A bar code scoring system for behavioral research

A data collection method using lap-top computers and bar codes was developed and used in behavioral research. The studies involved several common sampling methods and a variety of study subjects. Advantages and restrictions of the system are discussed. Overall, we found bar code technology to increase both efficiency and accuracy of behavioral data collection.     

Anthropogenic influences on primate antipredator behavior and implications for research and conservation

Predation risk affects prey species' behavior, even in the absence of a direct threat, but human-induced environmental change may disturb ecologically significant predator–prey interactions. Here, we propose various ways in which knowledge of antipredator tactics, behavioral risk effects, and primate–predator interactions could assist in identifying human-caused disruption to natural systems. Using behavior to evaluate primate responses to the ongoing environmental change should be a potentially effective way to make species conservation more predictive by identifying issues before a more dramatic population declines. A key challenge here is that studies of predation on primates often use data collected via direct observations of habituated animals and human presence can deter carnivores and influence subjects' perception of risk. Hence, we also review various indirect data collection methods to evaluate their effectiveness in identifying where environmental change threatens wild species, while also minimizing observer bias.     

Neurotrophins and the primate central nervous system: A minireview

The central nervous system (CNS) of primates is more complex than the CNS of other mammals. Details of the development and aging of the primate CNS have recently been revealed by various neurobiological techniques. It has become clear that the primate CNS has unique characteristics, for example, the capacity for the overproduction and elimination of fibers and synapses. Some differences have also been found in the distribution of and changes with development in levels of various neuroactive substances. Recent discoveries of a variety of neurotrophins in the mammalian CNS have led to research on the neurobiology of these molecules in the primate CNS. The distribution of and changes with development in levels of nerve growth factor (NGF) in the primate CNS are closely correlated with the cholinergic system of the basal forebrain. The administration of NGF into the monkey brain prevents the degeneration of the cholinergic neurons of the basal forebrain after axotomy, a result that suggests that neurotrophins might be very valuable agents for the future treatment of neurological diseases, such as Alzheimer's and Parkinson's diseases. This review is dedicted to Dr. Hans Thoenen.     

A scoring system for coat and tail condition in ringtailed lemurs,Lemur catta

Coat condition can be influenced by a wide variety of disorders and thus provides a useful tool for noninvasive health and welfare assessments in wild and captive animals. Using Lemur catta as an exemplar, we offer a 6‐step scoring system for coat and tail condition, ranging from perfectly fluffy to half or more of body and tail being hairless. The categories are described in detail and illustrated with sample pictures from a wild population in Berenty Reserve, Madagascar. Furthermore, we elaborate on intermediate conditions and discoloration of fur. Coat condition scoring allows the comparison between years, seasons, and the effect of toxin, disease or stress. Although this system was developed for wild L. catta, we believe it can also be of value for other species. We recommend scoring coat condition in healthy wild mammal populations to give a baseline on yearly and seasonal variations vs. deteriorating health conditions or pathology. Am. J. Primatol. 71:183–190, 2009. © 2009 Wiley‐Liss, Inc.     

Implementing long‐term baselines into primate tool‐use studies

Studies on primate tool‐use often involve the use of baseline conditions, as they allow for the examination of any differences in the subjects' behavior before and after the introduction of a tool‐use task. While these baseline conditions can be powerful for identifying the relative contributions of individual and social learning for the acquisition of tool‐use behaviors in naïve (usually captive) subjects, many have criticized them for being too short, and not allowing enough time for the behavior to develop spontaneously. Furthermore, some wild tool‐use behaviors such as chimpanzee nut‐cracking require animals to manipulate and familiarize themselves with the materials of the behavior within a “sensitive learning period” before it develops later on in life. One solution to this problem is to implement long‐term baselines, in which, with collaboration with zoological institutions, the materials of the behavior are left in the enclosure for an extended period. The keepers would then be asked not to demonstrate or train the animals in the target behavior, but to report back to the researchers if they observe the behavior emerge during this extended period. Alongside keeper reports, video cameras could be installed in the enclosure to minimize the chance of false negatives and to allow for coding and inter‐rater reliability to be carried out on the videos. These long‐term baselines therefore provide extended enrichment opportunities for the animals, alongside allowing the zoological institution to publicize their involvement with the study and guests to observe animals interacting with different testing apparatuses and tools. Finally, long‐term baselines can provide invaluable insight on the individual and social learning abilities of primates as well as the potential development stages and sensitive learning periods required for specific behaviors.     

