Monthly drought prediction based on ensemble models
Drought is a natural hazard, which is a result of a prolonged shortage of precipitation, high temperature and change in the weather pattern. Drought harms society, the economy and the natural environment, but it is difficult to identify and characterize. Many areas of Pakistan have suffered severe droughts during the last three decades due to changes in the weather pattern. A drought analysis with the incorporation of climate information has not yet been undertaken in this study region. Here, we propose an ensemble approach for monthly drought prediction and to define and examine wet/dry events. Initially, the drought events were identified by the short term Standardized Precipitation Index (SPI-3). Drought is predicted based on three ensemble models i.e., Equal Ensemble Drought Prediction (EEDP), Weighted Ensemble Drought Prediction (WEDP) and the Conditional Ensemble Drought Prediction (CEDP) model. Besides, two weighting procedures are used for distributing weights in the WEDP model, such as Traditional Weighting (TW) and the Weighted Bootstrap Resampling (WBR) procedure. Four copula families (i.e., Frank, Clayton, Gumbel and Joe) are used to explain the dependency relation between climate indices and precipitation in the CEDP model. Among all four copula families, the Joe copula has been found suitable for most of the times. The CEDP model provides better results in terms of accuracy and uncertainty as compared to other ensemble models for all meteorological stations. The performance of the CEDP model indicates that the climate indices are correlated with a weather pattern of four meteorological stations. Moreover, the percentage occurrence of extreme drought events that have appeared in the Multan, Bahawalpur, Barkhan and Khanpur are 1.44%, 0.57%, 2.59% and 1.71%, respectively, whereas the percentage occurrence of extremely wet events are 2.3%, 1.72%, 0.86% and 2.86%, respectively. The understanding of drought pattern by including climate information can contribute to the knowledge of future agriculture and water resource management.
Shaukat et al. (2020) Monthly drought prediction based on ensemble models. PeerJ 8:e9853 https://doi.org/10.7717/peerj.9853
Usefulness of the cytokines expression of Th1/Th2/Th17 and urinary CD80 excretion in adult-onset minimal change disease
Background Minimal change disease (MCD) is a common form of nephrotic syndrome in adults. However, the molecular mechanism underlying the pathogenesis of MCD remains incompletely understood. In this study, we aimed to investigate the role of the cytokines expression of Th1/Th2/Th17 and urinary CD80 excretion in adult-onset MCD patients. Methods The lymphocyte subsets, 34 cytokine levels of Th1/Th2/Th17, serum and urine concentrations of CD80, and expression of CD80 in glomeruli were analyzed in 28 cases (15 males and 13 females; average age: 34.1 years, age range: 18–56 years), including 10 patients with MCD in relapse, nine patients with MCD in remission and nine healthy controls. Results There was no significant difference of CD3+CD4+ cells proportion among patients with MCD in relapse, MCD in remission and healthy controls (P = 0.802). The cytokine levels of GM-CSF and tumor necrosis factor (TNF)-related activation-induced cytokine (TRANCE) in patients with MCD in relapse increased 1.5 times higher than those in remission. An evident increase in the excretion of urinary CD80 was found in patients with relapsed MCD compared with those in remission (598.4 ± 115.8 vs 81.78 ± 7.04 ng/g creatinine, P < 0.001) and healthy controls (598.4 ± 115.8 vs 67.44 ± 8.94 ng/g creatinine, P < 0.001). CD80 expression was observed in podocyte of MCD patient in relapse by immunofluorescence technique. Conclusions The cytokines GM-CSF and TRANCE are increased and the urinary CD80 levels are elevated in adult-onset MCD patients in relapse, indicating a disorder of Th1/Th2/Th17 balance and that the elevated excretion of CD80 may underlie the pathogenesis and development of adult-onset MCD.
