An Introduction to Adversarially Robust Deep Learning

The widespread success of deep learning in solving machine learning problems has fueled its adoption in many fields, from speech recognition to drug discovery and medical imaging. However, deep learning systems are extremely fragile: imperceptibly small modifications to their input data can cause the models to produce erroneous output. It is very easy to generate such adversarial perturbations even for state-of-the-art models, yet immunization against them has proven exceptionally challenging. Despite over a decade of research on this problem, our solutions are still far from satisfactory and many open problems remain. In this work, we survey some of the most important contributions in the field of adversarial robustness. We pay particular attention to the reasons why past attempts at improving robustness have been insufficient, and we identify several promising areas for future research.

Improving Turn Movement Count Using Cooperative Feedback

In this paper, we propose a new cooperative method that improves the accuracy of Turn Movement Count (TMC) under challenging conditions by introducing contextual observations from the surrounding areas. The proposed method focuses on the correct identification of the movements in conditions where current methods have difficulties. Existing vision-based TMC systems are limited under heavy traffic conditions. The main problems for most existing methods are occlusions between vehicles that prevent the correct detection and tracking of the vehicles through the entire intersection and the assessment of the vehicle's entry and exit points, incorrectly assigning the movement. The proposed method intends to overcome this incapability by sharing information with other observation systems located at neighboring intersections. Shared information is used in a cooperative scheme to infer the missing data, thereby improving the assessment that would otherwise not be counted or miscounted. Experimental evaluation of the system shows a clear improvement over related reference methods.

An Unsupervised Transfer Learning Framework for Visible-Thermal Pedestrian Detection

Dual cameras with visible-thermal multispectral pairs provide both visual and thermal appearance, thereby enabling detecting pedestrians around the clock in various conditions and applications, including autonomous driving and intelligent transportation systems. However, due to the greatly varying real-world scenarios, the performance of a detector trained on a source dataset might change dramatically when evaluated on another dataset. A large amount of training data is often necessary to guarantee the detection performance in a new scenario. Typically, human annotators need to conduct the data labeling work, which is time-consuming, labor-intensive and unscalable. To overcome the problem, we propose a novel unsupervised transfer learning framework for multispectral pedestrian detection, which adapts a multispectral pedestrian detector to the target domain based on pseudo training labels. In particular, auxiliary detectors are utilized and different label fusion strategies are introduced according to the estimated environmental illumination level. Intermediate domain images are generated by translating the source images to mimic the target ones, acting as a better starting point for the parameter update of the pedestrian detector. The experimental results on the KAIST and FLIR ADAS datasets demonstrate that the proposed method achieves new state-of-the-art performance without any manual training annotations on the target data.

Hunting pressure is a key contributor to the impending extinction of Bornean wild cattle

Widespread and unregulated hunting of ungulates in Southeast Asia is resulting in population declines and localised extinctions. Increased access to previously remote tropical forest following logging and changes in land-use facilitates hunting of elusive wild cattle in Borneo, which preferentially select secluded habitat. We collated the first population parameters for the Endangered Bornean banteng Bos javanicus lowi and developed population models to simulate the effect of different hunting offtake rates on survival and the recovery of the population using reintroduced captive-bred individuals. Our findings suggest that the banteng population in Sabah is geographically divided into 4 management units based on connectivity: the Northeast, Sipitang (West), Central and Southeast, which all require active management to prevent further population decline and local extinction. With only 1% offtake, population growth ceased in the Northeast and Sipitang. In the Southeast and Central units, growth ceased at 2 and 4% offtake, respectively. Extinction was estimated at 21-39 yr when offtake was 5%, occurring first in Sipitang and last in the Central unit. Supplementing the population with captive-bred individuals suggested that inbreeding was likely to limit population growth if using ≤20 founder individuals. Translocating 2 individuals for a 10 yr period, starting after 20 yr of captive breeding resulted in a faster population recovery over 100 yr and a lower extinction probability. Our results suggest that shielding the population against further losses from hunting will be key to their survival in the wild, provided that active management in the form of captive breeding is developed in the interim.

Shared decision-making in advance care planning for persons with dementia in nursing homes: a cross-sectional study

Background

Shared decision-making provides an approach to discuss advance care planning in a participative and informed manner, embodying the principles of person-centered care. A number of guided approaches to achieve shared decision-making already exist, such as the three-talk model. However, it is uncertain whether daily practice methods in nursing home wards for persons with dementia comply with the underpinnings of this model. It is also uncertain whether professionals consider shared decision-making to be important in this context, and whether they perceive themselves sufficiently competent to practice this approach frequently.

Methods

The study has a cross-sectional design, with 65 wards (46 Belgian nursing homes) participating in the study. We compared nursing home professionals’ and residents’ perspectives on the level of shared decision-making during advance care planning conversations with ratings from external raters. Residents and professionals rated the level of shared decision-making by means of a questionnaire, which included the topic of the conversation. External raters assessed audio recordings of the conversations. Professionals filled in an additional self-report questionnaire on the importance of shared decision-making, their competence in practicing the approach, and with what frequency.

Results

At ward level, professionals and residents rated the average achieved level of shared decision-making 71.53/100 (σ = 16.09) and 81.11/100 (σ = 19.18) respectively. Meanwhile, raters gave average scores of 26.97/100 (σ = 10.45). Only 23.8% of residents referred to advance care planning as the topic of the conversation. Professionals considered shared decision-making to be important (x̄=4.48/5, σ = 0.26). This result contrasted significantly with the frequency (x̄=3.48/5, σ = 0.51) and competence (x̄=3.76/5, σ = 0.27) with which these skills were practiced (P < 0.001).

