bluuebunny/crossref_metadata_2025_split huggingface dataset:
PARP inhibition impedes the maturation of nascent DNA strands during DNA replication
Authors: Vaitsiankova Alina , Burdova Kamila , Sobol Margarita , Gautam Amit , Benada Oldrich , Hanzlikova Hana , Caldecott Keith W. 
Published: March 2022

AbstractPoly(ADP-ribose) polymerase 1 (PARP1) is implicated in the detection and processing of unligated Okazaki fragments and other DNA replication intermediates, highlighting such structures as potential sources of genome breakage induced by PARP inhibition. Here, we show that PARP1 activity is greatly elevated in chicken and human S phase cells in which FEN1 nuclease is genetically deleted and is highest behind DNA replication forks. PARP inhibitor reduces the integrity of nascent DNA strands in both wild-type chicken and human cells during DNA replication, and does so in FEN1−/− cells to an even greater extent that can be detected as postreplicative single-strand nicks or gaps. Collectively, these data show that PARP inhibitors impede the maturation of nascent DNA strands during DNA replication, and implicate unligated Okazaki fragments and other nascent strand discontinuities in the cytotoxicity of these compounds.
Single-cell RNA sequencing of adult rat testes after Leydig cell elimination and restoration
Authors: Guan Xiaoju , Ji Minpeng , Wen Xin , Huang Fu , Zhao Xingyi , Chen Dan , Shao Jingjing , Wang Jiexia , Xie Jiajia , Tian Jing , Lin Han , Duan Ping , Zirkin Barry R. , Su Zhijian , Chen Haolin 
Published: March 2022

AbstractSpermatogenesis is an efficient, complex, and highly organized proliferation and differentiation process that relies on multiple factors including testosterone produced by the Leydig cells. Although the critical role played by testosterone in spermatogenesis is well recognized, the mechanism by which it works is still not completely understood, partially due to the inability to specifically and precisely monitor testosterone-dependent changes within developing germ cells. Here we present single-cell RNA sequencing data from10,983 adult rat testicular cells after the rats were treated with ethanedimethanesulfonate, which temporarily eliminates Leydig cells. The elimination and recovery of Leydig cells represented a complete testosterone depletion and restoration cycle. The dataset, which includes all developing germ cells from spermatogonia to spermatozoa, should prove useful for characterizing developing germ cells, their regulatory networks, and novel cell-specific markers. The dataset should be particularly useful for exploring the effects of the androgen environment on the regulation of spermatogenesis. As this is the first single-cell RNA-Seq dataset for rat testes, it can also serve as a reference for future studies.
The contribution of daytime sleepiness to impaired quality of life in NAFLD in an ethnically diverse population
Authors: Li Wenhao , Kadler Benjamin Karl , Brindley James Hallimond , Hood Gillian , Devalia Kalpana , Loy John , Syn Wing-kin , Alazawi William 
Published: March 2022

AbstractHealth-related quality of life (HRQoL) is lower in people with NAFLD compared to the general population. Sleep disturbance resulting in daytime sleepiness is common in patients with NAFLD, but the effect of daytime sleepiness on HRQoL in NAFLD is unclear. The prevalence and natural history of NAFLD vary in different ethnic groups, but there has been limited ethnic diversity in HrQoL studies to date. We aimed to assess whether daytime sleepiness is independently associated with reduced HRQoL in an ethnically diverse UK population. We conducted HRQoL assessments using SF-36 version 2 and Epworth Sleepiness Scale (ESS) questionnaires in 192 people with NAFLD. Multivariate linear regression was used to identify factors independently affecting HRQoL scales. People with NAFLD reported significantly reduced physical health-related SF-36 scores compared to the general UK population. South Asian NAFLD patients reported impairment in physical health, but not mental health, approximately a decade before White NAFLD patients. In multivariate linear regression, daytime sleepiness (ESS score > 10), was the most significant independent predictor of reduced physical health. Age, BMI and liver stiffness score were also significantly associated. HRQoL is impaired earlier in patients of South Asian ethnicity. ESS score > 10, indicative of excessive daytime sleepiness, is an independent predictor of reduced HRQoL in people with NAFLD regardless of ethnicity. Daytime sleepiness should be considered as a contributing factor to reduced HRQoL in clinical practice and when evaluating patient-related outcomes in clinical trials.
Sexual dimorphic impacts of systemic vincristine on lower urinary tract function
Authors: Iguchi Nao , Hecht Sarah L. , Gao Dexiang , Wilcox Duncan T. , Malykhina Anna P. , Cost Nicholas G. 
Published: March 2022