Chen et al. (2020) Usefulness of the cytokines expression of Th1/Th2/Th17 and urinary CD80 excretion in adult-onset minimal change disease. PeerJ 8:e9854 https://doi.org/10.7717/peerj.9854
Hypercarnivorous teeth and healed injuries to Canis chihliensis from Early Pleistocene Nihewan beds, China, support social hunting for ancestral wolves
Collaborative hunting by complex social groups is a hallmark of large dogs (Mammalia: Carnivora: Canidae), whose teeth also tend to be hypercarnivorous, specialized toward increased cutting edges for meat consumption and robust p4-m1 complex for cracking bone. The deep history of canid pack hunting is, however, obscure because behavioral evidence is rarely preserved in fossils. Dated to the Early Pleistocene (>1.2 Ma), Canis chihliensis from the Nihewan Basin of northern China is one of the earliest canines to feature a large body size and hypercarnivorous dentition. We present the first known record of dental infection in C. chihliensis, likely inflicted by processing hard food, such as bone. Another individual also suffered a displaced fracture of its tibia and, despite such an incapacitating injury, survived the trauma to heal. The long period required for healing the compound fracture is consistent with social hunting and family care (food-sharing) although alternative explanations exist. Comparison with abundant paleopathological records of the putatively pack-hunting Late Pleistocene dire wolf, Canis dirus, at the Rancho La Brea asphalt seeps in southern California, U.S.A., suggests similarity in feeding behavior and sociality between Chinese and American Canis across space and time. Pack hunting in Canis may be traced back to the Early Pleistocene, well before the appearance of modern wolves, but additional evidence is needed for confirmation.
Tong et al. (2020) Hypercarnivorous teeth and healed injuries to Canis chihliensis from Early Pleistocene Nihewan beds, China, support social hunting for ancestral wolves. PeerJ 8:e9858 https://doi.org/10.7717/peerj.9858
Mechanisms of diversity maintenance in dung beetle assemblages in a heterogeneous tropical landscape
Background Anthropized landscapes play a crucial role in biodiversity conservation, as they encompass about 90% of the remaining tropical forest. Effective conservation strategies require a deep understanding of how anthropic disturbances determine diversity patterns across these landscapes. Here, we evaluated how attributes and assembly mechanisms of dung beetle communities vary across the Selva El Ocote Biosphere Reserve (REBISO) landscape. Methods Community attributes (species diversity, abundance, and biomass) were assessed at the landscape scale, using spatial windows and vegetation classes. Windows were categorized as intact, variegated, or fragmented based on their percent cover of tropical forest. The vegetation classes analyzed were tropical forest, second-growth forest, and pastures. Results We collected 15,457 individuals and 55 species. Variegated windows, tropical forests, and second-growth forests showed the highest diversity values, while the lowest values were found in intact windows and pastures. Landscape fragmentation was positively and strongly related to dung beetle diversity and negatively related to their abundance; biomass was positively associated with forest cover. Beta diversity was the primary driver of the high dung beetle diversity in the landscape analyzed. Discussion The landscape heterogeneity and its biodiversity-friendly matrix facilitate the complementarity of dung beetle assemblages in the Selva El Ocote Biosphere Reserve. Random processes govern beta diversity patterns in intact and variegated windows. Therefore, vegetation cover in the region is sufficient to maintain a continuous flow of dung beetles between forested landscape segments. However, intense anthropic disturbances acted as deterministic environmental filters in fragmented windows and pastures sites, leading to biotic homogenization processes. Our results suggest that increasing habitat variegation in highly fragmented sites is an effective strategy to prevent or buffer homogenization processes in the REBISO landscape.
Rivera et al. (2020) Mechanisms of diversity maintenance in dung beetle assemblages in a heterogeneous tropical landscape. PeerJ 8:e9860 https://doi.org/10.7717/peerj.9860
Climatic influence on the growth pattern of Panthasaurus maleriensis from the Late Triassic of India deduced from paleohistology
Metoposaurids are representatives of the extinct amphibian clade Temnospondyli, found on almost every continent exclusively in the Late Triassic deposits. Osteohistologically, it is one of the best-known temnospondyl groups, analyzed with a wide spectrum of methods, such as morphology, morphometry, bone histology or computed modelling. The least known member of Metoposauridae is Panthasaurus maleriensis from the Pranhita-Godavari basin in Central India, being geographically the most southern record of this family. For the first time the bone histology of this taxon was studied with a focus on the intraspecific variability of the histological framework and the relationship between the observed growth pattern and climatic and/or environmental conditions. The studied material includes thin-sections of five long bones, a rib, an ilium and an intercentrum belonging most likely to eight individuals ranging from different ontogenetic stages. All bones have a large medullary region with progressively increasing remodeling, surrounded by a lamellar-zonal tissue type. The primary cortex consists of parallel-fibered matrix showing various degrees of organization, less organized collagen fibers in the zones and higher organized in the annuli. Growth marks occur in the form of alternating zones and annuli in every bone except the ilium and the intercentrum. The vascularity becomes less dense towards the outermost cortex in all sampled limb bones. Towards the outermost cortex the zone thickness is decreasing, in contrast to the avascular annuli, that become thicker or are of the same thickness. The growth pattern of P. maleriensis is uniform and represents changes in ontogenetic development. Multiple resting lines are prominent in the outer annuli of the limb bones and the rib and they presumably indicate climatic and environmental influence on the growth pattern. Therefore, a prolonged phase of slowed-down growth occurred during the unfavorable phase, but a complete cessation of growth indicated by Lines of Arrested Growth (LAGs) is not recorded in the studied samples. Based on the histological framework we conclude that the climate had an impact on the growth pattern. As we do not see any LAGs in the Indian metoposaurid, we assume that the local climate was relatively mild in India during the Late Triassic. A similar prolonged phase of slowed down growth without the occurrence of LAGs was observed in Metoposaurus krasiejowensis from the Late Triassic of Krasiejów (Poland). This is in contrast to Moroccan metoposaurid Dutuitosaurus ouazzoui from the Late Triassic of Argana Basin, where LAGs are regularly deposited throughout ontogeny indicating most likely harsher climatic conditions.
