Developing an automatic warning system for anomalous chicken dispersion and movement using deep learning and machine learning.

Chicken is a major source of dietary protein worldwide. The dispersion and movement of chickens constitute vital indicators of their health and status. This is especially evident in Taiwanese native chickens (TNCs), a local variety which is high in physical activity when healthy. Conventionally, the dispersion and movement of chicken flocks are observed in patrols. However, manual patrolling is laborious and time-consuming. Moreover, frequent patrols increase the risk of carrying pathogens into chicken farms. To address these issues, this study proposes an approach to develop an automatic warning system for anomalous dispersion and movement of chicken flocks in commercial chicken farms. Embendded systems were developed to acquire videos of chickens from overhead view in a chicken house, in which approximately 20,000 TNCs were raised for a period of 10 wk. Each video was 5-min in length. The videos were transmitted to a remote cloud server and were converted into images. A You Only Look Once-version 7 tiny (YOLOv7-tiny) object detection model was trained to detect chickens in the images. The dispersion of the chicken flocks in a 5-min long video was calculated using nearest neighbor index (NNI). The movement of the chicken flocks in a 5-min long video was quantified using simple online and real-time tracking algorithm (SORT). The normal ranges (i.e., 95% confidence intervals) of chicken dispersion and movement were established using an autoregressive integrated moving average (ARIMA) model and a seasonal autoregressive integrated moving average with exogenous factors (SARIMAX) model, respectively. The system allows farmers to check up on the chicken farm only when the dispersion or movement values were not in the normal ranges. Thus, labor time can be saved and the risk of carrying pathogens into chicken farms can be reduced. The trained YOLOv7-tiny model achieved an average precision of 98.2% in chicken detection. SORT achieved a multiple object tracking accuracy of 95.3%. The ARIMA and SARIMAX achieved a mean absolute percentage error 3.71% and 13.39%, respectively, in forecasting dispersion and movement. The proposed approach can serve as a solution for automatic monitoring of anomalous chicken dispersion and movement in chicken farming, alerting farmers of potential health risks and environmental hazards in chicken farms.

Effects of electron transport layer thickness on light extraction in corrugated OLEDs.

This study reported the effects of electron transport layer (ETL) thickness on light extraction in corrugated organic light-emitting diodes (OLEDs) and each layer in OLEDs exhibited a periodical corrugated structure, which was determined by depositing thin films on a glass substrate with a nanoimprinted blazed grating structure. The insight is that light extraction in corrugated OLEDs significantly depends on the ETL thickness. Varying the ETL thickness changed the distribution of carrier recombination and led to exciton formation and optical interference, thereby resulting in different attribution of optical loss modes in OLEDs, which increased or even decreased light extraction and device efficiency. Trapped light extraction from the surface plasmon polariton (SPP) and waveguide (WG) modes was identified by splitting the light into transverse electric and transverse magnetic emissions. Thus, the contributions from the individual SPP and WG modes to the external quantum efficiency (EQE) were distinctly clarified by comparing the experimental results with the theoretical calculations. At the ETL thickness of 115 nm, the corrugated OLED exhibited a significantly enhanced (1.83-fold) EQE compared to the planar one due to the effective extraction of trapped light from the SPP and WG modes. The EQE was enhanced by 0.5%, wherein 0.39% came from the WG mode and 0.11% came from the SPP mode.

The preventability of trauma-related death: A two-year cohort study in a trauma center in middle Taiwan.