AbstractVincristine (VCR) is one of the most common chemotherapy agents used in pediatric oncology. Despite the well-known VCR-induced peripheral neuropathy, potential impacts of VCR on lower urinary tract (LUT) function remain poorly defined. We investigated the effects of systemic VCR exposure in childhood on LUT function by using juvenile mice treated with VCR (4 mg/kg) or saline and evaluated at 5 weeks later. VCR induced a decreased urinary frequency with increased functional bladder capacity and non-void contractions. There were no changes in detrusor contractility between the groups. VCR exposure caused sexual dimorphic changes; in females, increased intravesical pressure at micturition and downregulations of a major player in bladder afferent firing, Htr3b, in the bladders, and Cav1.2 in the lumbosacral dorsal root ganglia (Ls-DRG), while male mice displayed increases in bladder compliance and detrusor activity, upregulations of IL-2, Trpa1 and Itga1 in the bladders and neuroinflammation-related genes, P2×4, P2×7, IL-2 and CD68 in the Ls-DRG. These results suggest that that systemic VCR exposure caused sensory neuropathy via sex-dimorphic mechanisms, leading to altered LUT function. These changes might clinically present as gender-specific signs or symptoms of LUT dysfunction, and follow-up urological assessment may be of benefit for pediatric cancer patients treated with VCR.
No indications for altered EEG oscillatory activity in patients with chronic post-burn itch compared to healthy controls
Authors: Millard Samantha K. , Bokelmann Klara , Schalbroeck Rik , van der Wee Nic J. A. , van Loey Nancy E. E. , van Laarhoven Antoinette I. M. 
Published: March 2022

AbstractA large proportion of patients with burn injuries develop chronic itch, which impacts quality of life. The underlying pathophysiological mechanisms are poorly understood. This cross-sectional pilot study investigates whether altered cortical oscillatory processes are involved in chronic post-burn itch. Continuous electroencephalography (EEG) data were recorded during rest and stimulation of non-injured skin, inducing itch (histamine and electrical) and cold-pressor task pain for 15 adults with chronic post-burn itch and 15 matched healthy controls. Quantitative metrics comprised oscillatory power and peak frequencies in theta, alpha, and beta bands. No statistical differences between patients and healthy controls were found in oscillatory activity during rest or stimulation, with Bayesian analysis suggesting equivocal evidence. However, post-traumatic stress symptoms and duration of chronic itch may be associated with changes in oscillatory activity. A lack of differences in cortical oscillatory processing and itch levels at non-injured sites, suggests that itch symptoms have a localised character in this sample of patients with post-burn itch. For future studies, a biopsychological approach with integration of peripheral and central nervous system techniques, linear and non-linear EEG analysis, injured and non-injured stimulation sites, and incorporation of individual characteristics is recommended. Insight into pathophysiological mechanisms underlying chronic post-burn itch could improve diagnostics and treatments.
Contactless radar-based breathing monitoring of premature infants in the neonatal intensive care unit
Authors: Beltrão Gabriel , Stutz Regine , Hornberger Franziska , Martins Wallace A. , Tatarinov Dimitri , Alaee-Kerahroodi Mohammad , Lindner Ulrike , Stock Lilly , Kaiser Elisabeth , Goedicke-Fritz Sybelle , Schroeder Udo , R. Bhavani Shankar M. , Zemlin Michael 
Published: March 2022