Baculum length and copulatory behavior in primates

The length of the baculum (os penis) was measured in 74 adult males representing 46 primate species. These data, and a review of previously published measurements, indicate that variation in baculum length among primates is related to taxonomic and behavioral differences. Thus, many New World monkeys have shorter bacula, relative to body weight, than Old World monkeys. The baculum is shorter in colobine monkeys than in cercopithecines. Among the great apes, reduction of the baculum is more pronounced in Pan and Gorilla than in Pongo. Very long bacula are found in some nocturnal prosimians (eg, Lorisidae) and also in Macaca arctoides. A comparison of baculum length relative to body weight was made in 34 species for which detailed information on copulatory behavi or was available. The presence of an elongated baculum was shown to correlate with copulatory patterns involving prolonged intromission and/or the maintenance of intromission during the postejaculatory interval (eg, Galago crassicaudatus, Loris tardigradus, M, arctoides). The evolutionary significance of these observations is discussed and it is suggeted that similar copulatory patterns may occur in species with elongated bacula (eg, Daubentonia, Perodicticus) for which behavioral data are lacking at present. The same hypothesis also applies to an extinct adapid primate which possessed a very large baculum.     

Technical note: Modeling primate occlusal topography using geographic information systems technology

Most functional analyses of primate tooth form have been limited to linear or area measurements. Such studies have offered but a limited glimpse at differences in occlusal relief among taxa. Such differences in dental topography may relate to tooth function and, so, have considerable implications for the inference of diet from fossil teeth. In this article, we describe a technique to model and compare primate molars in three dimensions using Geographic Resources Analysis Support System (GRASS) software. We examine unworn lower second molars of three extant hominoids with known differences in diet (Gorilla gorilla, Pan troglodytes, and Pongo pygmaeus), and two fossil forms, (Afropithecus turkanesis and Dryopithecus laietanus). First, we obtained approximately 400 landmarks on the occlusal surfaces of each tooth using an electromagnetic digitizer. Raster “terrain models” of occlusal surfaces were then created by interpolation of the coordinate data. We used GRASS terrain analysis automated techniques to quantify the volumes and slopes of individual cusps. We also used the GRASS watershed technique to identify the volume of liquid that would accumulate in each tooth's basin (a measure of basin area), and the directions and intensity of drainage over the occlusal surface. In sum, GRASS shows considerable potential for the characterization and comparison of tooth surfaces. Furthermore, techniques described here are not limited to the study of teeth, but may be broadly applicable to studies of skulls, joints, and other biological structures. Am J Phys Anthropol 107:137–142, 1998. © 1998 Wiley-Liss, Inc.     

Autophagy modulator scoring system: a user-friendly tool for quantitative analysis of methodological integrity of chemical autophagy modulator studies

ABSTRACT

Over the past 20 years (1999–2019), we have witnessed a rapid increase in publications involving chemical macroautophagy/autophagy modulators. However, an overview of the methodologies used in these studies is still lacking, and methodology flaws are frequently observed in some reports. To provide an objective and quantitative analysis of studies involving autophagy modulators, we present an Autophagy Modulator Scoring System (AMSS), which is designed to evaluate methodological integrity. AMSS-A includes the autophagy characterization by 4 aspects, namely, autophagosome quantification, autophagy-related biochemical changes, autophagy substrate degradation, and autophagic flux. AMSS-B contains the pharmacological and functional characteristics of chemical autophagy modulators, including lysosomal function, drug targets, autophagy-dependent pharmacological effects, and validation in multiple cell lines and in vivo models. Our analysis shows that of the 385 studies reporting chemical autophagy modulators, only 142 single studies had examined all 4 aspects of autophagy characterization in AMSS-A, and only 10 out of 142 studies had fulfilled all the AMSS criteria in a single study. A comprehensive analysis of the methodologies used in all the studies was made, along with a summary of studies that demonstrated the highest methodological integrity based on AMSS ranking. To test the reliability of the AMSS, a co-efficiency analysis of scores and co-citation values in the co-citation network was performed, and a significant co-efficiency was obtained. Collectively, AMSS provides insight into the methodological integrity of autophagy modulators studies and also offers a user-friendly toolkit to help choose appropriate assays to characterize autophagy modulators.