Conclusions

Residents with dementia are grateful when involved in discussing their care, but find it difficult to report what is discussed during these conversations. Receiving more information about advance care planning could provide them with the knowledge needed to prepare for such a conversation. External raters observe a discrepancy between the three-talk model and daily practice methods. Training programs should focus on providing professionals with better knowledge of and skills for shared decision-making. They should also promote team-based collaboration to increase the level of person-centered care in nursing home wards for persons with dementia.

Improving shared decision-making in advance care planning: Implementation of a cluster randomized staff intervention in dementia care

OBJECTIVE

Increasing staff engagement level of shared decision-making in advance care planning for persons with dementia in nursing homes. Perceived importance, competence and frequency of staff members applying shared decision-making were measured. Additionally, facilitators and barriers in the implementation process were described.

METHODS

In this pretest-posttest cluster randomized trial, 311 staff members from 65 Belgian nursing home wards participated. Key components of the intervention were knowledge on shared decision-making, role-play exercises and internal policies on advance care planning. Audio recordings of advance care planning conversations between residents, families and staff were compared before and after the intervention. Participants filled in questionnaires and provided feedback.

RESULTS

Wards demonstrated a higher level of shared decision-making after the intervention (p < 0.001) while time spent on the conversations did not increase. This effect persisted at 6 months follow-up (p < 0.001). Participants perceived shared decision-making as more important (p = 0.031) and felt more competent (p = 0.010), though frequency of use did not change (p = 0.201). High staff turnover and difficult co-operation with GP's were barriers.

CONCLUSION

Nursing home staff benefits from this training in shared decision-making.

PRACTICE IMPLICATIONS

Learning shared decision-making in advance care planning for persons with dementia is possible and sustainable in the time-constricted context of nursing homes.

'We DECide optimized' - training nursing home staff in shared decision-making skills for advance care planning conversations in dementia care: protocol of a pretest-posttest cluster randomized trial

Background

Due to the gradual loss of function, it is crucial for persons with dementia to discuss advance care planning in due course. However, nursing home staff, residents and their families feel uncomfortable to start this type of conversation, resulting in unknown (care) preferences. ‘We DECide optimized’ will provide tools to nursing home staff for discussing advance care planning. The primary objective is to enhance the level of shared decision-making in advance care planning conversations. We hypothesize that the training will enhance the perception of the importance, competence and frequency in which participants engage in advance care planning conversations. The secondary objective is to assess barriers and facilitators in the implementation of advance care planning policies at the ward level.

Methods

‘We DECide optimized’ will consist of two four-hour workshops and a homework assignment between sessions. Training components will include information on advance care planning and shared decision-making, role-play exercises and group discussions on implementation barriers at the ward level. Participating wards will receive supporting materials to stimulate residents and their families to initiate conversations. The study uses a cluster randomized controlled design, with 65 Flemish nursing home wards taking part (311 staff members). Data will be collected through a pretest-posttest model, with measurements up to 9 months after training. The RE-AIM framework will be used to evaluate the effectiveness of the implementation. Quantitative and qualitative data at the clinical, organizational and resident level will be collected.

Discussion

This study describes a hands-on, in-depth and multi-level training approach to improve shared decision-making in advance care planning conversations. By providing tools to ward staff, engaging the management and informing residents and their families, ‘We DECide optimized’ aims to decrease evidence-based barriers and to provide all stakeholders with incentives to engage in conversations about (care) preferences in an informative and participatory manner.

Electronic supplementary material

The online version of this article (10.1186/s12877-019-1044-z) contains supplementary material, which is available to authorized users.

[Somatic and pharmacological nurse care in 2b-teams in Flanders: a cross-sectional explorative study]

In the context of the Belgian mental health care reform (project 107), 2b-teams provide care to people with a serious mental illness (smi), a population encountering regular somatic comorbidity and limited compliance with medication. Team composition and care provided by these teams is rather unclear.<br /> AIM: To consider the team composition and to focus on the nurses' role within Flemish 2b-teams. Also, seen from different disciplines involved, to determine the desired future nursing role.<br /> METHOD: A structured interview was used to discover team characteristics and fidelity to the flexible assertive community treatment (fact) model in 12 Flemish 2b-teams. With a digital survey containing 16 questions we explored the actual and desired nursing care, according to 151 nurses and medical physicians.<br /> RESULTS: Despite the difference in team size and composition, it was not found to be significant. Flemish team's fact model-fidelity was average. Actual care was restricted to psychosocial interventions. Regarding desired care, significant differences were found between physicians and nurses. Caregivers within outreach teams scored items significantly higher on desired care compared to actual care.<br /> CONCLUSION: We conclude that the team composition of Flemish 2b-team varies, with an average fact model fidelity. Team care is restricted to psychosocial interventions, while more somatic and nursing care is desired.

Line-Constrained Camera Location Estimation in Multi-Image Stereomatching

Stereomatching is an effective way of acquiring dense depth information from a scene when active measurements are not possible. So-called lightfield methods take a snapshot from many camera locations along a defined trajectory (usually uniformly linear or on a regular grid-we will assume a linear trajectory) and use this information to compute accurate depth estimates. However, they require the locations for each of the snapshots to be known: the disparity of an object between images is related to both the distance of the camera to the object and the distance between the camera positions for both images. Existing solutions use sparse feature matching for camera location estimation. In this paper, we propose a novel method that uses dense correspondences to do the same, leveraging an existing depth estimation framework to also yield the camera locations along the line. We illustrate the effectiveness of the proposed technique for camera location estimation both visually for the rectification of epipolar plane images and quantitatively with its effect on the resulting depth estimation. Our proposed approach yields a valid alternative for sparse techniques, while still being executed in a reasonable time on a graphics card due to its highly parallelizable nature.

Coxiella burnetii (Q fever) prevalence in associated populations of humans and small ruminants in The Gambia

OBJECTIVES

To simultaneously estimate the prevalence of antibodies against Coxiella burnetii (Q fever) among adults and small ruminants, and C. burnetii shedding prevalence among small ruminants in households in the Kiang West district of The Gambia, and to assess associated risk factors.