INTRODUCTION: The preventable death rate (PDR) is an important parameter in the quality assurance of traumatic care. Medical errors or untimely management may occur during stressful trauma care, resulting in preventable deaths. We aimed to develop an applicable PDR model in a trauma center in middle Taiwan. MATERIALS AND METHODS: We identified adult trauma-related deaths which occurred from January 1, 2018 to December 31, 2019 at our hospital. Patients with a trauma and injury severity score (TRISS) <75% or ≥75% but with a chance of preventability, as determined by a trauma surgeon, were discussed by a panel comprising an emergency physician and surgeons specializing in different fields of medicine. Deaths were subsequently classified as definitely preventable (DP), potentially preventable (PP), or non-preventable (NP). Causes of DP or PP deaths were categorized as delayed diagnosis, delayed treatment, technical error, or inadequate infection prevention/control. The relationship between the time and cause of preventable deaths was also analyzed. RESULTS: This study included 127 trauma-related deaths, of which 39 were discussed by the panel. Eight patients (6.3%) were categorized as DP, eight (6.3%) as PP, and 111 (87.4%) as NP. Among patients with preventable deaths, inadequate infection prevention/control, delayed treatment, delayed diagnosis, and technical error were identified in six (37.5%), five (31.2%), three (18.8%), and two (12.5%) patients, respectively. Four patients in the inadequate infection prevention/control group (4/6, 66.7%) died of aspiration pneumonia during the recovery phase. CONCLUSION: A PDR evaluation model was developed and revealed that postoperative care is as important as a timely diagnosis and treatment to avoid preventable deaths following trauma.

Transcriptomic Analysis Suggests Auxin Regulation in Dorsal-Ventral Petal Asymmetry of Wild Progenitor Sinningia speciosa.

The establishment of dorsal-ventral (DV) petal asymmetry is accompanied by differential growth of DV petal size, shape, and color differences, which enhance ornamental values. Genes involved in flower symmetry in Sinningia speciosa have been identified as CYCLOIDEA (SsCYC), but which gene regulatory network (GRN) is associated with SsCYC to establish DV petal asymmetry is still unknown. To uncover the GRN of DV petal asymmetry, we identified 630 DV differentially expressed genes (DV-DEGs) from the RNA-Seq of dorsal and ventral petals in the wild progenitor, S. speciosa 'ES'. Validated by qRT-PCR, genes in the auxin signaling transduction pathway, SsCYC, and a major regulator of anthocyanin biosynthesis were upregulated in dorsal petals. These genes correlated with a higher endogenous auxin level in dorsal petals, with longer tube length growth through cell expansion and a purple dorsal color. Over-expression of SsCYC in Nicotiana reduced petal size by regulating cell growth, suggesting that SsCYC also controls cell expansion. This suggests that auxin and SsCYC both regulate DV petal asymmetry. Transiently over-expressed SsCYC, however, could not activate most major auxin signaling genes, suggesting that SsCYC may not trigger auxin regulation. Whether auxin can activate SsCYC or whether they act independently to regulate DV petal asymmetry remains to be explored in the future.

Nectar Guide Patterns on Developmentally Homologous Regions of the Subtribe Ligeriinae (Gesneriaceae).

Homology is a crucial concept that should be considered while conducting a comparative analysis between organisms. In particular, in the subtribe Ligeriinae, the nectar guide pattern is associated with high diversity in petal shapes and sizes. This largely limits researchers to exclusively examining the interspecific variation in nectar guide patterns on the developmentally homologous region. Thus, to solve this problem, we proposed an approach for defining a homologous region of interest (ROI) that aligns the petal image between specimens based on petal contours and vasculatures. We identified petal contours and vasculatures from the fresh petal image and its histological image through image processing. The homologous ROI was subsequently obtained by applying geometric transformation to the contour and vasculature. The qualification and quantification of nectar guide patterns were subsequently performed based on the homologous ROI. Four patterning modes, namely vascular, random, distal, and proximal, were defined for the qualitative analysis of nectar guide patterns. In the quantitative analysis, principal component (PC) analysis was applied to homologous ROIs, and the PC score of each specimen served as the trait values of nectar guide patterns. The results of the two analyses coincided, and both showed significant associations between nectar guide patterns and pollination types. The proximal mode (corresponding to PC1) and distal mode (corresponding to PC2) together showed the strongest association with pollination types. Species exhibiting the hummingbird and bee pollination types tended to recruit the distal and proximal modes, respectively. Our study conducted a comparative analysis of nectar guide patterns on the developmentally homologous region and provided a comprehensive view of the variation in the nectar guide patterns of Ligeriinae.

Automatic Identification of First-Order Veins and Corolla Contours in Three-Dimensional Floral Images.