Abbreviations: 3-MA: 3-methyladenine; AMSS: Autophagy Modulator Scoring System; ATG: autophagy-related; BAF: bafilomycin A₁; BECN1: beclin 1; CQ: chloroquine; GFP: green fluorescent protein; LC3: microtubule associated protein 1 light chain 3; mRFP: monomeric red fluorescent protein; MTOR: mechanistic target of rapamycin kinase; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate     

Leaping behavior of Pithecia pithecia and Chiropotes satanas in eastern Venezuela

I observed leaping behavior in the white-faced saki (Pithecia pithecia) and the black-bearded saki (Chiropotes satanas satanas) for 15 and 10 months, respectively, as part of a larger study of positional behavior in the tribe Pitheciini. I used focal animal instantaneous sampling to observe the two species on separate islands in their natural habitat at Guri Lake, Venezuela. Leaping behavior correlates with patterns of forest use and body size, and differences between the species relate more to habitat preferences than to habitat differences per se. Pithecia usually chose vertical or highly angled supports of lower tree portions for take-off and landing, and took off from a stationary posture. Chiropotes took off from the main crown or terminal branches, gaining momentum from locomotor movement before performing a leaping take-off. Pithecia's vertical body orientation and longer leap distance allowed it to assume a mid-flight tuck to prepare for a hindlimb-first landing onto a solid support, and to absorb landing forces with its relatively longer hindlimbs. Chiropotes remained more pronograde throughout its leaps, and minimized landing forces by landing on all four limbs onto numerous flexible supports in the terminal branches. The smaller-bodied P. pithecia is specialized for vertical clinging and leaping, and exhibits behavioral and morphological parallels with other vertical clingers and leapers. The larger C. satanas is a generalized leaper that lacks morphological specializations for leaping. Pithecia's use of solid supports in the lower tree portions allows it to move quietly through the forest-one of a suite of behaviors related to predator avoidance. This example of variation within one behavioral category has implications for devising locomotor classifications and interpreting fossil remains.     

Development of a preoperative prognostic scoring system to predict benefits of hepatic resection in advanced hepatocellular carcinoma patients

Objective: The present study aimed to identify risk factors for overall survival in advanced hepatocellular carcinoma (HCC) patients and establish a scoring system to select patients who would benefit from hepatic resection.Methods: Survival curves were analyzed using the Kaplan–Meier method and log-rank test. The prognostic scoring system was developed from training cohort using a Cox-regression model and validated in a external validation cohortResults: There were 401 patients in the training cohort, 163 patients in the external validation cohorts. The training cohort median survival in all patients was 12 ± 1.07 months, rate of overall survival was 49.6% at 1 year, 25.0% at 3 years, and 18.0% at 5 years. A prognostic scoring system was established based on age, body mass index, alkaline phosphatase, tumor number and tumor capsule. Patients were classified as low- risk group(≤3.5) or high-risk group(>3.5). High-risk patients had a median survival of 9 months, compared with 23 months in low-risk patients. The area under the receiver operating characteristic curve (AUC) of the prognostic scoring system was 0.747 (0.694–0.801), which is significantly better than AFP, Child-Pugh and ALBI. The AUC of validation cohorts was 0.716 (0.63–0.803).Conclusion: A prognostic scoring system for hepatic resection in advanced HCC patients has been developed based entirely on preoperative variables. Patients classified as low risk using this system may experience better prognosis after hepatic resection.     

The 10kTrees website: A new online resource for primate phylogeny

The comparative method plays a central role in efforts to uncover the adaptive basis for primate behaviors, morphological traits, and cognitive abilities. 1 - 4 The comparative method has been used, for example, to infer that living in a larger group selects for a larger neocortex, 5 , 6 that primate territoriality favors a longer day range relative to home range size, 7 and that sperm competition can account for the evolution of primate testes size. 8 , 9 Comparison is fundamental for reconstructing behavioral traits in the fossil record, for example, in studies of locomotion and diet. 10 - 13 Recent advances in comparative methods require phylogenetic information, 2 , 14 - 16 but our knowledge of phylogenetic information is imperfect. In the face of uncertainty about evolutionary relationships, which phylogeny should one use? Here we provide a new resource for comparative studies of primates that enables users to run comparative analyses on multiple primate phylogenies Importantly, the 10,000 trees that we provide are not random, but instead use recent systematic methods to create a plausible set of topologies that reflect our certainty about some nodes on the tree and uncertainty about other nodes, given the dataset. The trees also reflect uncertainty about branch lengths.     

