bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can the Rapid Antigen Test for COVID-19 Replace RT-PCR: A Meta-analysis of Test Agreement
Authors: Elmakaty Ibrahim , Elsayed Abdelrahman , Hommos Rama Ghassan , Abdo Ruba , Mohamed Amira , Yousif Zahra , Fakhroo Maryam , Alansari Abdulrahman , Coyle Peter V. , Doi Suhail A. R. 
Published: October 2021

SummaryBackgroundSeveral studies have compared the performance of reverse transcription-polymerase chain reaction (RT-PCR) and antigen rapid diagnostic tests (Ag-RDTs) as tools to diagnose SARS-CoV-2 disease (COVID-19). As the performance of Ag-RDT may vary among different products and viral load scenarios, the clinical utility of the Ag-RDT remains unclear. Our aim is to assess the diagnostic agreement between Ag-RDTs and RT-PCR in testing for COVID-19 across different products and cycle threshold (Ct) values.MethodsAn evidence synthesis and meta-analysis of Positive Percent Agreement (PPA) and Negative Percent Agreement (NPA) was conducted after an exhaustive search of five databases to locate published studies that compared Ag-RDT to RT-PCR and reported quantitative comparison results. After the screening, quality assessment, and data extraction, the synthesis of pooled estimates was carried out utilizing the quality-effects (QE) model and Freeman-Tukey double arcsine transformation (FTT) for variance stabilization. Subgroup analysis was also conducted to evaluate the tests’ diagnostic agreement across distinctive products and Ct-value thresholds.FindingsA total of 420 studies were screened by title and abstract, of which 39 were eventually included in the analysis. The overall NPA was 99.4% (95%CI 98.8-99.8, I2=91.40%). The PPA was higher in lower Ct groups such as groups with Ct <20 and Ct <25, which had an overall PPA of 95.9% (95%CI 92.7-98.2, I2=0%) and 96.8% (95%CI 95.2-98.0, I2=50.1%) respectively. This is in contrast to groups with higher Ct values, which had relatively lower PPA. Panbio and Roche Ag-RDTs had the best consistent overall PPA across different Ct groups especially in groups with Ct <20 and Ct <25.InterpretationThe findings of our meta-analysis support the use of Ag-RDTs in lieu of RT-PCR for decision making regarding COVID-19 control measures, since the enhanced capacity of RT-PCR to detect disease in those that are Ag-RDT negative will be unlikely to have much public health utility. This step will drastically reduce the cost and time in testing for COVID-19.FundingThis research did not receive any specific funding.
Antennapedia and optix regulate metallic silver wing scale development and cell shape in Bicyclus anynana butterflies
Authors: Prakash Anupama , Finet Cédric , Banerjee Tirtha Das , Saranathan Vinodkumar , Monteiro Antónia 
Published: October 2021

AbstractButterfly wing scale cells can develop very intricate cuticular nanostructures that interact with light to produce structural colors including silvery hues, but the genetic basis of such nanostructures is mostly unexplored. Here, we first identified that optix is necessary for metallic scale development in the butterfly Bicyclus anynana. We then characterized different subtypes of wildtype metallic silver scales and addressed the function of five genes – apterous A, Ultrabithorax, doublesex, Antennapedia, and optix – in the differentiation of silver scales, at a single-cell resolution, by leveraging crispants that exhibited either ectopic gains or losses of silver scales. Wildtype silver scales were generally rounded and had low amounts of pigmentation, exhibiting a common ultrastructural modification for metallic broadband reflectance, i.e., an undulatory air layer enclosed by an upper and lower lamina. Our results indicated that the varying air layer thickness was the important parameter of the bilaminate scale for producing a broadband reflectance across visible wavelengths. While a single lamina of the appropriate thickness could also produce broadband colors, the bilaminate structure is advantageous as it increases the overall reflectivity. Crispant brown scales differed from wildtype silver scales via the loss of the continuous upper lamina, increased lower lamina thickness, and increased pigmentation. The reverse was seen when brown scales became silver. We identified Antennapedia and optix as high-level regulators in the network differentiating different silver scale subtypes and determining overall cell shape in both sexes. In addition, Antp exhibits a novel, post-embryonic role in the determination of ridge and crossrib orientation.
Cables1 links Slit/Robo and Wnt/Frizzled signaling in commissural axon guidance
Authors: Zuñiga Nikole , Stoeckli Esther T. 
Published: October 2021

