bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iterative data-driven forecasting of the transmission and management of SARS-CoV-2/COVID-19 using social interventions at the county-level
Authors: Newcomb Ken , Smith Morgan E. , Donohue Rose E. , Wyngaard Sebastian , Reinking Caleb , Sweet Christopher R. , Levine Marissa J. , Unnasch Thomas R. , Michael Edwin 
Published: January 2022

AbstractThe control of the initial outbreak and spread of SARS-CoV-2/COVID-19 via the application of population-wide non-pharmaceutical mitigation measures have led to remarkable successes in dampening the pandemic globally. However, with countries beginning to ease or lift these measures fully to restart activities, concern is growing regarding the impacts that such reopening of societies could have on the subsequent transmission of the virus. While mathematical models of COVID-19 transmission have played important roles in evaluating the impacts of these measures for curbing virus transmission, a key need is for models that are able to effectively capture the effects of the spatial and social heterogeneities that drive the epidemic dynamics observed at the local community level. Iterative forecasting that uses new incoming epidemiological and social behavioral data to sequentially update locally-applicable transmission models can overcome this gap, potentially resulting in better predictions and policy actions. Here, we present the development of one such data-driven iterative modelling tool based on publicly available data and an extended SEIR model for forecasting SARS-CoV-2 at the county level in the United States. Using data from the state of Florida, we demonstrate the utility of such a system for exploring the outcomes of the social measures proposed by policy makers for containing the course of the pandemic. We provide comprehensive results showing how the locally identified models could be employed for accessing the impacts and societal tradeoffs of using specific social protective strategies. We conclude that it could have been possible to lift the more disruptive social interventions related to movement restriction/social distancing measures earlier if these were accompanied by widespread testing and contact tracing. These intensified social interventions could have potentially also brought about the control of the epidemic in low- and some medium-incidence county settings first, supporting the development and deployment of a geographically-phased approach to reopening the economy of Florida. We have made our data-driven forecasting system publicly available for policymakers and health officials to use in their own locales, so that a more efficient coordinated strategy for controlling SARS-CoV-2 region-wide can be developed and successfully implemented.
Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians
Authors: Kundu Shantanu , Pakrashi Avas , Kamalakannan Manokaran , Singha Devkant , Tyagi Kaomud , Banerjee Dhriti , Venkatraman Chinnadurai , Kumar Vikas 
Published: January 2022

AbstractThe Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome ofT. nicobaricato elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, exceptnad6and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found inT. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering ofT. nicobaricawith high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The16S rRNAdataset corroborates the taxonomic rank of two subspecies ofT. nicobaricafrom the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.
Morphological and vascular characteristics of the optic nerve head of normal guinea pigs
Authors: Guo Lei , Tao Jun , Tong Yang , Chen Shichao , Zhao Xin , Hua Rui 
Published: January 2022

AbstractThe morphological and vascular characteristics of the optic nerve head (ONH) of normal guinea pigs have not been fully recognized. Therefore, we aimed to investigate them using optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA). We measured the refractive error, axial length, and intraocular pressure (IOP) and performed OCT and OCTA of the ONH of 3- and 4-week-old tricolour guinea pigs. A total of 208 right eyes from 208 normal guinea pigs were examined. The refractive error (both myopic and hyperopic) of the 3-week group was significantly higher than that of the 4-week group (p < 0.001), the IOP of the 3-week group was significantly lower than that of the 4-week group (p = 0.014), and the circumpapillary retinal nerve fibre layer (cpRNFL) of the 3-week group was significantly thicker than that of the 4-week group (p = 0.048). There were no significant differences in the average vessel area, vascular density, total number of junctions, total vessel length, total number of endpoints, and vascular diameter between the two groups. However, an age-adjusted linear regression analysis revealed that the total vessel length was positively associated with the cpRNFL thickness (p = 0.024) and negatively associated with IOP (p = 0.016). This is the first report on morphological and vascular characteristics of the ONH in normal guinea pigs based on in vivo OCT and OCTA imaging and quantification of ONH parameters. These results may contribute to further research on myopia using guinea pig models.
Morphologic, genetic, and biogeographic continua among subspecies hinder the conservation of threatened taxa: the case of Centaurea aspera ssp. scorpiurifolia (Asteraceae)
Authors: Garmendia Alfonso , Merle Hugo , Sanía Marta , López Carmelo , Ferriol María 
Published: January 2022

