covid19.Explorer: a web application and R package to explore United States COVID-19 data
Appearing at the end of 2019, a novel virus (later identified as SARS-CoV-2) was characterized in the city of Wuhan in Hubei Province, China. As of the time of writing, the disease caused by this virus (known as COVID-19) has already resulted in over three million deaths worldwide. SARS-CoV-2 infections and deaths, however, have been highly unevenly distributed among age groups, sexes, countries, and jurisdictions over the course of the pandemic. Herein, I present a tool (the covid19.Explorer R package and web application) that has been designed to explore and analyze publicly available United States COVID-19 infection and death data from the 2020/21 U.S. SARS-CoV-2 pandemic. The analyses and visualizations that this R package and web application facilitate can help users better comprehend the geographic progress of the pandemic, the effectiveness of non-pharmaceutical interventions (such as lockdowns and other measures, which have varied widely among U.S. states), and the relative risks posed by COVID-19 to different age groups within the U.S. population. The end result is an interactive tool that will help its users develop an improved understanding of the temporal and geographic dynamics of the SARS-CoV-2 pandemic, accessible to lay people and scientists alike.
Revell (2021) covid19.Explorer: a web application and R package to explore United States COVID-19 data. PeerJ 9:e11489 https://doi.org/10.7717/peerj.11489
Alterations in brain structure and function in patients with osteonecrosis of the femoral head: a multimodal MRI study
Background Pain, a major symptom of osteonecrosis of the femoral head (ONFH), is a complex sensory and emotional experience that presents therapeutic challenges. Pain can cause neuroplastic changes at the cortical level, leading to central sensitization and difficulties with curative treatments; however, whether changes in structural and functional plasticity occur in patients with ONFH remains unclear. Methods A total of 23 ONFH inpatients who did not undergo surgery (14 males, nine females; aged 55.61 ± 13.79 years) and 20 controls (12 males, eight females; aged 47.25 ± 19.35 years) were enrolled. Functional indices of the amplitude of low-frequency fluctuation (ALFF), regional homogeneity (ReHo), and a structural index of tract-based spatial statistics (TBSS) were calculated for each participant. The probability distribution of fiber direction was determined according to the ALFF results. Results ONFH patients demonstrated increased ALFF in the bilateral dorsolateral superior frontal gyrus, right medial superior frontal gyrus, right middle frontal gyrus, and right supplementary motor area. In contrast, ONFH patients showed decreased ReHo in the left superior parietal gyrus and right inferior temporal gyrus. There were no significant differences in TBSS or probabilistic tractography. Conclusion These results indicate cerebral pain processing in ONFH patients. It is advantageous to use functional magnetic resonance imaging to better understand pain pathogenesis and identify new therapeutic targets in ONFH patients.
Ma et al. (2021) Alterations in brain structure and function in patients with osteonecrosis of the femoral head: a multimodal MRI study. PeerJ 9:e11759 https://doi.org/10.7717/peerj.11759
A molecular phylogeny of the Chinese Sinopoda spiders (Sparassidae, Heteropodinae): implications for taxonomy
Sinopoda spiders are a diverse group with limited dispersal ability. They are remarkably sympatric among related species, which often results in misidentification and incorrect matching of sexes. In order to understand the evolutionary relationships and revise the taxonomy problems in this genus, we offer the first molecular phylogeny of Sinopoda. Our results strongly support the monophyly of Sinopoda and its sister relationship with Spariolenus and reject the monophyly of the S. okinawana species group. We establish three new species groups based on both molecular and morphological data. Our phylogeny also illuminates some taxonomic issues and clarifies some species limits: (1) Supporting the newly revised matching of sexes in S. longiducta and S. yaanensis by Zhong et al. (2019). (2) The original description of S. campanacea was based on mismatched sexes. S. changde is proposed as a junior synonymy of S. campanacea, while the original female ‘S. campanacea’ is here described as a new species: S. papilionaceous Liu sp. nov. (3) The type series of S. serpentembolus contains mismatched sexes. The female is considered as S. campanacea, while we here report the correctly matched females of S. serpentembolus. (4) We describe one additional new species: S. wuyiensis Liu sp. nov. Our first molecular phylogeny of Sinopoda provides a tool for comparative analyses and a solid base for the future biodiversity and taxonomic work on the genus.