METHODS

Sera of 599 adults and 615 small ruminants from 125 compounds within 12 villages were tested for antibodies against C. burnetii using ELISA. Vaginal swabs and milk samples of 155 small ruminants were tested using PCR to investigate shedding of C. burnetii.

RESULTS

A total of 3.8-9.7% of adults, depending on ELISA test cut-off, and 24.9% of small ruminants in Kiang West were seropositive. Having at least one seropositive animal in one's compound was a risk factor for human seropositivity (OR: 3.35, 95% CI: 1.09-14.44). A grazing area within a village was a risk factor for seropositivity in small ruminants (OR: 2.07, 95% CI: 1.26-3.50); others were having lambed (OR: 2.75, 95% CI: 1.37-5.76) and older age of the animals (OR: 2.75, 95% CI: 1.37-5.76 for 1-3 years and OR 5.84, 95% CI: 3.10-11.64 for >3 years); 57.4% of sampled small ruminants were shedding C. burnetii.

CONCLUSION

Coxiella burnetii infection is endemic among both humans and small ruminants in this area of The Gambia. Human and animal exposure to C. burnetii were related at compound level. Further research into the clinical relevance of C. burnetii infection in West Africa is needed.

Low Seroprevalence of Brucellosis in Humans and Small Ruminants in the Gambia

Background

Brucellosis is a worldwide zoonosis with significant impact on rural livelihoods and a potentially underestimated contributor to febrile illnesses. The aim of this study was to estimate the seroprevalence of brucellosis in humans and small ruminants in The Gambia.

Methods

The study was carried out in rural and urban areas. In 12 rural villages in Kiang West district, sera were collected from humans (n = 599) and small ruminants (n = 623) from the same compounds. From lactating small ruminants, milk samples and vaginal swabs were obtained. At the urban study sites, sera were collected from small ruminants (n = 500) from slaughterhouses and livestock markets. Information on possible risk factors for seropositivity was collected through questionnaires. Sera were screened for antibodies against Brucella spp. with the Rose Bengal Test, ELISA and Micro Agglutination Test (human sera only). PCR was performed on 10 percent of the milk samples and vaginal swabs from small ruminants.

Results

One human and 14 sheep sera were positive by the Rose Bengal Test. The rest were negative in all serological tests used. The PCR results were all negative.

Conclusions

The results suggest that brucellosis is currently not a generalized problem in humans or small ruminants in The Gambia.

MATE: Machine Learning for Adaptive Calibration Template Detection

The problem of camera calibration is two-fold. On the one hand, the parameters are estimated from known correspondences between the captured image and the real world. On the other, these correspondences themselves—typically in the form of chessboard corners—need to be found. Many distinct approaches for this feature template extraction are available, often of large computational and/or implementational complexity. We exploit the generalized nature of deep learning networks to detect checkerboard corners: our proposed method is a convolutional neural network (CNN) trained on a large set of example chessboard images, which generalizes several existing solutions. The network is trained explicitly against noisy inputs, as well as inputs with large degrees of lens distortion. The trained network that we evaluate is as accurate as existing techniques while offering improved execution time and increased adaptability to specific situations with little effort. The proposed method is not only robust against the types of degradation present in the training set (lens distortions, and large amounts of sensor noise), but also to perspective deformations, e.g., resulting from multi-camera set-ups.

Optimal Joint Detection and Estimation That Maximizes ROC-Type Curves

Combined detection-estimation tasks are frequently encountered in medical imaging. Optimal methods for joint detection and estimation are of interest because they provide upper bounds on observer performance, and can potentially be utilized for imaging system optimization, evaluation of observer efficiency, and development of image formation algorithms. We present a unified Bayesian framework for decision rules that maximize receiver operating characteristic (ROC)-type summary curves, including ROC, localization ROC (LROC), estimation ROC (EROC), free-response ROC (FROC), alternative free-response ROC (AFROC), and exponentially-transformed FROC (EFROC) curves, succinctly summarizing previous results. The approach relies on an interpretation of ROC-type summary curves as plots of an expected utility versus an expected disutility (or penalty) for signal-present decisions. We propose a general utility structure that is flexible enough to encompass many ROC variants and yet sufficiently constrained to allow derivation of a linear expected utility equation that is similar to that for simple binary detection. We illustrate our theory with an example comparing decision strategies for joint detection-estimation of a known signal with unknown amplitude. In addition, building on insights from our utility framework, we propose new ROC-type summary curves and associated optimal decision rules for joint detection-estimation tasks with an unknown, potentially-multiple, number of signals in each observation.

Coxiella burnetii seroprevalence in small ruminants in The Gambia

Background

Q fever is a zoonosis caused by Coxiella burnetii, a Gram negative bacterium present worldwide. Small ruminants are considered the main reservoirs for infection of humans. This study aimed to estimate the extent of C. burnetii infection among sheep and goats in part of The Gambia.

Methodology/Principal Findings

This survey was carried out from March to May 2012 at two areas in The Gambia. The first area comprised a cluster of seven rural villages situated 5–15 km west of Farafenni as well as the local abattoir. A second sampling was done at the central abattoir in Abuko (30 km from the capital, Banjul) in the Western Region. Serum samples were obtained from 490 goats and 398 sheep. In addition, 67 milk samples were obtained from lactating dams. Sera were tested with a Q fever ELISA kit. C. burnetii DNA was extracted from milk samples and then detected using a specific quantitative multiplex PCR assay, targeting the IS1111a element. A multivariable mixed logistic regression model was used to examine the relationship between seropositivity and explanatory variables. An overall seroprevalence of 21.6% was found. Goats had a significantly higher seroprevalence than sheep, respectively 24.2% and 18.5%. Seropositive animals were significantly older than seronegative animals. Animals from the villages had a significantly lower seroprevalence than animals from the central abattoir (15.1% versus 29.1%). C. burnetii DNA was detected in 2 out of 67 milk samples, whereas 8 samples gave a doubtful result.