AbstractSubspecies are widely included as conservation units because of their potential to become new species. However, their practical recognition includes variable criteria, such as morphological, genetic, geographic and other differences. Centaurea aspera ssp. scorpiurifolia is a threatened taxon endemic to Andalusia (Spain), which coexists in most of its distribution area with similar taxa. Because of the difficulty to identify it using morphology alone, we aimed to sample all the populations cited as ssp. scorpiurifolia as exhaustively as possible, morphologically characterise them, and analyse their genetic structuring using microsatellites, to better understand difficulties when conserving subspecies. Three different Centaurea species were found which were easily identified. Within C. aspera, two genetic populations and some admixed individuals were observed, one including ssp. scorpiurifolia individuals and the other including individuals identified as subspecies aspera, stenophylla, and scorpiurifolia. A morphological continuum between these two genetic populations and a wide overlapping of their biogeographic distribution were also found. This continuum can affect the conservation of ssp. scorpiurifolia because of potential misidentifications and harmful effects of subspecific hybridization. Misidentifications could be partly overcome by using as many different traits as possible, and conservation priority should be given to populations representative of the ends of this continuum.
Machine learning assisted real-time deformability cytometry of CD34+ cells allows to identify patients with myelodysplastic syndromes
Authors: Herbig Maik , Jacobi Angela , Wobus Manja , Weidner Heike , Mies Anna , Kräter Martin , Otto Oliver , Thiede Christian , Weickert Marie‑Theresa , Götze Katharina S. , Rauner Martina , Hofbauer Lorenz C. , Bornhäuser Martin , Guck Jochen , Ader Marius , Platzbecker Uwe , Balaian Ekaterina 
Published: January 2022

AbstractDiagnosis of myelodysplastic syndrome (MDS) mainly relies on a manual assessment of the peripheral blood and bone marrow cell morphology. The WHO guidelines suggest a visual screening of 200 to 500 cells which inevitably turns the assessor blind to rare cell populations and leads to low reproducibility. Moreover, the human eye is not suited to detect shifts of cellular properties of entire populations. Hence, quantitative image analysis could improve the accuracy and reproducibility of MDS diagnosis. We used real-time deformability cytometry (RT-DC) to measure bone marrow biopsy samples of MDS patients and age-matched healthy individuals. RT-DC is a high-throughput (1000 cells/s) imaging flow cytometer capable of recording morphological and mechanical properties of single cells. Properties of single cells were quantified using automated image analysis, and machine learning was employed to discover morpho-mechanical patterns in thousands of individual cells that allow to distinguish healthy vs. MDS samples. We found that distribution properties of cell sizes differ between healthy and MDS, with MDS showing a narrower distribution of cell sizes. Furthermore, we found a strong correlation between the mechanical properties of cells and the number of disease-determining mutations, inaccessible with current diagnostic approaches. Hence, machine-learning assisted RT-DC could be a promising tool to automate sample analysis to assist experts during diagnosis or provide a scalable solution for MDS diagnosis to regions lacking sufficient medical experts.
Differential expression of CD11c defines two types of tissue-resident macrophages with different origins in steady-state salivary glands
Authors: Lu Lu , Kuroishi Toshinobu , Tanaka Yukinori , Furukawa Mutsumi , Nochi Tomonori , Sugawara Shunji 
Published: January 2022

