution of Cognition Research Group at the Max Planck Institute of Animal Behavior in Konstanz, Germany. The eFAI was calculated based on a ratio of GPS points taken at fixed intervals throughout the focal follow to GPS points taken whenever the focal individual was feeding. I divided orangutans into four age-sex classes: adult females, flanged males, unflanged males, and independent immatures. The results show that the comparison of behavioral and GPS data was needed to validate the accuracy of GPS points, complement feeding locations, and improve the eFAI calculation. A bootstrapping analysis revealed a minimum number of 10 follows per month to be an appropriate threshold. Regarding the traditional, habitat-centered fruit availability (termed hFAI in this study), I confirmed that Sumatran orangutans at Suaq do not face fruit scarcity throughout the year. Nevertheless, experienced food availability (eFAI) varied depending on the age-sex classes. Results suggest that flanged males spend extended time exploiting one resource rather than switching between resources. Independent immatures are most likely less competent at locating big food patches, and thus they end up switching between food patches faster than other individuals. However, I noticed that orangutans of different age-sex classes have similar diet compositions, except for adult females that showed broader diets, which may relate to maintaining lactation and pregnancy by consuming nutrient- and protein-rich food. The spatial and temporal analysis of the eFAI suggests that fruit availability patterns may be associated with the layout of the research site and vary between forest types. In contrast, non-fruit food items can be found everywhere. In the second part, I investigated the effect of food availability on socio-spatial movement patterns. Therefore, I derived the Day Journey Length (DJL), Total Displacement Distance (TDD), and two tortuosity indices, the Straightness Index (SI) and the sinuosity index for the different age-sex classes and individuals. Fruit eFAI and non-fruit eFAI showed contradicting effects on the DJLs of orangutans and highlighted that an overall eFAI can explain less variation in ranging behavior. Fruit availability in the habitat (hFAI) could not explain any variation in the movement of orangutans, as expected based on the findings of previous studies, most likely because of the high abundance of fruit in Suaq. In contrast, I detected significant effects of fruit eFAI and non-fruit eFAI on DJL and sinuosity of movement but not on TDD and SI. When flanged males increased their non-fruit consumption, they had shorter DJL. Shorter distances may relate to longer feeding times at their feeding locations. Further results suggest that adult females move the shortest distances but the most tortuous. Moving after independently moving but still dependent offspring or carrying their young offspring may lead to higher sinuosity and slow adult females down. Furthermore, adult females traveled longer and straighter distances when consuming more fruit but shorter distances when focusing on non-fruit food items. This behavior suggests that adult females know the locations of the fruit trees and how to get to them when fruit are available. However, on a focal level, I found that older females tend to stay put when more non-fruit food items are available, and younger females tend to travel more, suggesting they actively search for those items. Results for unflanged males and independent immatures suggest that the ranging behavior of both age-sex classes is not influenced by food availability. For unflanged males, the mating strategy may have a greater effect on their ranging behavior than food availability. In contrast, for independent immatures, social factors most likely play a more prominent role as they are more gregarious and social than adult orangutans. In conclusion, comparing and complementing data sets and establishing new ways of representing food availability for Suaq proved to be meaningful, as I discovered different significant effects of experienced food availability on the movement parameters of Sumatran orangutans. However, differentiating between the availability of different food types is essential when looking at the effects of food availability on ranging. I suggest testing the approach in this thesis further at other research sites, which may help to understand the ranging behavior of orangutans better and protect them

Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n = 28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection

Write-optimized indexing with partitioned B-trees

Database management systems (DBMS) are critical performance components in large scale applications under modern update intensive workloads. Additional access paths accelerate look-up performance in DBMS for frequently queried attributes, but the required maintenance slows down update performance. The ubiquitous B+ tree is a commonly used key-indexed access path that is able to support many required functionalities with logarithmic access time to requested records. Modern processing and storage technologies and their characteristics require reconsideration of matured indexing approaches for today's workloads. Partitioned B-trees (PBT) leverage characteristics of modern hardware technologies and complex memory hierarchies as well as high update rates and changes in workloads by maintaining partitions within one single B+-Tree. This paper includes an experimental evaluation of PBTs optimized write pattern and performance improvements. With PBT transactional throughput under TPC-C increases 30%; PBT results in beneficial sequential write patterns even in presence of updates and maintenance operations

Indexing large updatable datasets in multi-version database management systems

Database Management Systems (DBMS) need to handle large updatable datasets in on-line transaction processing (OLTP) workloads. Most modern DBMS provide snapshots of data in multi-version concurrency control (MVCC) transaction management scheme. Each transaction operates on a snapshot of the database, which is calculated from a set of tuple versions. High parallelism and resource-efficient append-only data placement on secondary storage is enabled. One major issue in indexing tuple versions on modern hardware technologies is the high write amplification for tree-indexes. Partitioned B-Trees (PBT) [5] is based on the structure of the ubiquitous B+ Tree [8]. They achieve a near optimal write amplification and beneficial sequential writes on secondary storage. Yet they have not been implemented in a MVCC enabled DBMS to date. In this paper we present the implementation of PBTs in PostgreSQL extended with SIAS. Compared to PostgreSQL’s B+–Trees PBTs have 50% better transaction throughput under TPC-C and a 30% improvement to standard PostgreSQL with Heap-Only Tuples