AbstractVital sign monitoring systems are essential in the care of hospitalized neonates. Due to the immaturity of their organs and immune system, premature infants require continuous monitoring of their vital parameters and sensors need to be directly attached to their fragile skin. Besides mobility restrictions and stress, these sensors often cause skin irritation and may lead to pressure necrosis. In this work, we show that a contactless radar-based approach is viable for breathing monitoring in the Neonatal intensive care unit (NICU). For the first time, different scenarios common to the NICU daily routine are investigated, and the challenges of monitoring in a real clinical setup are addressed through different contributions in the signal processing framework. Rather than just discarding measurements under strong interference, we present a novel random body movement mitigation technique based on the time-frequency decomposition of the recovered signal. In addition, we propose a simple and accurate frequency estimator which explores the harmonic structure of the breathing signal. As a result, the proposed radar-based solution is able to provide reliable breathing frequency estimation, which is close to the reference cabled device values most of the time. Our findings shed light on the strengths and limitations of this technology and lay the foundation for future studies toward a completely contactless solution for vital signs monitoring.
Census-independent population estimation using representation learning
Authors: Neal Isaac , Seth Sohan , Watmough Gary , Diallo Mamadou S. 
Published: March 2022

AbstractKnowledge of population distribution is critical for building infrastructure, distributing resources, and monitoring the progress of sustainable development goals. Although censuses can provide this information, they are typically conducted every 10 years with some countries having forgone the process for several decades. Population can change in the intercensal period due to rapid migration, development, urbanisation, natural disasters, and conflicts. Census-independent population estimation approaches using alternative data sources, such as satellite imagery, have shown promise in providing frequent and reliable population estimates locally. Existing approaches, however, require significant human supervision, for example annotating buildings and accessing various public datasets, and therefore, are not easily reproducible. We explore recent representation learning approaches, and assess the transferability of representations to population estimation in Mozambique. Using representation learning reduces required human supervision, since features are extracted automatically, making the process of population estimation more sustainable and likely to be transferable to other regions or countries. We compare the resulting population estimates to existing population products from GRID3, Facebook (HRSL) and WorldPop. We observe that our approach matches the most accurate of these maps, and is interpretable in the sense that it recognises built-up areas to be an informative indicator of population.
Comparisons of plasma and fecal pharmacokinetics of danofloxacin and enrofloxacin in healthy and Mannheimia haemolytica infected calves
Authors: Beyi Ashenafi Feyisa , Mochel Jonathan P. , Magnin Géraldine , Hawbecker Tyler , Slagel Clare , Dewell Grant , Dewell Renee , Sahin Orhan , Coetzee Johann F. , Zhang Qijing , Plummer Paul J. 
Published: March 2022

AbstractDanofloxacin and enrofloxacin are fluoroquinolones (FQs) used to treat and control bovine respiratory disease (BRD) complex. While low toxicity, high bactericidal activity, and availability in single and multiple dosing regimens make them preferable, the increasing incidence of FQ-resistance in foodborne pathogens and effects on gut microbiota necessitate evaluating their pharmacokinetics (PKs). The objective of this study was to determine the exposure level of gut microbiota to subcutaneously administered FQs and compare their PKs between plasma and feces in healthy and Mannheimia haemolytica infected calves. A single dose of danofloxacin (8 mg/kg), low dose (7.5 mg/kg), or high dose (12.5 mg/kg) of enrofloxacin was administered to calves. Blood and feces were collected from calves under experimental conditions over 48 h, and FQ concentrations were measured using Ultra High-Pressure Liquid Chromatography. While moderate BRD signs were exhibited in most calves in the infected cohorts, the plasma PKs were similar between healthy and sick calves. However, the fecal danofloxacin concentration was lower in the BRD group (area under concentration–time curve [AUCinf], BRD median = 2627, healthy median = 2941 h*μg/mL, adj.P = 0.005). The dose normalized plasma and fecal danofloxacin concentrations were higher than those of enrofloxacin and its metabolite ciprofloxacin. Further, FQs had several fold higher overall concentrations in feces than in plasma in both groups. In conclusion, parenterally administered FQs expose gut microbiota to high concentrations of the antibiotics.
TeachMe: a web-based teaching system for annotating abdominal lymph nodes
Authors: Chen Shuaihua , Huang Hao , Yang Xuyang , Wang Han , Wei Mingtian , Zhang Haixian , Wang Ziqiang , Yi Zhang 
Published: March 2022