Conclusion/Significance

A substantial C. burnetii seroprevalence in sheep and goats in The Gambia was demonstrated. People living in close proximity to small ruminants are exposed to C. burnetii. Q fever should be considered as a possible cause of acute febrile illness in humans in The Gambia. Future studies should include a simultaneous assessment of veterinary and human serology, and include aetiology of febrile illness in local clinics.

Channelized model observer for the detection and estimation of signals with unknown amplitude, orientation, and size

As a task-based approach for medical image quality assessment, model observers (MOs) have been proposed as surrogates for human observers. While most MOs treat only signal-known-exactly tasks, there are few studies on signal-known-statistically (SKS) MOs, which are clinically more relevant. In this paper, we present a new SKS MO named channelized joint detection and estimation observer (CJO), capable of detecting and estimating signals with unknown amplitude, orientation, and size. We evaluate its estimation and detection performance using both synthesized (correlated Gaussian) backgrounds and real clinical (magnetic resonance) backgrounds. The results suggest that the CJO has good performance in the SKS detection-estimation task.

Vocal acoustics in the endangered proboscis monkey (Nasalis larvatus)

The endangered proboscis monkey (Nasalis larvatus) is a sexually highly dimorphic Old World primate endemic to the island of Borneo. Previous studies focused mainly on its ecology and behavior, but knowledge of its vocalizations is limited. The present study provides quantified information on vocal rate and on the vocal acoustics of the prominent calls of this species. We audio-recorded vocal behavior of 10 groups over two 4-month periods at the Lower Kinabatangan Wildlife Sanctuary in Sabah, Borneo. We observed monkeys and recorded calls in evening and morning sessions at sleeping trees along riverbanks. We found no differences in the vocal rate between evening and morning observation sessions. Based on multiparametric analysis, we identified acoustic features of the four common call-types "shrieks," "honks," "roars," and "brays." "Chorus" events were also noted in which multiple callers produced a mix of vocalizations. The four call-types were distinguishable based on a combination of fundamental frequency variation, call duration, and degree of voicing. Three of the call-types can be considered as "loud calls" and are therefore deemed promising candidates for non-invasive, vocalization-based monitoring of proboscis monkeys for conservation purposes.

Short communication: prevalence of antibodies against Coxiella burnetii (Q fever) in children in The Gambia, West Africa

OBJECTIVE

To estimate the prevalence of antibodies against Coxiella burnetii (Q fever) among children in eight villages in The Gambia, West Africa.

METHODS

Sera of 796 children aged 1-15 years were tested for presence of antibodies against phase II of C. burnetii by ELISA.

RESULTS

IgG and/or IgM phase II antibodies against C. burnetii were detectable in 8.3% (66/796) of all serum samples analysed with significant differences in seroprevalence between villages. Highest prevalence was found in the age group 1-4 years.

CONCLUSIONS

Exposure to C. burnetii is considerable in the early years of life in The Gambia, and further studies are warranted to estimate the role of Q fever in acute febrile illness in The Gambia and elsewhere in Africa.

Channelized Hotelling observers for the assessment of volumetric imaging data sets

Current clinical practice is rapidly moving in the direction of volumetric imaging. For two-dimensional (2D) images, task-based medical image quality is often assessed using numerical model observers. For three-dimensional (3D) images, however, these models have been little explored so far. In this work, first, two novel designs of a multislice channelized Hotelling observer (CHO) are proposed for the task of detecting 3D signals in 3D images. The novel designs are then compared and evaluated in a simulation study with five different CHO designs: a single-slice model, three multislice models, and a volumetric model. Four different random background statistics are considered, both gaussian (noncorrelated and correlated gaussian noise) and non-gaussian (lumpy and clustered lumpy backgrounds). Overall, the results show that the volumetric model outperforms the others, while the disparity between the models decreases for greater complexity of the detection task. Among the multislice models, the second proposed CHO could most closely approach the volumetric model, whereas the first new CHO seems to be least affected by the number of training samples.

Image denoising using mixtures of projected Gaussian Scale Mixtures

We propose a new statistical model for image restoration in which neighborhoods of wavelet subbands are modeled by a discrete mixture of linear projected Gaussian Scale Mixtures (MPGSM). In each projection, a lower dimensional approximation of the local neighborhood is obtained, thereby modeling the strongest correlations in that neighborhood. The model is a generalization of the recently developed Mixture of GSM (MGSM) model, that offers a significant improvement both in PSNR and visually compared to the current state-of-the-art wavelet techniques. However, the computation cost is very high which hampers its use for practical purposes. We present a fast EM algorithm that takes advantage of the projection bases to speed up the algorithm. The results show that, when projecting on a fixed data-independent basis, even computational advantages with a limited loss of PSNR can be obtained with respect to the BLS-GSM denoising method, while data-dependent bases of Principle Components offer a higher denoising performance, both visually and in PSNR compared to the current wavelet-based state-of-the-art denoising methods.

Removal of correlated noise by modeling the signal of interest in the wavelet domain

Images, captured with digital imaging devices, often contain noise. In literature, many algorithms exist for the removal of white uncorrelated noise, but they usually fail when applied to images with correlated noise. In this paper, we design a new denoising method for the removal of correlated noise, by modeling the significance of the noise-free wavelet coefficients in a local window using a new significance measure that defines the "signal of interest" and that is applicable to correlated noise. We combine the intrascale model with a hidden Markov tree model to capture the interscale dependencies between the wavelet coefficients. We propose a denoising method based on the combined model and a less redundant wavelet transform. We present results that show that the new method performs as well as the state-of-the-art wavelet-based methods, while having a lower computational complexity.