Zhang et al. (2021) A molecular phylogeny of the Chinese Sinopoda spiders (Sparassidae, Heteropodinae): implications for taxonomy. PeerJ 9:e11775 https://doi.org/10.7717/peerj.11775
Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer
Background Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Both 3D digitizer arms and structured light surface scanners are portable, easy to use, and relatively cheap, which makes these two capturing devices obvious choices for geometric morphometrics. While digitizer arms have been the “gold standard”, benefits of having full 3D models are manifold. We assessed the measurement error and investigate bias associated with the use of an open-source, high-resolution structured light scanner called SeeMaLab against the popular Microscribe 3D digitizer arm. Methodology The analyses were based on 22 grey seal (Halichoerus grypus) skulls. 31 fixed anatomical landmarks were annotated both directly using a Microscribe 3D digitizer and on reconstructed 3D digital models created from structured light surface scans. Each skull was scanned twice. Two operators annotated the landmarks, each twice on all the skulls and 3D models, allowing for the investigation of multiple sources of measurement error. We performed multiple Procrustes ANOVAs to compare the two devices in terms of within- and between-operator error, to quantify the measurement error induced by device, to compare between-device error with other sources of variation, and to assess the level of scanning-related error. We investigated the presence of general shape bias due to device and operator. Results Similar precision was obtained with both devices. If landmarks that were identified as less clearly defined and thus harder to place were omitted, the scanner pipeline would achieve higher precision than the digitizer. Between-operator error was biased and seemed to be smaller when using the scanner pipeline. There were systematic differences between devices, which was mainly driven by landmarks less clearly defined. The factors device, operator and landmark replica were all statistically significant and of similar size, but were minor sources of total shape variation, compared to the biological variation among grey seal skulls. The scanning-related error was small compared to all other error sources. Conclusions As the scanner showed precision similar to the digitizer, a scanner should be used if the advantages of obtaining detailed 3D models of a specimen are desired. To obtain high precision, a pre-study should be conducted to identify difficult landmarks. Due to the observed bias, data from different devices and/or operators should not be combined when the expected biological variation is small, without testing the landmarks for repeatability across platforms and operators. For any study necessitating the combination of landmark measurements from different operators, the scanner pipeline will be better suited. The small scanning-related error indicates that by following the same scanning protocol, different operators can be involved in the scanning process without introducing significant error.
Messer et al. (2021) Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer. PeerJ 9:e11804 https://doi.org/10.7717/peerj.11804
Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa
Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa. Methods Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced. Results This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this study do not match those from specimens in China and India, respectively. Further research is required to resolve the species complexes detected and also to refine the use of names by fishermen over a wider geographic range.
Simon et al. (2021) Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa. PeerJ 9:e11847 https://doi.org/10.7717/peerj.11847
Association of serum fetuin-B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide
Background and Aims Fetuin-B has been reported to be involved in glucose and lipid metabolism and associated with the occurrence of diabetes. The main purpose of this study is to explore the changes of circulating fetuin-B in young women with pre-diabetes and to analyze the relationship between fetuin-B and the occurrence and development of IR. Methods A total of 304 women were enrolled in this study and subjected to both OGTT and EHC. A subgroup of 26 overweight/obese womenwas treated with Lira for 24 weeks. serum fetuin-B concentrations were measured by ELISA. Results In IGT and IR-NG groups, serum fetuin-B levels were higher than those in the NGT group. The serum fetuin-B levels in the IGT group were higher than those in the IR-NG group. serum fetuin-B was positively correlated with BMI, WHR, 2h-BG, FIns, HbA1c, and HOMA2-IR, but negatively correlated with the M-value in all study populations. Multiple stepwise regression analysis showed that the M-value was independently and inversely associated with serum fetuin-B. Logistic regression analysis showed that serum fetuin-B was independently associated with IGT and significantly increased the risk of IGT. During the OGTT, serum fetuin-B increased significantly in the NGT group, but there were no significant changes in other groups. During the EHC, serum fetuin-B increased in the IGT group, but there was no change in other groups. After Lira intervention, serum fetuin-B decreased significantly in IGT women. Conclusions serum fetuin-B levels are elevated in young women with IR or IGT and may be associated with IR.