Defining and quantifying corolla traits are essential for studying corolla shape variation. Three-dimensional (3D) images of corollas contain comprehensive information regarding corolla structures and are optimal for studying corolla shapes. Conventionally, corolla traits are identified and quantified manually from 3D images. Manual identification is time consuming and labor intensive. In this study, approaches are proposed to automatically identify first-order veins and corolla contours in 3D corolla images. The first-order veins of the corollas were identified using Hessian of Gaussian and Dijkstra's algorithm. The contours of the corollas were identified using vector harmony and node distance thresholding. A total of 130 3D images of 28 species in the subtribe Ligeriinae were collected and used to test the proposed approaches. The successful detection rate reached 86.54%. Two derived traits, contour-vein ratio and corolla angle, were defined and quantified using the first-order veins and corolla contour results to investigate the relationship between corolla shapes and pollination types of the subtribe Ligeriinae. Analyses revealed that the mean corolla contour, mean absolute corolla angle, and mean contour-vein ratio of the ornithophilic species were significantly smaller compared with the other species. The mean corolla contour, mean corolla angle, and mean contour-vein ratio of the melittophilic species were significantly larger compared with those of the ornithophilic species. The proposed method was also applied to certain Gesneriaceae species in the subtribes Gloxiniinae, Streptocarpinae, and Didymocarpinae. The results revealed that the method could be applied to most fresh sympetalous flowers for identifying first-order veins and corolla contours.

3D revelation of phenotypic variation, evolutionary allometry, and ancestral states of corolla shape: a case study of clade Corytholoma (subtribe Ligeriinae, family Gesneriaceae).

BACKGROUND: Quantification of corolla shape variations helps biologists to investigate plant diversity and evolution. 3D images capture the genuine structure and provide comprehensive spatial information. RESULTS: This study applied X-ray micro-computed tomography (µCT) to acquire 3D structures of the corollas of clade Corytholoma and extracted a set of 415 3D landmarks from each specimen. By applying the geometric morphometrics (GM) to the landmarks, the first 4 principal components (PCs) in the 3D shape and 3D form analyses, respectively, accounted for 87.86% and 96.34% of the total variance. The centroid sizes of the corollas only accounted for 5.46% of the corolla shape variation, suggesting that the evolutionary allometry was weak. The 4 morphological traits corresponding to the 4 shape PCs were defined as tube curvature, lobe area, tube dilation, and lobe recurvation. Tube curvature and tube dilation were strongly associated with the pollination type and contained phylogenetic signals in clade Corytholoma. The landmarks were further used to reconstruct corolla shapes at the ancestral states. CONCLUSIONS: With the integration of µCT imaging into GM, the proposed approach boosted the precision in quantifying corolla traits and improved the understanding of the morphological traits corresponding to the pollination type, impact of size on shape variation, and evolution of corolla shape in clade Corytholoma.

Parapharyngeal fat pad area at the subglosso-supraglottic level is associated with corresponding lateral wall collapse and apnea-hypopnea index in patients with obstructive sleep apnea: a pilot study.

The aim of this study was to assess associations between fat pad areas at various anatomic levels and the sites of lateral wall collapse and disease severity in adult patients with obstructive sleep apnea (OSA). Forty-one patients with OSA who prospectively underwent drug-induced sleep computed tomography were included. Areas of parapharyngeal fat pads and degrees of lateral wall collapse at three representative anatomic levels (nasopharynx, oropharynx, and subglosso-supraglottis), and apnea-hypopnea index (AHI) were measured. In the subglosso-supraglottic region, the parapharyngeal fat pad area in 17 (41%) patients with complete lateral wall collapse was significantly larger than that in 24 (59%) patients without complete collapse (median, 236.0 mm2 vs 153.0 mm2; P = 0.02). In multivariate regression analysis, the parapharyngeal fat pad area at the subglosso-supraglottic level (ß = 0.02; P = 0.01) and body mass index (ß = 3.24; P = 0.01) were independently associated with AHI. Our preliminary results supported that parapharyngeal fat pads at the subglosso-supraglottic level may be involved in the development of lateral wall collapse and then determine the severity of OSA. Further studies are warranted to investigate the effect of reducing parapharyngeal fat pads in the treatment of OSA.

Corrugated organic light-emitting diodes to effectively extract internal modes.