Riverine effects on mitochondrial structure of Bornean orangutans (Pongo pygmaeus) at two spatial scales

We examined mitochondrial DNA control region sequences of 73 Kinabatangan orangutans to test the hypothesis that the phylogeographical structure of the Bornean orangutan is influenced by riverine barriers. The Lower Kinabatangan Wildlife Sanctuary contains one of the most northern populations of orangutans (Pongo pygmaeus) on Borneo and is bisected by the Kinabatangan River, the longest river in Sabah. Orang-utan samples on either side of the river were strongly differentiated with a high Phi(ST) value of 0.404 (P < 0.001). Results also suggest an east-west gradient of genetic diversity and evidence for population expansion along the river, possibly reflecting a postglacial colonization of the Kinabatangan floodplain. We compared our data with previously published sequences of Bornean orangutans in the context of river catchment structure on the island and evaluated the general relevance of rivers as barriers to gene flow in this long-lived, solitary arboreal ape.

Molecular analysis of dispersal in giant pandas

Although dispersal in the giant panda (Ailuropoda melanoleuca) is a demographic mechanism which can potentially counteract the negative effect of habitat fragmentation, little is known about dispersal in this species because of difficulties in observing individuals. Using data from faecal microsatellite genotyping, we compared the spatial distribution of giant pandas in two populations and the proximity of relatives in one key population to infer their dispersal pattern. We conclude that giant pandas exhibit female-biased dispersal because: (i) vAIc (variance of assignment index) for females was significantly larger than for males, suggesting that females comprise both 'local' and 'foreign' genotypes; (ii) the average spatial distance of related female dyads was significantly larger than that of males; (iii) larger r (relatedness), F(ST) (genetic variance among populations) and mAIc (mean of assignment index) values were found in males using the software FSTAT, although the differences were not significant; (iv) males set up territories neighbouring to their birth place; (v) significant population structure using microsatellites with a concomitant lack of mitochondrial structure was found in a previous study, possibly indicating more extensive female dispersal; and (vi) female-biased dispersal was strongly supported by evidence from concomitant ecological studies. Considering previous ecological data and life-history characteristics of the giant panda, female-biased dispersal is most likely to be due to competition for birth dens among females, inbreeding avoidance and enhancing inclusive fitness among related males.

Philopatry and reproductive success in Bornean orang-utans (Pongo pygmaeus)

Behavioural observations suggest that orang-utans are semi-solitary animals with females being philopatric and males roaming more widely in search of receptive partners, leading to the prediction that females are more closely related than males at any given site. In contrast, our study presents evidence for male and female philopatry in the orang-utan. We examined patterns of relatedness and parentage in a wild orang-utan population in Borneo using noninvasively collected DNA samples from animals observed to defecate, and microsatellite markers to assess dispersal and mating strategies. Surprisingly, resident females were equally as related to other resident females (mean r(xy) = 0.303) as resident males were to other resident males (mean r(xy) = 0.305). Moreover, resident females were more related to each other and to the resident males than they were to nonresident females, and resident males were more related to each other (and resident females) than they were to nonresident males. We assigned genetic mothers to 12 individuals in the population, while sires could be identified for eight. Both flanged males and unflanged males achieved paternity, similar to findings reported for Sumatran orang-utans.

Trypanosomosis prevalence in cattle on Mafia Island (Tanzania)

During two consecutive surveys (February and August/Sept 2002), a total of 970 cattle from the cattle population of Mafia Island (United Republic of Tanzania) were blood-sampled. All blood samples were microscopically screened for the presence of trypanosomes and a portion of these were checked for antibodies with an Ab-ELISA and for the presence of trypanosomal DNA with PCR. Microscopic evidence of trypanosomes of the congolense group (sub-genus Nannomonas) was found in 0.8% of the animals (8/970) and in two cases the species identified was confirmed by PCR as Trypanosoma congolense savannah type. Non-pathogenic Trypanosoma theileri were detected in 3.2% (31/970) of the samples using the Dark Ground-Buffy Coat (DG-BC) technique. For survey 1 (S1), detection of antibodies (Ab-ELISA) against pathogenic trypanosomes indicated a seroprevalence of 14.2% (68/480). Of the samples, either DG positive or with a PCV lower then 25, examined by PCR, a total of 8.4% (5/59) (selected from 970 samples), were found positive for T. congolense. The low prevalence of pathogenic trypanosomes on Mafia Island is intriguing, especially in view of the omnipresence of the tsetse fly Glossina brevipalpis. Although the presence of detected trypanosomal antibodies does not necessarily indicate a current infection, the combination of serological/parasitological examinations and the results of the PCR do support this low prevalence of trypanosomosis in cattle. Despite the low prevalence, pathogenic trypanosomes are present on Mafia Island and possible reasons for this low infection rate, taking account of the relation between Glossina species present, transmission risk and trypanosomes found in cattle, are discussed also in view of a future appropriate intervention strategy.

Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia

We investigated the genetic structure within and among Bornean orang-utans (Pongo pygmaeus) in forest fragments of the Lower Kinabatangan flood plain in Sabah, Malaysia. DNA was extracted from hair and faecal samples for 200 wild individuals collected during boat surveys on the Kinabatangan River. Fourteen microsatellite loci were used to characterize patterns of genetic diversity. We found that genetic diversity was high in the set of samples (mean H(E) = 0.74) and that genetic differentiation was significant between the samples (average F(ST) = 0.04, P < 0.001) with F(ST) values ranging from low (0.01) to moderately large (0.12) values. Pairwise F(ST) values were significantly higher across the Kinabatangan River than between samples from the same river side, thereby confirming the role of the river as a natural barrier to gene flow. The correlation between genetic and geographical distance was tested by means of a series of Mantel tests based on different measures of geographical distance. We used a Bayesian method to estimate immigration rates. The results indicate that migration is unlikely across the river but cannot be completely ruled out because of the limited F(ST) values. Assignment tests confirm the overall picture that gene flow is limited across the river. We found that migration between samples from the same side of the river had a high probability indicating that orang-utans used to move relatively freely between neighbouring areas. This strongly suggests that there is a need to maintain migration between isolated forest fragments. This could be done by restoring forest corridors alongside the river banks and between patches.

Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management

The Jersey is a ubiquitous and successful breed of cattle that originates from the UK Channel Island of Jersey. While the breed has been exported extensively, no imports have taken place to the island since 1789, leading to a concern regarding possible losses of genetic diversity and increased inbreeding. We have conducted the first large-scale genetic analysis of the Jersey cattle using only samples from the island. A total of 223 cattle from all parishes except one were genotyped for 12 microsatellite loci. The average number of alleles per locus and expected heterozygosity were found to be comparatively high (n(A)=4, H(e)=0.64) with respect to that observed in a number of continental breeds. Only breeds that have been upgraded and are therefore the result of admixture are clearly more variable than the Jersey. We also found a significant but limited amount of genetic differentiation between parishes (F(st)=0.013), or even between farms (F(st)=0.035) despite an apparent lack of movement. This is confirmed by the application of two recent statistical methods. A Bayesian partition analysis shows that the most probable value of K, the number of possible hidden partitions, is 1 (P approximately 0.98). K=2 has a much lower probability (P approximately 0.02) while other values are essentially zero. Similarly, we were able to show that there was no support for departure from panmixia other than due to population structure, and thus that there is sufficient background gene flow across the island to overcome local drift. Overall, it appears that the current level of genetic diversity and its distribution within the island means it is unnecessary to import unrelated genetic material to the island for management purposes.

Susceptibility of trypanotolerant West African Dwarf goats and F1 crosses with the susceptible Sahelian breed to experimental Trypanosoma congolense infection and interactions with helminth infections and different levels of diet

Forty pure West African Dwarf (WAD) goats and 35 of its F1 crosses with the Sahelian breed were used in a multifactorial experimental design to evaluate the effects of an experimental Trypanosoma congolense infection and interactions with natural helminth infections and different levels of diet on health and productivity of these two breeds. Trypanosome infection caused a severe drop in packed cell volume (PCV), but this was not significantly affected by breed. Neither deworming nor diet had any effect on the course of anaemia after trypanosome infection. The mean score of parasitaemia tended to be higher in crossbreeds than in WAD goats although this was not significant (P>0.05). Similarly, the antibody response to trypanosome infection was not significantly different between breeds. Parasitaemia level was significantly influenced by the level of diet with the group under high supplementation having a higher mean parasitaemia score than the group under low supplementation. Weight loss due to trypanosome infection tended to be greater in crossbreeds than in WAD goats (P>0.05). During this study, there was no difference in mean helminth egg output between crossbred and WAD goats. However, between weeks 4 and 10 after trypanosome infection (corresponding to a period of heavy rainfall and highly infective pastures), the mean egg output was higher in the crossbreeds. The immunosuppressive effect of trypanosome infections was revealed by a lower antibody response to Haemonchus contortus in infected animals compared to the uninfected controls. Trypanosome infection tended to increase strongyle egg output. This study did no reveal any superior trypanotolerance of WAD goats compared to crossbreeds.

Prevalence and incidence of trypanosomosis in horses and donkeys in the Gambia

In a study of the prevalence and incidence of trypanosomosis in horses and donkeys in two regions of the Gambia, surveys were carried out at Niamina east and Bansang south with a high and low to moderate tsetse challenge, respectively. Eleven horses and 67 donkeys were sampled monthly from August 1997 to September 1998. Blood samples were examined for trypanosomes using the buffy-coat (BC) method and polymerase chain reaction (PCR). Three primer sets were used, specific for either Trypanosoma vivax (TVW), Trypanosoma congolense (GOL) or Trypanosoma brucei (ORPHON5J). The BC results showed that the prevalence (August 1997) and the average monthly incidence (September 1997-1998) of trypanosome infections in horses (45.5 and 16%, respectively) were significantly higher than in donkeys (6.2 and 9%, respectively). Using PCR, the number of detected cases was seven times higher than using the BC. T. congolense was the most frequently observed species, followed by T. vivax and T. brucei. This study confirms earlier observations by other authors that donkeys, which are exposed to a similar tsetse challenge as horses, are significantly less infected with trypanosomes than the latter.

Mating system and reproductive skew in the black rhinoceros

Only approximately 2600 black rhinoceros survive today, mainly in small, isolated populations of < 100 animals. The management of remaining black rhinoceros populations aims at preserving natural levels of genetic relatedness and optimizing breeding success, which requires an accurate knowledge of the mating system, reproductive skew and effective population size. DNA was extracted from faecal samples from a community of 35 wild black rhinoceros, and microsatellites were used to characterize patterns of paternity of 19 offspring born from eight females in this community. Paternity could be ascribed unequivocally for each offspring. Although our conclusions must be considered tentative, we present the first genetic evidence that black rhinoceros males are polygynous, with a high variance in reproductive success. We also describe a noninvasive management tool that can be used for the genetic management of this critically endangered species, both in the wild and in captivity.

Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps

The genetic structure of the Alpine marmot, Marmota marmota, was studied by an analysis of five polymorphic microsatellite loci. Eight locations were sampled in the French Alps, one from Les Ecrins valley (n = 160), another from La Sassière valley (n = 289) and the six others from the Maurienne valley (n = 139). Information on social group structure was available for both Les Ecrins and La Sassière but not for the other samples. The high levels of genetic diversity observed are at odds with the results obtained using microsatellites, minisatellites and allozymes on Alpine marmots from Germany, Austria and Switzerland. Strong deficits in heterozygotes were found in Les Ecrins and La Sassière. They are caused by a Wahlund effect due to the family structure (i.e. differentiation between the family groups). The family groups exhibit excess of heterozygotes rather than deficits. This may be caused by outbreeding and this is compatible with recent results from the genetics of related social species when information on the social structure is taken into account. The observed outbreeding could be the result of females mating with transient males or males coming from neighbouring colonies. Both indicate that the species may not be as monogamous as is usually believed. The results are also compatible with a male-biased dispersal but do not allow us to exclude some female migration. We also found a significant correlation between geographical and genetic distance indicating that isolation by distance could be an issue in marmots. This study is the first that analysed populations of marmots taking into account the social structure within populations and assessing inbreeding at different levels (region, valley, population, and family groups). Our study clearly demonstrated that the sampling strategy and behavioural information can have dramatic effects on both the results and interpretation of the genetic data.

Some biochemical changes following Trypanosoma congolense infection in Djallonké ewe lambs and breeding ewes fed on two levels of nutrition

The effects of artificial Trypanosoma congolense infection and dietary level on biochemical changes were observed in 24 ewe lambs (Experiment 1) and 42 breeding ewes (Experiment 2). All animals belonged to the Djallonké breed which is known to be trypanotolerant. For both experiments, there were four treatment combinations, of which two were kept on a restricted diet (L), the other two on an at libitum diet (H). Half of each dietary group was infected with T. congolense (LI, HI), while the remainder served as uninfected controls (LC, HC). Artificial T. congolense infection took place at the age of 200+/-7 days in Experiment 1 and at the peak of oestrus in Experiment 2. Irrespective of dietary levels offered, total proteins in lambs and ewes and albumin in lambs declined significantly (P<0.001) post infection. Plasma glucose concentration was reduced by the low dietary level and not by infection. Although plasma urea concentrations were slightly increased in the infected ewe lambs, adult ewes in the HI group demonstrated increased plasma urea concentrations (P<0.05) due to an interaction between infection and diet. Neither infection nor the imposed diet induced significant changes on plasma creatinine concentrations. Transitory peaks in non-esterified fatty acids (NEFA) and beta-hydroxy butyric acid (BHBA) levels in infected ewes on low dietary level indicated temporary changes in the energy metabolism of the host. It was concluded from this study that, inspite of their trypanotolerance, Djallonké lambs and ewes demonstrated an infection effect on host metabolism pattern due to T. congolense infection. These changes reflected to some extent trypanosome-induced alteration of the nutrient metabolism, which could not always be negated by diet supplements. Nutrition, as an independent factor, did confer added benefits against the debilitating effects of trypanosomosis under the conditions of the present study.

The effects of prophylactic anthelmintic treatment on the productivity of traditionally managed Djallonke sheep and West African Dwarf goats kept under high trypanosomosis risk

The effects of a prophylactic anthelmintic intervention on the productivity of village based sheep and goats was studied in an area of high trypanosomosis risk in The Gambia during 2 and 3 years, respectively. In total, 223 sheep and 385 goats from five villages were included. Allocation to treatment groups (treated-control) was randomised by village, based on age and sex. Three treatments per rainy season were applied with Fenbendazole (Panacur, Hoechst, 2.5%, 5 mg/kg). Mean nematode egg excretion per gram faeces (EPG) of the treated groups were significantly reduced by prophylactic anthelmintic treatment, indicating the efficiency of the treatment despite the risk of rapid reinfestation. Weight gain benefits of anthelmintic treatment were observed in all age categories (> 6 month) of sheep but not in goats. Kidding rates were significantly increased whilst the same positive trends were observed for other reproductive parameters (litter size, parturition interval) in both goats and sheep without reaching statistical significance. Birth weights of offspring born out of treated does and ewes were higher (P < 0.05) than those from the controls. In contrast, growth rates until 3 months of age were not influenced by the treatment status of the dam. Mortality rates until the age of 3 months of kids from treated does were significantly lower than of those from control does. Mean Packed Red Cell Volume (PCV) levels during the rains were significantly higher in treated goats than in control goats. The same trend was observed in sheep. In general, there were no interactions between trypanosome infections and effect of anthelmintic treatment, thus both factors acted independently. Finally, the live weight productivity index (12 months old-offspring in kg/year per dam) for treated dams was 24% and 47% higher than in control ewes and does, respectively. It can be concluded that, despite the continuous risk of trypanosome infections which has a negative impact on their productivity, a beneficial effect of anthelmintic treatment was observed in both species but most obviously in goats, measured as an increased production and improved health status. A cost-benefit analysis should be carried out in order to confirm whether prophylactic anthelmintic treatment can be recommended to farmers to increase their income from small ruminant production. Nevertheless, anthelmintic treatment will certainly optimise the trypanotolerance in these breeds.

The susceptibility of Djallonké and Djallonké-Sahelian crossbred sheep to Trypanosoma congolense and helminth infection under different diet levels

Forty two Djallonké and 27 Djallonké-Sahelian crossbred sheep were compared during 34 weeks for their disease resistance and productivity in a multifactorial experiment including trypanosome infection, helminth infections and dietary level. Eight treatment combinations were formed in which the two breeds were balanced. Pyrexia was observed following trypanosome infection and was not different between the two breeds. However, a significant higher parasitaemia level, a shorter prepatent period and a lower antibody response in the crossbreds following infection, indicated a significant reduction of the trypanotolerance and confirmed the genetic origin of the trait. Neither helminth infection nor dietary level influenced the onset and level of parasitaemia or the level of antibody response following trypanosome infection. Trypanosome infection, helminth infection and low supplementary feeding caused independently significant reductions in PCV level and weight gain but these declines were not worse in crossbreds as compared to Djallonké. Independently, of the studied factors, crossbreds were generally heavier than Djallonké and also grew faster, especially during the second phase of the study. Crossbreds had significantly higher mean nematode egg output (epg) compared to Djallonké sheep but reduction of epg following deworming was similar in both breeds. The lower epg in the Djallonké breed indicated an innate resistance to helminths and/or more efficient immune response. Trypanosome infection tended to increase epg, confirming the immunosuppressive effect of the former. The higher body temperature in the Djallonké compared to crossbreds suggested a better heat tolerance in the former breed. From this study it was concluded that Djallonké-Sahelian crossbred sheep inspite of a reduced trypanotolerance and lower resistance to helminth infection, posses a higher potential to intensify mutton production as compared to the pure Djallonké. However, appropriate measures should be taken to limit disease and stress factors in order to optimise production environment for this crossbred sheep.