A computerized plankton counter

A portable computerized plankton counting system is presented, which has the potential to enumerate 255 different species per sample. The software is used to count phytoplankton samples and produce summary data. The hardware allows the results to be reproduced in the form of a hardcopy, stored on a cassette tape, or transferred to a larger computer for analysis.     

optiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters

Amplified fragment length polymorphism (AFLP), a widely used method for DNA fingerprinting, has shifted from polyacrylamide gel to capillary electrophoresis over the last years. Currently, most AFLP data are generated in a computer-readable format, and several programs are available that automatically score raw data into binary profiles. Good scoring parameters are the key to good AFLP profiles. optiFLP is the first open source program for automatic optimization of AFLP scoring parameters. It searches parameter space to maximize the contrast among groups of AFLP profiles, with the allocation of profiles to groups in either a supervised or an unsupervised mode. The software produces output files ready for use in a range of downstream applications.     

Validation and utility of a body condition scoring system for chimpanzees (Pan troglodytes)

Obesity is a problem in captive chimpanzee colonies that can lead to increased risk for disease; therefore, implementation of effective weight management strategies is imperative. To properly implement a weight management program, captive managers should be able to noninvasively identify and assess overweight or obese individuals. Traditional means of categorizing obese individuals involve sedating the animals to obtain body weights or skin fold measurements. The current study aimed to validate a noninvasive, subjective body condition score (BCS) system for captive chimpanzees. The system utilizes a 10-point scale, with one rated as “emaciated,” five as “normal,” and 10 as “extremely obese.” Between 2013 and 2014, 158 chimpanzees were weighed and scored using this system (a) while sedated and (b) while awake in their social group within 1–3 days of sedation (“In-group” ratings). We found high inter-rater reliability between In-group raters, as well as between sedated and In-group scores. BCSs, which require observation only, were significantly positively correlated with weight (an objective measure of obesity often requiring anesthetization), supporting the scale's validity. The BCS system identified 36 individuals as “overweight,” while the use of weights alone identified only 26 individuals as “overweight.” Furthermore, the BCS system was able to classify individuals of the same sex and weight as having different BCSs, ranging from normal to overweight. Lastly, using focal animal behavioral observations from 2016 to 2018 (N = 120), we found that In-group BCS predicted individual levels of inactive behavior more than 2 years later, demonstrating the predictive validity of the scale. These results illustrate the utility of the BCS system as a noninvasive, reliable, and valid technique that may be more sensitive than traditional methods in identifying and quantifying obesity in chimpanzees. This system can be a useful tool for captive managers to monitor and manage the weight of chimpanzees and other nonhuman primates.     

The case for primate V3

The visual system in primates is represented by a remarkably large expanse of the cerebral cortex. While more precise investigative studies that can be performed in non-human primates contribute towards understanding the organization of the human brain, there are several issues of visual cortex organization in monkey species that remain unresolved. In all, more than 20 areas comprise the primate visual cortex, yet there is little agreement as to the exact number, size and visual field representation of all but three. A case in point is the third visual area, V3. It is found relatively early in the visual system hierarchy, yet over the last 40 years its organization and even its very existence have been a matter of debate among prominent neuroscientists. In this review, we discuss a large body of recent work that provides straightforward evidence for the existence of V3. In light of this, we then re-examine results from several seminal reports and provide parsimonious re-interpretations in favour of V3. We conclude with analysis of human and monkey functional magnetic resonance imaging literature to make the case that a complete V3 is an organizational feature of all primate species and may play a greater role in the dorsal stream of visual processing.     

Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models

Docking programs can generate subsets of a compound collection with an increased percentage of actives against a target (enrichment) by predicting their binding mode (pose) and affinity (score), and retrieving those with the highest scores. Using the QXP and GOLD programs, we compared the ability of six single scoring functions (PLP, Ligscore, Ludi, Jain, ChemScore, PMF) and four composite scoring models (Mean Rank: MR, Rank-by-Vote: Vt, Bayesian Statistics: BS and PLS Discriminant Analysis: DA) to separate compounds that are active against CDK2 from inactives. We determined the enrichment for the entire set of actives (IC50 < 10 microM) and for three activity subsets. In all cases, the enrichment for each subset was lower than for the entire set of actives. QXP outperformed GOLD at pose prediction, but yielded only moderately better enrichments. Five to six scoring functions yielded good enrichments with GOLD poses, while typically only two worked well with QXP poses. For each program, two scoring functions generally performed better than the others (Ligscore2 and Ludi for GOLD; QXP and Jain for QXP). Composite scoring functions yielded better results than single scoring functions. The consensus approaches MR and Vt worked best when separating micromolar inhibitors from inactives. The statistical approaches BS and DA, which require training data, performed best when distinguishing between low and high nanomolar inhibitors. The key observation that all hit rate profiles for all four activity intervals for all scoring schemes for both programs are significantly better than random, is evidence that docking can be successfully applied to enrich compound collections.