We report a corrugated structure to effectively extract the surface plasmon polaritons (SPP) and waveguiding modes in organic light-emitting diodes (OLEDs). This structure is formed by nano-imprint of blazed gratings. To study the optimum extraction condition in terms of grating pitches, we compare the light extraction efficiency of corrugated OLEDs with three kinds of pitches, showing a 42.00% external quantum efficiency (EQE) enhancement ratio with this internal structure. Due to the transfer of SPP and waveguiding modes into substrate mode, the EQE enhancement ratio can be further pushed to 103.02% by attaching a macrolens. The simulation verifies the experimental results and shows the extraction mechanism of the corrugated structure towards transverse electric (TE) and transverse magnetic (TM) waves. We foresee that this method is able to enhance the optical efficiency of devices for both mass-production OLED lighting and display in a cost-effective way.

Improving Indirect Revascularization for Effective Treatment of Adult Moyamoya Disease: A Prospective Clinical, Cerebral Angiographic, and Perfusion Study.

BACKGROUND: Indirect revascularization is simple and safe, but it is not commonly used in adult moyamoya disease owing to its unreliable effect. This prospective study aimed to evaluate the effectiveness of indirect revascularization in treating adult moyamoya disease after refinement of the surgical technique and perioperative care. METHODS: Adult patients who underwent indirect revascularization as the primary treatment for moyamoya disease between November 2013 and January 2017 were studied. The indirect revascularization procedures included encephalo-duro-arterio-synangiosis and encephalo-myo-synangiosis in the temporal region and encephalo-pericranio-synangiosis in other hypoperfusion areas. The preoperative and postoperative clinical conditions, cerebral angiography findings, and time-to-peak prolongation areas on magnetic resonance perfusion studies were assessed to evaluate the revascularization effect. Refinements of the surgical technique included the selection of surgical area based on perfusion imaging, craniotomy size, and number of affected hemispheres, along with the inclusion of a dural flap in every procedure. RESULTS: Nineteen patients (17 females and 2 males), and a total of 31 cerebral hemispheres, were included. The mean patient age was 32.7 ± 11.4 years. After a mean follow-up of 38.6 ± 11.5 months, all patients showed clinical improvement or stabilization. Available postoperative angiography demonstrated Matsushima grade A or B in 19 of 21 hemispheres. The mean time-to-peak prolongation index of all 31 hemispheres improved from 24.09 ± 9.83% preoperatively to 12.82 ± 6.75% at 3-6 months after surgery (P < 0.001). The complication rate was 12.9%, and all complications were transient. CONCLUSIONS: With refinements of surgical techniques and perioperative care, indirect revascularization is more reliable and can be a viable alternative treatment for adult moyamoya disease. In our cohort, outcomes were satisfactory, with mean 38.6-month follow-up.

Association between Petal Form Variation and CYC2-like Genotype in a Hybrid Line of Sinningia speciosa.

This study used three-dimensional (3D) micro-computed tomography (µCT) imaging to examine petal form variation in a hybrid cross of Sinningia speciosa between a cultivar with actinomorphic flowers and a variety with zygomorphic flowers. The major objectives were to determine the genotype-phenotype associations between the petal form variation and CYCLOIDEA2-like alleles in S. speciosa (SsCYC) and to morphologically investigate the differences in petal types between actinomorphic and zygomorphic flowers. In this study, µCT was used to accurately acquire 3D floral images. Landmark-based geometric morphometrics (GM) was applied to evaluate the major form variations of the petals. Nine morphological traits of the petals were defined according to the form variations quantified through the GM analysis. The results indicated that the outward curvature of dorsal petals, the midrib asymmetry of lateral petals, and the dilation of ventral region of the tube were closely associated with the SsCYC genotype. Multiple analyses of form similarity between the petals suggested that the dorsal and ventral petals of actinomorphic plants resembled the ventral petals of zygomorphic plants. This observation indicated that the transition from zygomorphic to actinomorphic flowers in S. speciosa might be caused by the ventralization of the dorsal petals. We demonstrated that the 3D-GM approach can be used to determine genotype-phenotype associations and to provide morphological evidence for the transition of petal types between actinomorphic and zygomorphic flowers in S. speciosa.

Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers.

The quantification of floral shape variations is difficult because flower structures are both diverse and complex. Traditionally, floral shape variations are quantified using the qualitative and linear measurements of two-dimensional (2D) images. The 2D images cannot adequately describe flower structures, and thus lead to unsatisfactory discrimination of the flower shape. This study aimed to acquire three-dimensional (3D) images by using microcomputed tomography (µCT) and to examine the floral shape variations by using geometric morphometrics (GM). To demonstrate the advantages of the 3D-µCT-GM approach, we applied the approach to a second-generation population of florist's gloxinia (Sinningia speciosa) crossed from parents of zygomorphic and actinomorphic flowers. The flowers in the population considerably vary in size and shape, thereby served as good materials to test the applicability of the proposed phenotyping approach. Procedures were developed to acquire 3D volumetric flower images using a µCT scanner, to segment the flower regions from the background, and to select homologous characteristic points (i.e., landmarks) from the flower images for the subsequent GM analysis. The procedures identified 95 landmarks for each flower and thus improved the capability of describing and illustrating the flower shapes, compared with typically lower number of landmarks in 2D analyses. The GM analysis demonstrated that flower opening and dorsoventral symmetry were the principal shape variations of the flowers. The degrees of flower opening and corolla asymmetry were then subsequently quantified directly from the 3D flower images. The 3D-µCT-GM approach revealed shape variations that could not be identified using typical 2D approaches and accurately quantified the flower traits that presented a challenge in 2D images. The approach opens new avenues to investigate floral shape variations.

MicroRNA396-Targeted SHORT VEGETATIVE PHASE Is Required to Repress Flowering and Is Related to the Development of Abnormal Flower Symptoms by the Phyllody Symptoms1 Effector.

Leafy flowers are the major symptoms of peanut witches' broom (PnWB) phytoplasma infection in Catharanthus roseus. The orthologs of the phyllody symptoms1 (PHYL1) effector of PnWB from other species of phytoplasma can trigger the proteasomal degradation of several MADS box transcription factors, resulting in leafy flower formation. In contrast, the flowering negative regulator gene SHORT VEGETATIVE PHASE (SVP) was up-regulated in PnWB-infected C. roseus plants, but most microRNA (miRNA) genes had repressed expression. Coincidentally, transgenic Arabidopsis (Arabidopsis thaliana) plants expressing the PHYL1 gene of PnWB (PHYL1 plants), which show leafy flower phenotypes, up-regulate SVP of Arabidopsis (AtSVP) but repress a putative regulatory miRNA of AtSVP, miR396. However, the mechanism by which PHYL1 regulates AtSVP and miR396 is unknown, and the evidence of miR396-mediated AtSVP degradation is lacking. Here, we show that miR396 triggers AtSVP messenger RNA (mRNA) decay using genetic approaches, a reporter assay, and high-throughput degradome profiles. Genetic evidence indicates that PHYL1 plants and atmir396a-1 mutants have higher AtSVP accumulation, whereas the transgenic plants overexpressing MIR396 display lower AtSVP expression. The reporter assay indicated that target-site mutation results in decreasing the miR396-mediated repression efficiency. Moreover, degradome profiles revealed that miR396 triggers AtSVP mRNA decay rather than miRNA-mediated cleavage, implying that AtSVP caused miR396-mediated translation inhibition. We hypothesize that PHYL1 directly or indirectly interferes with miR396-mediated AtSVP mRNA decay and synergizes with other effects (e.g. MADS box transcription factor degradation), resulting in abnormal flower formation. We anticipate our findings to be a starting point for studying the posttranscriptional regulation of PHYL1 effectors in symptom development.

Effect of side chain length on intrahelical interactions between carboxylate- and guanidinium-containing amino acids.