AbstractThe detection and characterization of lymph nodes through interpreting abdominal medical images are significant for diagnosing and treating colorectal cancer recurrence. However, interpreting abdominal medical images manually is labor-intensive and time-consuming. The related radiology education has many limitations as well. In this context, we seek to build an extensive collection of abdominal medical images with ground truth labels for lymph nodes recognition research and help junior doctors to train their interpretation skills. Therefore, we develop TeachMe, which is a web-based teaching system for annotating abdominal lymph nodes. The system has a three-level annotation-review workflow to construct an expert database of abdominal lymph nodes and a feedback mechanism helping junior doctors to learn the tricks of interpreting abdominal medical images. TeachMe’s functionalities make itself stand out against other platforms. To validate these functionalities, we invite a medical team from Gastrointestinal Surgery Center, West China Hospital, to participate in the data collection workflow and experience the feedback mechanism. With the help of TeachMe, an expert dataset of abdominal lymph nodes has been created and an automated detection model for abdominal lymph nodes with incredible performances has been proposed. Moreover, through three rounds of practicing via TeachMe, our junior doctors’ interpretation skills have been improved.
New approaches suggest term and preterm human fetal membranes may have distinct biomechanical properties
Authors: Bhunia Sudeshna , O’Brien Shaughn , Ling Yuting , Huang Zhihong , Wu Pensée , Yang Ying 
Published: March 2022

AbstractPreterm prelabour rupture of membranes is the leading cause of preterm birth and its associated infant mortality and morbidity. However, its underlying mechanism remains unknown. We utilized two novel biomechanical assessment techniques, ball indentation and Optical Coherence Elastography (OCE), to compare the mechanical properties and behaviours of term (≥ 37 weeks) and preterm (33–36 weeks) human fetal membranes from ruptured and non-ruptured regions. We defined the expression levels of collagen, sulfated glycosaminoglycans (sGAG), matrix metalloproteinase (MMP-9, MMP-13), fibronectin, and interleukin-1β (IL-1β) within membranes by biochemical analysis, immunohistochemical staining and Western blotting, both with and without simulated fetal movement forces on membrane rupture with a new loading system. Preterm membranes showed greater heterogeneity in mechanical properties/behaviours between ruptured and non-ruptured regions compared with their term counterparts (displacement rate: 36% vs. 15%; modulus: 125% vs. 34%; thickness: 93% vs. 30%; collagen content: 98% vs. 29%; sGAG: 85% vs 25%). Furthermore, simulated fetal movement forces triggered higher MMP-9, MMP-13 and IL-1β expression in preterm than term membranes, while nifedipine attenuated the observed increases in expression. In conclusion, the distinct biomechanical profiles of term and preterm membranes and the abnormal biochemical expression and activation by external forces in preterm membranes may provide insights into mechanisms of preterm rupture of membranes.
An intergenerational approach to parasitoid fitness determined using clutch size
Authors: Samková Alena , Raška Jan , Hadrava Jiří , Skuhrovec Jiří 
Published: March 2022