ABSTRACTDuring neural circuit formation, axons navigate from one intermediate target to the next, until they find their final target. At intermediate targets, axons switch from being attracted to being repelled by changing the guidance receptors on the growth cone surface. For smooth navigation of the intermediate target and the continuation of their journey, the switch in receptor expression has to be orchestrated in a precisely timed manner. As an alternative to changes in expression, receptor function could be regulated by phosphorylation of receptors or components of signaling pathways. We identifed Cables1 as a linker between floor-plate exit of commissural axons regulated by Slit/Robo signaling and the rostral turn of post-crossing axons regulated by Wnt/Frizzled signaling. Cables1 localizes β-Catenin phosphorylated at tyrosine 489 by Abelson kinase to the distal axon, which in turn is necessary for the correct navigation of post-crossing commissural axons in the developing chicken spinal cord.
Encapsulated actomyosin patterns drive cell-like membrane shape changes
Authors: Bashirzadeh Yashar , Moghimianavval Hossein , Liu Allen P. 
Published: October 2021

AbstractCell shape changes from locomotion to cytokinesis are, to a large extent, driven by myosin-driven remodeling of cortical actin patterns. Passive crosslinkers such as α-actinin and fascin as well actin nucleator Arp2/3 complex largely determine the architecture and connectivity of actin network patterns; consequently, they regulate network remodeling and membrane shape changes. Membrane constriction in animal cell cytokinesis proceeds by assembly and contraction of a contractile ring pattern rich in α-actinin and myosin at the equator of the cell cortex, with which the ring is contiguous. Here we reconstitute actomyosin networks inside cell-sized lipid bilayer vesicles and show that, depending on vesicle size and concentrations of α-actinin and fascin, actomyosin networks assemble into ring and aster-like patterns. Anchoring actin to the membrane enhances the interaction of the contractile networks with lipid membrane but does not change the architecture of the patterns. A membrane-bound actomyosin ring exerts force and constricts the membrane. An Arp2/3 complex-mediated actomyosin cortex is shown to assemble a ring-like pattern at the equatorial cortex and contribute to myosin-driven clustering of the cortex and consequently membrane deformation. An active gel theory unifies a model for the observed membrane constriction and protrusion induced by the membrane-bound actomyosin networks.
A Recombinant Multivalent Vaccine (rCpa1) Induces Protection for C57BL/6 and HLA Transgenic Mice Against Pulmonary Infection with Both Species of Coccidioides
Authors: Campuzano Althea , Pentakota Komali Devi , Liao Yu-Rou , Zhang Hao , Wiederhold Nathan , Ostroff Gary , Hung Chiung-Yu 
Published: October 2021

AbstractCoccidioidomycosis is caused by Coccidioides posadasii (Cp) and Coccidioides immitis (Ci) that have 4-5% differences in their genomic sequences. There is an urgent need to develop a human vaccine against both species. A previously created recombinant antigen (rCpa1) that contains multiple peptides derived from Cp isolate C735 is protective against the autologous isolate. The focus of this study is to evaluate cross-protective efficacy and immune correlates by the rCpa1- based vaccine against both species of Coccidioides. DNA sequence analyses of the homologous genes for the rCpa1 antigen were conducted for 39 and 17 clinical isolates of Cp and Ci, respectively. Protective efficacy and vaccine-induced immunity were evaluated for both C57BL/6 and human HLA-DR4 transgenic mice against 5 highly virulent isolates of Cp and Ci. There are a total of 7 amino acid substitutions in the rCpa1 antigen between Cp and Ci. Both C57BL/6 and HLA-DR4 mice that were vaccinated with a rCpa1 vaccine resulted in significant reduction of fungal burden and increased numbers of IFN-γ- and IL-17-producing CD4+ T cells in the first 2 weeks post-challenge. These data support that rCpa1 has cross-protection activity against Cp and Ci pulmonary infection through activation of early Th1 and Th17 responses.
Assessment of Tuberculosis Prevention and Care Measures in Mining Industries of Malawi, 2019
Authors: Dimba Andrew , Ng’ambi Wingston Felix , Banda Knox , Soundappan Kathirvel , Chongwe Gershom , Banda Pilirani , Rambiki Ethel , Mpunga James , Chanda- Kapata Pascalina , Lwanda Levi , Matu Martin , Girma Belaineh , Gowelo Happy , Kapokosa Mphatso , Kathyola Damson 
Published: October 2021