The charge-containing hydrophilic functionalities of encoded charged amino acids are linked to the backbone via different numbers of hydrophobic methylenes, despite the apparent electrostatic nature of protein ion pairing interactions. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on ion pairing interactions, α-helical peptides containing Zbb-Xaa (i, i + 3), (i, i + 4) and (i, i + 5) (Zbb = carboxylate-containing residues Aad, Glu, Asp in decreasing length; Xaa = guanidinium residues Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by circular dichroism spectroscopy (CD). The helicity of Aad- and Glu-containing peptides was similar and mostly pH independent, whereas the helicity of Asp-containing peptides was mostly pH dependent. Furthermore, the Arg-containing peptides consistently exhibited higher helicity compared to the corresponding Agp-, Agb-, and Agh-containing peptides. Side chain conformational analysis by molecular mechanics calculations showed that the Zbb-Xaa (i, i + 3) and (i, i + 4) interactions mainly involved the χ 1 dihedral combinations (g+, g+) and (g-, g+), respectively. These low energy conformations were also observed in intrahelical Asp-Arg and Glu-Arg salt bridges of natural proteins. Accordingly, Asp and Glu provides variation in helix characteristics associated with Arg, but Aad does not provide features beyond those already delivered by Glu. Importantly, nature may have chosen the side chain length of Arg to support helical conformations through inherent high helix propensity coupled with stabilizing intrahelical ion pairing interactions with the carboxylate-containing residues.

Helix formation and capping energetics of arginine analogs with varying side chain length.

Arginine (Arg) has been used for recognizing negatively charged biological molecules, cell penetration, and oligosaccharide mass signal enhancement. The versatility of Arg has inspired the need to develop Arg analogs and to research the structural effects of incorporating Arg analogs. Accordingly, we investigated the effect of Arg side chain length on helix formation by studying 12 Ala-based peptides containing the Arg analogs (S)-2-amino-6-guanidino-hexanoic acid (Agh), (S)-2-amino-4-guanidinobutyric acid (Agb), and (S)-2-amino-3-guanidinopropionic acid (Agp). Solid phase guanidinylation with orthogonal protection strategies was necessary to synthesize Agb- and Agp-containing peptides using Fmoc-based chemistry. The fraction helix for the peptides was determined by circular dichroism spectroscopy, and used to derive the statistical mechanical parameters and energetics for N-capping, C-capping, and helix propagation (propensity). All four Arg analogs were unfavorable for N-capping. The C-cap parameter followed the trend AgpAgh, highlighting the uniqueness of the Arg side chain length in helix formation. Molecular mechanics calculations and a survey on protein structures were consistent with the experimental results. Furthermore, calculations and survey both showed that the g- conformation for the χ1 dihedral was present for the first two residues at the N-terminus of helices, but not favored in the center or C-terminus of helices due to sterics. These results should serve as the foundation for developing Arg-related bioactive compounds and technologies.

Positional effects on helical Ala-based peptides.

Helix-coil equilibrium studies are important for understanding helix formation in protein folding, and for helical foldamer design. The quantitative description of a helix using statistical mechanical models is based on experimentally derived helix propensities and the assumption that helix propensity is position-independent. To investigate this assumption, we studied a series of 19-residue Ala-based peptides, to measure the helix propensity for Leu, Phe, and Pff at positions 6, 11, and 16. Circular dichroism spectroscopy revealed that substituting Ala with a given amino acid (Leu, Phe, or Pff) resulted in the following fraction helix trend: KXaa16 > KXaa6 > KXaa11. Helix propensities for Leu, Phe, and Pff at the different positions were derived from the CD data. For the same amino acid, helix propensities were similar at positions 6 and 11, but much higher at position 16 (close to the C-terminus). A survey of protein helices revealed that Leu/Phe-Lys (i, i + 3) sequence patterns frequently occur in two structural patterns involving the helix C-terminus; however, these cases include a left-handed conformation residue. Furthermore, no Leu/Phe-Lys interaction was found except for the Lys-Phe cation-π interaction in two cases of Phe-Ala-Ala-Lys. The apparent high helix propensity at position 16 may be due to helix capping, adoption of a 310-helix near the C-terminus perhaps with Xaa-Lys (i, i + 3) interactions, or proximity to the peptide chain terminus. Accordingly, helix propensity is generally position-independent except in the presence of alternative structures or in the proximity of either chain terminus. These results should facilitate the design of helical peptides, proteins, and foldamers.