Simuliidae

The ‘mice_of’ dataset was used to evaluate performance for tracking mice under optimal imaging conditions (high contrast) and with variable numbers of animals. The dataset consisted of videos from C57BL/6J male (n = 17) and female (n = 20) mice acquired from Jackson Laboratory (RRID:IMSR_JAX:000664, Jackson Laboratory). Groups of four and five mice were formed from same-sex littermates, and groups of two same-sex mice were picked randomly from different litters and interacted with each other in the open field for the first time. During video recording, mice moved freely in a 45.7 × 45.7-cm open-field arena with a clear acrylic floor. Videos were captured from below with infrared illumination using a Point Grey Blackfly S camera at a resolution of 1.97 pixels per mm at 80 FPS.
Experimental procedures were approved by the Princeton University Institutional Animal Care and Use Committee and conducted in accordance with the National Institutes of Health guidelines for the humane care and use of laboratory animals. Mice used in this study had at least 1 week of acclimation to the Princeton Neuroscience Institute vivarium in group cages with food and water ad libitum under a reversed 12-h–12-h dark–light cycle (light, 19:30–07:30) and were habituated in the dark test room for at least 30 min before experimental procedures were performed.
For this dataset, we labeled 1,000 frames (2,950 instances) with a skeleton consisting of 11 nodes: nose, neck, ‘L_ear’, ‘R_ear’, ‘L_Fr_paw’, ‘R_Fr_paw’, ‘tail_base’, ‘L_Hi_paw’, ‘R_Hi_paw’, ‘tail_mid’ and ‘tail_end’; and ten edges: neck to ‘L_Fr_paw’, neck to ‘R_Fr_paw’, ‘tail_base’ to ‘R_Hi_paw’, ‘tail_base’ to ‘L_Hi_paw’, ‘tail_base’ to ‘tail_mid’, ‘tail_mid’ to ‘tail_end’, neck to nose, neck to ‘R_ear’, neck to ‘L_ear’ and ‘tail_base’ to neck. Labels were randomly split into 800 training, 100 validation and 100 test frames.

The present study was conducted in the Bafia (4°45′00″N, 11°14′00″E) and Yabassi (4°27′16″N, 9°57′56″E) health districts (HD), belonging to the Centre 1 and Littoral 2 CDTI projects, respectively.
The Bafia HD is located in the Mbam and Inoubou Division (Centre Region), at 120 km north from Yaoundé, the political capital of Cameroon. In 2014, its population was 226,073 inhabitants, based on a census conducted by community-directed distributors (CDD). The altitude of this region varies from 1,100 to 1,300 m. It is a forest-savanna transition zone, irrigated by many fast-flowing rivers including Sanaga and its tributaries, as well as the Mbam and Noun rivers. The main activities of inhabitants are agriculture (mainly cocoa), fishing and sand mining.
The Yabassi HD is located in the Nkam Division (Littoral Region), at 100 km north-east from Douala, the economic capital of the country. According to the 2014 CDD census, its population was 21,459 inhabitants. The relief is undulating, showing an alternation of valleys and plains. Altitude of the region varies from 10 to 800 m. This district is irrigated by many fast-flowing rivers comprising Nkam, Dibamba, Mabombé, Njanga and Mahé which are favorable to blackfly breeding. The vegetation is mainly dense humid forest. Agriculture is the main activity, interesting at least 60 % of inhabitants.

All procedures described below were approved by The Institutional Animal Care and Use Committee at Emory University. Anesthesia was induced with an initial dose of 4% isoflurane in oxygen provided in an induction chamber with 2 L/minute rate and maintained with 3% isoflurane at 1 L/minute. Following this, rats received a subcutaneous injection of 1mg/kg Meloxicam, a subcutaneous injection of 1% Lidocaine and topical application of lidocaine ointment (5%) at each incision site. Myomatrix threads were implanted in the triceps muscle using the “intramuscular” method. EMG data were then recorded while animals walked on a treadmill at speeds ranging from 8–25 cm/sec. Kinematics were quantified using a circular arrangement of four high-speed FLIR Black Fly S USB3 cameras (BFS-U3-16S2M-CS, Mono), each running at 125 FPS. We used DeepLabCut to label pixel locations of each of ten anatomical landmarks on the limbs and body, which we then transformed into 3D cartesian coordinates using Anipose (Karashchuk et al. 2021 (link); Mathis et al. 2018 (link)). We then defined the onset of each swing/stance cycle by using local minima in the rat’s forelimb endpoint position along the direction of locomotion.