AbstractGland macrophages are primed for gland development and functions through interactions within their niche. However, the phenotype, ontogeny, and function of steady-state salivary gland (SG) macrophages remain unclear. We herein identified CD11c+and CD11c−subsets among CD64+macrophages in steady-state murine SGs. CD11c−macrophages were predominant in the SGs of embryonic and newborn mice and decreased with advancing age. CD11c+macrophages were rarely detected in the embryonic period, but rapidly expanded after birth. CD11c+, but not CD11c−, macrophage numbers decreased in mice treated with a CCR2 antagonist, suggesting that CD11c+macrophages accumulate from bone marrow-derived progenitors in a CCR2-dependent manner, whereas CD11c−macrophages were derived from embryonic progenitors in SGs. CD11c+and CD11c−macrophages strongly expressed colony-stimulating factor (CSF)-1 receptor, the injection of an anti-CSF-1 receptor blocking antibody markedly reduced both subsets, and SGs strongly expressed CSF-1, indicating the dependency of SG resident macrophage development on CSF-1. The phagocytic activity of SG macrophages was extremely weak; however, the gene expression profile of SG macrophages indicated that SG macrophages regulate gland development and functions in SGs. These results suggest that SG CD11c+and CD11c−macrophages are developed and instructed to perform SG-specific functions in steady-state SGs.
Chemotherapy significantly improves long-term survival of small lesion node negative metaplastic breast carcinoma in T1c population rather than T1a and T1b
Authors: Chen Qitong , Zhou Qin , He Hongye , He Yeqing , Yuan Yunchang , Zou Qiongyan , Yi Wenjun 
Published: January 2022

AbstractMetaplastic breast carcinoma (MpBC) is considered a highly aggressive disease, the outcome of chemotherapy on small lesions (T1abcN0M0) MpBC patients remain unclear. We identified 890 female MpBC patients in the Surveillance, Epidemiology, and End Results (SEER) database from 2000 to 2016. After propensity score matching (PSM), 584 patients were matched. Survival probability was compared among T1a, T1b, and T1c patients and between patients with and without chemotherapy using Kaplan–Meier analysis and Cox proportional hazard analysis. Significance was set at two-sided P < 0.05. We classified 49, 166, and 675 patients as T1a, T1b, and T1c MpBC, respectively. The chemotherapy group included 404 patients (45.4%). Following PSM, survival analysis indicated that the patients who underwent chemotherapy had higher OS (P = 0.0002) and BCSS (P = 0.0276) in the T1c substage, but no significant difference was detected in T1a or T1b patients. In this population-based study, small lesion MpBC showed a favorable prognosis. Chemotherapy improved the prognosis of T1c MpBC patients but not T1a and T1b patients to a beneficial extent. Our findings may offer novel insight into a therapeutic strategy for MpBC.
Identification of stomatal-regulating molecules from de novo arylamine collection through aromatic C–H amination
Authors: Toda Yosuke , Perry Gregory J. P. , Inoue Shimpei , Ito Eri , Kawakami Takahiro , Narouz Mina R. , Takahashi Koji , Aihara Yusuke , Maeda Bumpei , Kinoshita Toshinori , Itami Kenichiro , Murakami Kei 
Published: January 2022