Teschner et al. (2020) Climatic influence on the growth pattern of Panthasaurus maleriensis from the Late Triassic of India deduced from paleohistology. PeerJ 8:e9868 https://doi.org/10.7717/peerj.9868
Development of limb bone laminarity in the homing pigeon (Columba livia)
Background Birds show adaptations in limb bone shape that are associated with resisting locomotor loads. Whether comparable adaptations occur in the microstructure of avian cortical bone is less clear. One proposed microstructural adaptation is laminar bone in which the proportion of circumferentially-oriented vascular canals (i.e., laminarity) is large. Previous work on adult birds shows elevated laminarity in specific limb elements of some taxa, presumably to resist torsion-induced shear strain during locomotion. However, more recent analyses using improved measurements in adult birds and bats reveal lower laminarity than expected in bones associated with torsional loading. Even so, there may still be support for the resistance hypothesis if laminarity increases with growth and locomotor maturation. Methods Here, we tested that hypothesis using a growth series of 17 homing pigeons (15–563 g). Torsional rigidity and laminarity of limb bones were measured from histological sections sampled from midshaft. Ontogenetic trends in laminarity were assessed using principal component analysis to reduce dimensionality followed by beta regression with a logit link function. Results We found that torsional rigidity of limb bones increases disproportionately with growth, consistent with rapid structural compensation associated with locomotor maturation. However, laminarity decreases with maturity, weakening the hypothesis that high laminarity is a flight adaptation at least in the pigeon. Instead, the histological results suggest that low laminarity, specifically the relative proportion of longitudinal canals aligned with peak principal strains, may better reflect the loading history of a bone.
McGuire et al. (2020) Development of limb bone laminarity in the homing pigeon (Columba livia). PeerJ 8:e9878 https://doi.org/10.7717/peerj.9878
Spatial ecology of little egret (Egretta garzetta) in Hong Kong uncovers preference for commercial fishponds
Many natural wetlands have been converted to human-influenced wetlands. In some instances, human-influenced wetlands could provide complementary habitats for waterbirds, compensating for the loss of natural wetlands. Inner Deep Bay in Hong Kong is composed of both natural and human-influenced wetlands and is under immense development pressure. From an ecology perspective, we need to understand if different wetland types play the same ecological role. To achieve this, we tracked nine little egrets (Egretta garzetta) using GPS loggers for 14 months to study their spatial ecology, home range, movement and habitat use. We found that over 88% of the home range of all individuals comprised of wetlands (commercial fishponds, mangrove, gei wai, channel, and intertidal mudflat). Among these wetland types, nearly all (seven of nine) individuals preferred commercial fishponds over other habitats in all seasons. Little egrets exhibited seasonal movement and habitat use among seasons, with largest home range, greatest movement, and most frequent visits to commercial fishponds in winter compared to spring and autumn. Our results highlight the significant role of commercial fishponds, providing a feeding ground for little egrets. However, other wetland types cannot be ignored, as they were also used considerably. These findings underscore the importance of maintaining a diversity of wetland types as alternative foraging and breeding habitats.