AbstractParasitoids, as important natural enemies, occur in high numbers and help maintain balance in natural ecosystems. Their fitness is traditionally studied as fertility based on the number of offspring in the F1 generation. Here, using gregarious parasitoids as models, we show that this traditional approach omits one important parameter: the clutch size–body size–fertility correlation among offspring. As a result of this correlation, when females adjust the number of offspring laid in a host, they determine not only the number of offspring produced but also the body size and reproductive potential of those offspring. Although parasitoid fertility has been determined several times from clutch size, here we use Anaphes flavipes to demonstrate the use of this relationship in an upgraded intergenerational approach to parasitoid fitness. We show that with a range of hosts simultaneously utilized by female parasitoids, identical fertility in the F1 generation can lead to distinctly different fertility values in the F2 generation. Even with the same number of hosts, lower fertility in the F1 generation can generate higher fertility in the F2 generation. Our approach provides an intergenerational perspective for determining individual fitness of gregarious parasitoids and new possibilities for the modelling of parasitoid population density.
The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction
Authors: Moshiri Niema , Fisch Kathleen M. , Birmingham Amanda , DeHoff Peter , Yeo Gene W. , Jepsen Kristen , Laurent Louise C. , Knight Rob 
Published: March 2022

AbstractThroughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, with great sequencing comes great computation, and while cloud computing platforms bring high-performance computing directly into the hands of all who seek it, optimal design and configuration of a cloud compute cluster requires significant system administration expertise. We developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence datasets leveraging Amazon Web Services (AWS) cloud compute resources and the Reflow system. ViReflow was developed specifically in response to the COVID-19 pandemic, but it is general to any viral pathogen. Importantly, when utilized with sufficient compute resources, ViReflow can trim, map, call variants, and call consensus sequences from amplicon sequence data from 1000 SARS-CoV-2 samples at 1000X depth in < 10 min, with no user intervention. ViReflow’s simplicity, flexibility, and scalability make it an ideal tool for viral molecular epidemiological efforts.
The influence of risk perceptions on close contact frequency during the SARS-CoV-2 pandemic
Authors: Wambua James , Hermans Lisa , Coletti Pietro , Verelst Frederik , Willem Lander , Jarvis Christopher I. , Gimma Amy , Wong Kerry L. M. , Lajot Adrien , Demarest Stefaan , Edmunds W. John , Faes Christel , Beutels Philippe , Hens Niel 
Published: March 2022

AbstractHuman behaviour is known to be crucial in the propagation of infectious diseases through respiratory or close-contact routes like the current SARS-CoV-2 virus. Intervention measures implemented to curb the spread of the virus mainly aim at limiting the number of close contacts, until vaccine roll-out is complete. Our main objective was to assess the relationships between SARS-CoV-2 perceptions and social contact behaviour in Belgium. Understanding these relationships is crucial to maximize interventions’ effectiveness, e.g. by tailoring public health communication campaigns. In this study, we surveyed a representative sample of adults in Belgium in two longitudinal surveys (survey 1 in April 2020 to August 2020, and survey 2 in November 2020 to April 2021). Generalized linear mixed effects models were used to analyse the two surveys. Participants with low and neutral perceptions on perceived severity made a significantly higher number of social contacts as compared to participants with high levels of perceived severity after controlling for other variables. Our results highlight the key role of perceived severity on social contact behaviour during a pandemic. Nevertheless, additional research is required to investigate the impact of public health communication on severity of COVID-19 in terms of changes in social contact behaviour.
Complementary catalysis and analysis within solid state additively manufactured metal micro flow reactors
Authors: Monaghan T. , Harding M. J. , Christie S. D. R. , Harris R. A. , Friel R. J. 
Published: March 2022

AbstractAdditive Manufacturing is transforming how researchers and industrialists look to design and manufacture chemical devices to meet their specific needs. In this work, we report the first example of a flow reactor formed via the solid-state metal sheet lamination technique, Ultrasonic Additive Manufacturing (UAM), with directly integrated catalytic sections and sensing elements. The UAM technology not only overcomes many of the current limitations associated with the additive manufacturing of chemical reactionware but it also significantly increases the functionality of such devices. A range of biologically important 1, 4-disubstituted 1, 2, 3-triazole compounds were successfully synthesised and optimised in-flow through a Cu mediated Huisgen 1, 3-dipolar cycloaddition using the UAM chemical device. By exploiting the unique properties of UAM and continuous flow processing, the device was able to catalyse the proceeding reactions whilst also providing real-time feedback for reaction monitoring and optimisation.