Health and productivity of traditionally managed Djallonke sheep and West African dwarf goats under high and moderate trypanosomosis risk

Trypanosome infections, packed red cell volume levels (PCV), body weight and nematode faecal egg counts of village-based small ruminants were monitored in two areas in The Gambia with either moderate or high trypanosomosis risk for 24 and 30 months respectively. Outflows from the flock and new-born animals were recorded and data on housing and management were compiled. Reported mortality rates were higher in goats than in sheep, but for both species highest in the moderate risk area. The peak of trypanosome infections lagged the peak of tsetse densities by 1-3 months in both areas. Trypanosoma vivax was the predominant species found in the infected animals, followed by T. congolense. Trypanosome prevalence was, in general, higher in sheep than in goats but only significantly higher during Year 1 in the moderate risk area. Trypanosome infection reduced the PCV level significantly and seasonal effects indicated significantly lower PCV levels during the rains. Trypanosome infection significantly depressed weight gain in both species at periods where infection rates were highest. In both species considerably lower weight gains were observed during the rainy season. Abortion rates were higher in goats than in sheep in both study sites, and highest in the high-risk site. Trypanosome infection in ewes in the high risk area increased lamb mortality significantly but had no effect on birth weights, nor on growth rates up to 4 months. Offspring mortality up to 4 months was generally high at both sites. Trypanosome infection in the dam between 3.5 to 7 months post parturition significantly increased parturition interval in both species. Peak faecal egg output occurred at the end of the rainy season and was highest for both species in the moderate risk site. Poor grazing management was found responsible for a seasonal nutritional constraint. Based on these results, these breeds of sheep and goats can be considered as trypanotolerant since they are able to remain productive under high and moderate levels of trypanosome challenge. Nevertheless, trypanosomosis affected their health and production level as shown by reduced PCV levels, depressed weight gains, longer parturition intervals and higher lamb mortality. In addition, during the rains, helminth infections and poor management leading to nutritional constraints had also a negative impact on health and production and therefore influenced the innate resilience to trypanosomosis in those indigenous breeds. Adaptations in management may have an equal impact as certain disease control measures to improve biological and economical returns from small ruminants in tsetse infested rural areas.

Effects of Trypanosoma congolense infection and diet on puberty, age at first lambing and haematology changes in Djallonké ewe lambs

The interactions between T. congolense infection and nutritional supplements on onset of puberty and age at first lambing were observed in 24 young Djallonké ewes. As experimental design, a randomised complete block design was used with four treatment combinations, of which two were kept on a restricted diet (L), the remainder on an unrestricted diet (H) and half of each nutritional group being infected with T. congolense (LI and HI), the remainder serving as controls (LC and HC). Infection with T. congolense took place at an average age of 6 months and 15 days. Mortality due to trypanosome infection was zero and clinical symptoms were not obvious. Intensity of parasitaemia and packed cell volume (PCV) drop following trypanosome infection were similar in both infected groups (HI and LI). High dietary supplementation resulted temporarily in a better haematopoietic response following trypanosome infection, measured as a macrocytic anaemia. Dry matter intake (DMI) was significantly depressed in the HI group immediately following infection. Trypanosome infection had a negative effect on live weight gain during the chronic phase, with the difference being most obvious in the HI group (interaction diet x infection; p< or =0.05). Whereas trypanosome infection had no significant effect, high supplementary feeding significantly reduced the age at first cycling. Age at first lambing was similarly reduced by the diet. Trypanosome infection tended (p< or =0.09) to delay age at first lambing with a mean difference of 31.5+/-22.4 days between infected and controls. Interactions between diet and infection for age at first cycling/lambing were not significant, indicating these effects were just additive. Neither birth weights nor growth rates of offspring born to the experimental animals were significantly affected by previous trypanosome infection, nor by the diet of the dam. In contrast, lamb mortality up to 3 months of age was significantly increased by infection of the dam and most losses arose in group LI. In conclusion, the effects of trypanosome infection on puberty and age at first lambing were indirectly mediated through depression of growth rates. Nutritional supplementation enabled a better erythropoietic response to T. congolense infection and better offspring survival rates but resulted in more depressed weight gains. The results however clearly indicated the delaying effect of insufficient feeding on onset of puberty and reproductive performance in young Djallonké sheep.

PCR primer evaluation for the detection of trypanosome DNA in naturally infected goats

The buffy coat of 76 roaming goats from the Bansang and Missira regions in Gambia, was examined for the presence of trypanosomes. From these animals, extractions from dry blood samples on filter paper were subjected to PCR using three different primer sets, ORPHON5J, GOL and TVW, specific for Trypanosoma brucei/Trypanosoma evansi, Trypanosoma congolense and Trypanosoma vivax, respectively. PCR results for T. congolense were 100% concordant with buffy coat examination. Besides the three T. vivax buffy coat-positive samples, another 15 yielded positive with the TVW primers. The ORPHON5J primers yielded no positive results. Analyses with the GOL primers of putatively negative samples, yielded aberrant band patterns whose diagnostic significance still remains to be determined.