AbstractStomata—small pores generally found on the leaves of plants—control gas exchange between plant and the atmosphere. Elucidating the mechanism that underlies such control through the regulation of stomatal opening/closing is important to understand how plants regulate photosynthesis and tolerate against drought. However, up-to-date, molecular components and their function involved in stomatal regulation are not fully understood. We challenged such problem through a chemical genetic approach by isolating and characterizing synthetic molecules that influence stomatal movement. Here, we describe that a small chemical collection, prepared during the development of C–H amination reactions, lead to the discovery of a Stomata Influencing Molecule (SIM); namely, a sulfonimidated oxazole that inhibits stomatal opening. The starting molecule SIM1 was initially isolated from screening of compounds that inhibit light induced opening of dayflower stomata. A range of SIM molecules were rapidly accessed using our state-of-the-art C–H amination technologies. This enabled an efficient structure–activity relationship (SAR) study, culminating in the discovery of a sulfonamidated oxazole derivative (SIM*) having higher activity and enhanced specificity against stomatal regulation. Biological assay results have shed some light on the mode of action of SIM molecules within the cell, which may ultimately lead to drought tolerance-conferring agrochemicals through the control of stomatal movement.
Maternal postpartum depressive symptoms partially mediate the association between preterm birth and mental and behavioral disorders in children
Authors: Girchenko Polina , Robinson Rachel , Rantalainen Ville Juhani , Lahti-Pulkkinen Marius , Heinonen-Tuomaala Kati , Lemola Sakari , Wolke Dieter , Schnitzlein Daniel , Hämäläinen Esa , Laivuori Hannele , Villa Pia M. , Kajantie Eero , Räikkönen Katri 
Published: January 2022

AbstractPreterm birth has been linked with postpartum depressive (PPD) disorders and high symptom levels, but evidence remains conflicting and limited in quality. It remains unclear whether PPD symptoms of mothers with preterm babies were already elevated before childbirth, and whether PPD symptoms mediate/aggravate the effect of preterm birth on child mental disorders. We examined whether preterm birth associated with maternal PPD symptoms, depressive symptoms trajectories from antenatal to postpartum stage, and whether PPD symptoms mediated/aggravated associations between preterm birth and child mental disorders. Mothers of preterm (n = 125) and term-born (n = 3033) children of the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction study reported depressive symptoms four times within 8 weeks before and twice within 12 months after childbirth. Child mental and behavioral disorder diagnoses until age 8.4–12.8 years came from medical register. Preterm birth associated with higher PPD symptoms (mean difference = 0.19 SD, 95% CI 0.01, 0.37, p = 0.04), and higher odds (odds ratio = 2.23, 95% CI 1.22, 4.09, p = 0.009) of the mother to belong to a group that had consistently high depressive symptoms levels trajectory from antenatal to postpartum stage. PPD symptoms partially mediated and aggravated the association between preterm birth and child mental disorders. Preterm birth, maternal PPD symptoms and child mental disorders are associated, calling for timely prevention interventions.
Dissipation of mesoscale eddies at a western boundary via a direct energy cascade
Authors: Evans D. Gwyn , Frajka-Williams Eleanor , Naveira Garabato Alberto C. 
Published: January 2022

AbstractThe fate of mesoscale eddy kinetic energy represents a large source of uncertainty in the global ocean energy budget. Satellite altimetry suggests that mesoscale eddies vanish at ocean western boundaries. However, the fate of the eddies’ kinetic energy remains poorly known. Here we show that the generation of small-scale turbulence as eddy flow impinges on the steep and corrugated slope of an ocean western boundary plays a dominant role in the regional decay of mesoscale eddy kinetic energy. We compare altimetry-based estimates of mesoscale eddy kinetic energy decline with measurements of turbulent dissipation. Mesoscale eddies are found to decay at a rate of 0.016 ± 0.012 GW and 0.023 ± 0.017 GW for anticyclonic and cyclonic eddies, respectively, similar to the observed turbulent dissipation rate of 0.020 ± 0.011 GW. This demonstrates that a major direct transfer of mesoscale eddy kinetic energy to small, dissipative scales can be effectively triggered by the eddies’ interaction with the western boundary topography.
Automated evaluation of retinal pigment epithelium disease area in eyes with age-related macular degeneration
Authors: Motozawa Naohiro , Miura Takuya , Ochiai Koji , Yamamoto Midori , Horinouchi Takaaki , Tsuzuki Taku , Kanda Genki N. , Ozawa Yosuke , Tsujikawa Akitaka , Takahashi Koichi , Takahashi Masayo , Kurimoto Yasuo , Maeda Tadao , Mandai Michiko 
Published: January 2022