Xia et al. (2021) Association of serum fetuin-B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide. PeerJ 9:e11869 https://doi.org/10.7717/peerj.11869
Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb
Background Anecdotally, people living with Complex Regional Pain Syndrome (CRPS) often report difficulties in localising their own affected limb when it is out of view. Experimental attempts to investigate this report have used explicit tasks and yielded varied results. Methods Here we used a limb localisation task that interrogates implicit mechanisms because we first induce a compelling illusion called the Disappearing Hand Trick (DHT). In the DHT, participants judge their hands to be close together when, in fact, they are far apart. Sixteen volunteers with unilateral upper limb CRPS (mean age 39 ± 12 years, four males), 15 volunteers with non-CRPS persistent hand pain (‘pain controls’; mean age 58 ± 13 years, two males) and 29 pain-free volunteers (‘pain-free controls’; mean age 36 ± 19 years, 10 males) performed a hand-localisation task after each of three conditions: the DHT illusion and two control conditions in which no illusion was performed. The conditions were repeated twice (one for each hand). We hypothesised that (1) participants with CRPS would perform worse at hand self-localisation than both the control samples; (2) participants with non-CRPS persistent hand pain would perform worse than pain-free controls; (3) participants in both persistent pain groups would perform worse with their affected hand than with their unaffected hand. Results Our first two hypotheses were not supported. Our third hypothesis was supported —when visually and proprioceptively encoded positions of the hands were incongruent (i.e. after the DHT), relocalisation performance was worse with the affected hand than it was with the unaffected hand. The similar results in hand localisation in the control and pain groups might suggest that, when implicit processes are required, people with CRPS’ ability to localise their limb is preserved.
Bellan et al. (2021) Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb. PeerJ 9:e11882 https://doi.org/10.7717/peerj.11882
Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia
Background Schizophrenia is a severely multifactorial neuropsychiatric disorder, and the majority of cases are due to genetic variations. In this study, we evaluated the genetic association between the C-Maf-inducing protein (CMIP) gene and schizophrenia in the Han Chinese population. Methods In this case-control study, 761 schizophrenia patients and 775 healthy controls were recruited. Tag single-nucleotide polymorphisms (SNPs; rs12925980, rs2287112, rs3751859 and rs77700579) from the CMIP gene were genotyped via matrix-assisted laser desorption/ionization time of flight mass spectrometry. We used logistic regression to estimate the associations between the genotypes/alleles of each SNP and schizophrenia in males and females, respectively. The in-depth link between CMIP and schizophrenia was explored through linkage disequilibrium (LD) and further haplotype analyses. False discovery rate correction was utilized to control for Type I errors caused by multiple comparisons. Results There was a significant difference in rs287112 allele frequencies between female schizophrenia patients and healthy controls after adjusting for multiple comparisons (χ2 = 12.296, Padj = 0.008). Females carrying minor allele G had 4.445 times higher risk of schizophrenia compared with people who carried the T allele (OR = 4.445, 95% CI [1.788–11.046]). Linkage-disequilibrium was not observed in the subjects, and people with haplotype TTGT of rs12925980–rs2287112–rs3751859–rs77700579 had a lower risk of schizophrenia (OR = 0.42, 95% CI [0.19–0.94]) when compared with CTGA haplotypes. However, the association did not survive false discovery rate correction. Conclusion This study identified a potential CMIP variant that may confer schizophrenia risk in the female Han Chinese population.
Fu et al. (2021) Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia. PeerJ 9:e11907 https://doi.org/10.7717/peerj.11907
Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish
From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
Cárcamo-Tejer et al. (2021) Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish. PeerJ 9:e11917 https://doi.org/10.7717/peerj.11917
A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China
Brachiosauridae is a lineage of titanosauriform sauropods that includes some of the most iconic non-avian dinosaurs. Undisputed brachiosaurid fossils are known from the Late Jurassic through the Early Cretaceous of North America, Africa, and Europe, but proposed occurrences outside this range have proven controversial. Despite occasional suggestions that brachiosaurids dispersed into Asia, to date no fossils have provided convincing evidence for a pan-Laurasian distribution for the clade, and the failure to discover brachiosaurid fossils in the well-sampled sauropod-bearing horizons of the Early Cretaceous of Asia has been taken to evidence their genuine absence from the continent. Here we report on an isolated sauropod maxilla from the middle Cretaceous (Albian–Cenomanian) Longjing Formation of the Yanji basin of northeast China. Although the specimen preserves limited morphological information, it exhibits axially twisted dentition, a shared derived trait otherwise known only in brachiosaurids. Referral of the specimen to the Brachiosauridae receives support from phylogenetic analysis under both equal and implied weights parsimony, providing the most convincing evidence to date that brachiosaurids dispersed into Asia at some point in their evolutionary history. Inclusion in our phylogenetic analyses of an isolated sauropod dentary from the same site, for which an association with the maxilla is possible but uncertain, does not substantively alter these results. We consider several paleobiogeographic scenarios that could account for the occurrence of a middle Cretaceous Asian brachiosaurid, including dispersal from either North America or Europe during the Early Cretaceous. The identification of a brachiosaurid in the Longshan fauna, and the paleobiogeographic histories that could account for its presence there, are hypotheses that can be tested with continued study and excavation of fossils from the Longjing Formation.
Liao et al. (2021) A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China. PeerJ 9:e11957 https://doi.org/10.7717/peerj.11957