Multi-version indexing and modern hardware technologies

Characteristics of modern computing and storage technologies fundamentally differ from traditional hardware. There is a need to optimally leverage their performance, endurance and energy consumption characteristics. Therefore, existing architectures and algorithms in modern high performance database management systems have to be redesigned and advanced. Multi Version Concurrency Control (MVCC) approaches in data-base management systems maintain multiple physically independent tuple versions. Snapshot isolation approaches enable high parallelism and concurrency in workloads with almost serializable consistency level. Modern hardware technologies benefit from multi-version approaches. Indexing multi-version data on modern hardware is still an open research area. In this paper, we provide a survey of popular multi-version indexing approaches and an extended scope of high performance single-version approaches. An optimal multi-version index structure brings look-up efficiency of tuple versions, which are visible to transactions, and effort on index maintenance in balance for different workloads on modern hardware technologies

Increased myocardial SERCA expression in early type 2 diabetes mellitus is insulin dependent: In vivo and in vitro data

Background Calcium (Ca2+) handling proteins are known to play a pivotal role in the pathophysiology of cardiomyopathy. However little is known about early changes in the diabetic heart and the impact of insulin treatment (Ins). Methods Zucker Diabetic Fatty rats treated with or without insulin (ZDF +/- Ins, n = 13) and lean littermates (controls, n = 7) were sacrificed at the age of 19 weeks. ZDF + Ins (n = 6) were treated with insulin for the last 6 weeks of life. Gene expression of Ca2+ ATPase in the cardiac sarcoplasmatic reticulum (SERCA2a, further abbreviated as SERCA) and phospholamban (PLB) were determined by northern blotting. Ca2+ transport of the sarcoplasmatic reticulum (SR) was assessed by oxalate-facilitated 45Ca-uptake in left ventricular homogenates. In addition, isolated neonatal cardiomyocytes were stimulated in cell culture with insulin, glucose or triiodthyronine (T3, positive control). mRNA expression of SERCA and PLB were measured by Taqman PCR. Furthermore, effects of insulin treatment on force of contraction and relaxation were evaluated by cardiomyocytes grown in a three-dimensional collagen matrix (engineered heart tissue, EHT) stimulated for 5 days by insulin. By western blot phosphorylations status of Akt was determed and the influence of wortmannin. Results SERCA levels increased in both ZDF and ZDF + Ins compared to control (control 100 +/- 6.2 vs. ZDF 152 +/- 26.6* vs. ZDF + Ins 212 +/- 18.5*# % of control, *p < 0.05 vs. control, #p < 0.05 vs. ZDF) whereas PLB was significantly decreased in ZDF and ZDF + Ins (control 100 +/- 2.8 vs. ZDF 76.3 +/- 13.5* vs. ZDF + Ins 79.4 +/- 12.9* % of control, *p < 0.05 vs control). The increase in the SERCA/PLB ratio in ZDF and ZDF +/- Ins was accompanied by enhanced Ca2+ uptake to the SR (control 1.58 +/- 0.1 vs. ZDF 1.85 +/- 0.06* vs. ZDF + Ins 2.03 +/- 0.1* mug/mg/min, *p < 0.05 vs. control). Interestingly, there was a significant correlation between Ca2+ uptake and SERCA2a expression. As shown by in-vitro experiments, the effect of insulin on SERCA2a mRNA expression seemed to have a direct effect on cardiomyocytes. Furthermore, long-term treatment of engineered heart tissue with insulin increased the SERCA/PLB ratio and accelerated relaxation time. Akt was significantly phosphorylated by insulin. This effect could be abolished by wortmannin. Conclusion The current data demonstrate that early type 2 diabetes is associated with an increase in the SERCA/PLB ratio and that insulin directly stimulates SERCA expression and relaxation velocity. These results underline the important role of insulin and calcium handling proteins in the cardiac adaptation process of type 2 diabetes mellitus contributing to cardiac remodeling and show the important role of PI3-kinase- kt-SERCA2a signaling cascade

MV-PBT: multi-version indexing for large datasets and HTAP workloads

Modern mixed (HTAP)workloads execute fast update-transactions and long running analytical queries on the same dataset and system. In multi-version (MVCC) systems, such workloads result in many short-lived versions and long version-chains as well as in increased and frequent maintenance overhead. Consequently, the index pressure increases significantly. Firstly, the frequent modifications cause frequent creation of new versions, yielding a surge in index maintenance overhead. Secondly and more importantly, index-scans incur extra I/O overhead to determine, which of the resulting tuple versions are visible to the executing transaction (visibility-check) as current designs only store version/timestamp information in the base table – not in the index. Such index-only visibility-check is critical for HTAP workloads on large datasets. In this paper we propose the Multi Version Partitioned B-Tree (MV-PBT) as a version-aware index structure, supporting index-only visibility checks and flash-friendly I/O patterns. The experimental evaluation indicates a 2x improvement for analytical queries and 15% higher transactional throughput under HTAP workloads. MV-PBT offers 40% higher tx. throughput compared to WiredTiger’s LSM-Tree implementation under YCSB