AbstractThe retinal pigment epithelium (RPE) is essential for the survival and function of retinal photoreceptor cells. RPE dysfunction causes various retinal diseases including age-related macular degeneration (AMD). Clinical studies on ES/iPS cell-derived RPE transplantation for RPE dysfunction-triggered diseases are currently underway. Quantification of the diseased RPE area is important to evaluate disease progression or the therapeutic effect of RPE transplantation. However, there are no standard protocols. To address this issue, we developed a 2-step software that enables objective and efficient quantification of RPE-disease area changes by analyzing the early-phase hyperfluorescent area in fluorescein angiography (FA) images. We extracted the Abnormal region. This extraction was based on deep learning-based discrimination. We scored the binarized extracted area using an automated program. Our program’s performance for the same eye from the serial image captures was within 3.1 ± 7.8% error. In progressive AMD, the trend was consistent with human assessment, even when FA images from two different visits were compared. This method was applicable to quantifying RPE-disease area changes over time, evaluating iPSC-RPE transplantation images, and a disease other than AMD. Our program may contribute to the assessment of the clinical course of RPE-disease areas in routine clinics and reduce the workload of researchers.
Designing a multilayer film via machine learning of scientific literature
Authors: Fukada Kenta , Seyama Michiko 
Published: January 2022

AbstractScientists who design chemical substances often use materials informatics (MI), a data-driven approach with either computer simulation or artificial intelligence (AI). MI is a valuable technique, but applying it to layered structures is difficult. Most of the proposed computer-aided material search techniques use atomic or molecular simulations, which are limited to small areas. Some AI approaches have planned layered structures, but they require a physical theory or abundant experimental results. There is no universal design tool for multilayer films in MI. Here, we show a multilayer film can be designed through machine learning (ML) of experimental procedures extracted from chemical-coating articles. We converted material names according to International Union of Pure and Applied Chemistry rules and stored them in databases for each fabrication step without any physicochemical theory. Compared with experimental results which depend on authors, experimental protocol is superiority at almost unified and less data loss. Connecting scientific knowledge through ML enables us to predict untrained film structures. This suggests that AI imitates research activity, which is normally inspired by other scientific achievements and can thus be used as a general design technique.
Effectiveness of negative pressure wound therapy with instillation and dwelling after stoma closure: a retrospective and propensity score matching analysis
Authors: Yane Yoshinori , Hida Jin-ichi , Chiba Yasutaka , Makutani Yusuke , Ushijima Hokuto , Yoshioka Yasumasa , Iwamoto Masayoshi , Wada Toshiaki , Daito Koji , Tokoro Tadao , Ueda Kazuki , Kawamura Junichiro 
Published: January 2022

AbstractThe use of temporary diverting stoma has become more common in low colorectal anastomosis to reduce anastomotic complications. Surgical site infection (SSI) at the stoma closure site has been one of the most frequent postoperative complications. The aim of this study was to compare the short-term outcomes between conventional primary suture closure and negative pressure wound therapy with instillation and dwelling (NPWTi-d) therapy following purse-string suturing, using propensity score matching analysis. We retrospectively evaluated the medical records of 107 patients who underwent stoma closure between January 2016 and October 2020. The primary outcome was the proportion of SSI. The secondary outcome was the day of postoperative length of stay. Propensity score matching with one-to-one match was performed for reducing treatment selection bias. Of a total of 107 patients, 67 patients had been treated with conventional primary closure and 40 with NPWTi-d therapy. The propensity score matching derived 37 pairs. The respective SSI proportions were 0% and 16.2% in the groups with NPWTi-d and primary closure (P = 0.025). The respective median days of postoperative hospital stay were 9.0 and 10.0 in the groups with NPWTi-d and primary closure (P = 0.453). NPWTi-d therapy with purse-string suturing was effective in reducing SSI after stoma closure.