All procedures described below were approved by The Institutional Animal Care and Use Committee at Emory University. Anesthesia was induced with an initial dose of 4% isoflurane in oxygen provided in an induction chamber with 2 L/minute rate and maintained with 3% isoflurane at 1 L/minute. Following this, rats received a subcutaneous injection of 1mg/kg Meloxicam, a subcutaneous injection of 1% Lidocaine and topical application of lidocaine ointment (5%) at each incision site. Myomatrix threads were implanted in the triceps muscle using the “intramuscular” method. EMG data were then recorded while animals walked on a treadmill at speeds ranging from 8–25 cm/sec. Kinematics were quantified using a circular arrangement of four high-speed FLIR Black Fly S USB3 cameras (BFS-U3–16S2MCS, Mono), each running at 125 FPS. We used DeepLabCut to label pixel locations of each of ten anatomical landmarks on the limbs and body, which we then transformed into 3D cartesian coordinates using Anipose ^{51 (link),53 (link)}. We then defined the onset of each swing/stance cycle by using local minima in the raťs forelimb endpoint position along the direction of locomotion.

Black soldier fly larvae (BSFL; Hermetia illucens) were obtained from the commercial BSF producing company Bestico, (Berkel en Rodenrijs, The Netherlands). The following substrates were tested: chicken feed (CF; control diet), pig manure slurry mixed with roadside silage grass (PMLSG), the organic wet fraction of municipal household waste (OWF), secondary sludge from slaughter waste (SW), fast food waste (FFW), mushroom stems (MS) and pig manure solid (PMS). Chicken feed is a commercial broiler feed which was used as the control diet [33 (link),36 (link),37 (link)]. Pig manure slurry was a mixture of pig feces and urine, and it was mixed with roadside silage grass (1:1 w/w) to produce PMLSG. The organic wet fraction used in this experiment makes around 30–35% of the municipal household waste. It was contaminated by physical contaminants such as glass and plastic that were not removed. The solid phase of the secondary sludge from slaughter waste was also used as an experimental substrate. The fast food waste consisted of fries, vegetables, bread and meat products but not any non-food waste and was collected within maximum 4 days after disposal. The mushroom stems are a soft substrate and may have been contaminated by soil. The different substrates were selected based on the results of a prior study published by Veldkamp [33 (link)].
Substrates were obtained one week before the start of the rearing cycle and stored at 4 °C until use. Some of the substrates were pre-treated in a cutter to decrease particle size which included PMLSG (~2 cm), FFW (~1 cm) and MS substrates (~0.5 cm). All substrates are brought to 35% dry matter by adding water and/or cellulose/wood shavings to decrease or increase the DM in the substrate, respectively. Since the used substrates all have a different weight-to-volume ratio, different quantities of substrates and larvae were added to the containers to maintain a substrate layer of approximately 5 cm such that every BSFL gets 0.54 g of the wet substrate (Table 1). The containers were filled one day before starting the experiment, thus allowing them to adapt to the ambient temperature in the climate chamber without any external heating. On top of each substrate, 1850 starter BSFL (8 day old) per kilogram of wet substrate were incubated in 21 plastic containers (75 cm × 47 cm × 15 cm). Each substrate was tested in triplicate in a climate chamber (7 treatments × 3 replicates). The chamber temperature was set to 28 °C and the relative humidity (RH) was 70% from day 0 until day 5 and was 40–60% from day 6 until the end of the experiment. The rearing chamber was dark. The plastic containers were stacked in three columns each with seven containers (one container per repetition) arranged based on escaping probability, i.e., the containers with the highest moisture content were placed at the bottom to avoid escaping larvae falling into containers below them. Each column was placed in a non-escape box (cubic box; 120 cm × 100 cm × 60 cm). The experimental period was 7 to 8 days which was determined by visual checking of the substrate consumption or the presence of ~10% prepupae.