Pang et al. (2020) Spatial ecology of little egret (Egretta garzetta) in Hong Kong uncovers preference for commercial fishponds. PeerJ 8:e9893 https://doi.org/10.7717/peerj.9893
Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan City, China, late in December 2019 is an example of an emerging zoonotic virus that threatens public health and international travel and commerce. When such a virus emerges, there is often insufficient specific information available on mechanisms of virus dissemination from animal-to-human or from person-to-person, on the level or route of infection transmissibility or of viral release in body secretions/excretions, and on the survival of virus in aerosols or on surfaces. The effectiveness of available virucidal agents and hygiene practices as interventions for disrupting the spread of infection and the associated diseases may not be clear for the emerging virus. In the present review, we suggest that approaches for infection prevention and control (IPAC) for SARS-CoV-2 and future emerging/re-emerging viruses can be invoked based on pre-existing data on microbicidal and hygiene effectiveness for related and unrelated enveloped viruses.
Ijaz et al. (2020) Combating SARS-CoV-2: leveraging microbicidal experiences with other emerging/re-emerging viruses. PeerJ 8:e9914 https://doi.org/10.7717/peerj.9914
Overexpression of KIAA1199 is an independent prognostic marker in laryngeal squamous cell carcinoma
Background KIAA1199 is a recently identified novel gene that is upregulated in various human cancers with poor survival, but its role and the underlying mechanisms in laryngeal squamous cell carcinoma (LSCC) remain unknown. Here, we collected tissues from 105 cases of LSCC to investigate the relationships between KIAA1199 protein expression and clinical factors. Methods Western blotting and real-time quantitative PCR (RT-PCR) were used for detect the protein and mRNA expression of KIAA1199 in LSCC tissue. Immunohistochemistry (IHC) staining was used to detect the expression of KIAA1199. Patient clinical information, for instance sex, age, pathological differentiation, clinical region, T stage, N stage, clinical stage, operation type, neck lymph dissection, smoking status, and drinking status were recorded. Kaplan–Meier survival analysis and Cox analysis were applied to identify the relationship between KIAA1199 and LSCC. Results Western blotting results showed KIAA1199 protein was significantly higher in tumor tissues vs. adjacent non-cancerous tissues (0.9385 ± 0.1363 vs. 1.838 ± 0.3209, P = 0.04). The KIAA1199 mRNA expression was considerably higher in tumor tissues (P < 0.001) than in adjacent non-cancerous tissues by RT-PCR. IHC results showed up-regulated KIAA1199 expression was related with some severe clinicopathological parameters: pathologic differentiation (P = 0.002), T stage (P < 0.001), N stage (P < 0.001), clinical stage (P < 0.001), survival time (P = 0.008) and survival status (P < 0.001). Kaplan–Meier survival analysis showed that patients with high KIAA1199 protein expression had poor overall survival (OS) (P < 0.05). Cox analysis suggested that the KIAA1199 protein expression constituted an independent prognostic marker for LSCC patients (P < 0.001). Conclusion Our findings revealed that KIAA1199 protein expression may be used to predict LSCC patient outcome.
Huang et al. (2020) Overexpression of KIAA1199 is an independent prognostic marker in laryngeal squamous cell carcinoma. PeerJ 8:e9637 https://doi.org/10.7717/peerj.9637
Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A
Candida parapsilosis is a major fungal pathogen that leads to sepsis. New and more effective antifungal agents are required due to the emergence of resistant fungal strains. MAF-1A is a cationic antifungal peptide isolated from Musca domestica that is effective against a variety of Candida species. However, the mechanism(s) of its antifungal activity remains undefined. Here, we used RNA-seq to identify differentially expressed genes (DEGs) in Candida parapsilosis following MAF-1A exposure. The early (6 h) response included 1,122 upregulated and 1,065 downregulated genes. Late (18 h) responses were associated with the increased expression of 101 genes and the decreased expression of 151 genes. Upon MAF-1A treatment for 18 h, 42 genes were upregulated and 25 genes were downregulated. KEGG enrichment showed that the DEGs in response to MAF-1A were mainly involved in amino acid synthesis and metabolism, oxidative phosphorylation, sterol synthesis, and apoptosis. These results indicate that MAF-1A exerts antifungal activity through interference with Candida parapsilosis cell membrane integrity and organelle function. This provides new insight into the interaction between Candida parapsilosis and this antimicrobial peptide and serves as a reference for future Candida parapsilosis therapies.
Cheng et al. (2020) Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A. PeerJ 8:e9767 https://doi.org/10.7717/peerj.9767