AbstractSettingKaronga, Rumphi, Kasungu and Lilongwe districts of Malawi in 2019.ObjectivesTo determine the availability and utilization of TB preventive and care services in fifteen licensed mining industries in four selected districts in Malawi in 2019.DesignWe conducted a cross-sectional study using mixed-methods. Qualitative data were analysed using content analysis and thematic approach. We calculated the frequencies, proportions, median and interquartile range in STATA v16.0. Qualitative data was analysed using content analysis. We triangulated the qualitative and quantitative results.ResultsOf the 373 miners, 215 (58%) indicated that they were provided with annual TB screening while 43 (12%) had TB screened before being recruited in the mine, 171 (46%) were provided with masks, and 25 (7%) were aware of compensation after being sick while working in a mine. Of the 171 miners that indicated that masks were provided, 110 (64%) cited N95, 55 (32%) cited surgical mask, and 6 (4%) cited cotton wasters. The common OHS measures at the mines were banning of smoking within the mining site, sensitization of the miners on TB and adequate ventilation. The key challenges were the absence of the national Occupational Health and Safety Policy (OHSP), limited financial resources to consistently procure the PPE, and poor coordination between the mines, labour and health offices at district level.ConclusionThe mining industries of Malawi have implemented an array of the expected measures however most of these are available at a sub-optimal level. The absence of the national OHSP has provided a loophole for non-adherence of the mining industries to providing OHS to the miners. Therefore, Malawi should put in place OHSP to safeguard the health and social protection as well as compensation of the miners and ex-miners.
Hydraulic synchrony of spawning sites amongst Earth’s riverine fishes
Authors: O’Sullivan Antóin M. , Morgan Alexander M. , Newbury Robert , Linnansaari Tommi , Kurylyk Barret L. , Helminen Jani , Wegscheider Bernhard , Johns Robert C. , Samways Kurt , Alex Kari I. , Curry R. Allen , Cunjak Richard A. 
Published: October 2021

AbstractEarth’s riverine fishes utilize a suite of reproductive guilds, broadly following four guilds: nest guarders, broadcast pelagic spawners, broadcast benthic spawners and nest non-guarders 1,2, and these guilds utilize different mechanisms to aerate eggs 3,4. Globally, river fishes populations are declining5, and spawning habitat rehabilitation has become a popular tool to counter these declines6. However, there is a lack of understanding as to what classifies suitable spawning habitats for riverine fishes, thereby limiting the efficacy of these efforts and thus the restoration of the target species. Using data from n = 220 peer-reviewed papers and examining n = 128 unique species, we show the existence of a hydraulic pattern (defined by Froude number (Fr), a non-dimensional hydraulic parameter) that characterizes the reproductive guilds of riverine fishes. We found nest guarders, broadcast pelagic spawners, benthic spawners, and nest non-guarders selected sites with mean Fr = 0.05, 0.11, 0.22, and 0.28, respectively. Some of the fishes in this study are living fossils, suggesting that that these hydraulic preference patterns may be consistent across time. Our results suggest this hydraulic pattern can guide spawning habitat rehabilitation for all riverine fish species globally in absence of specific spawning habitat information for a species, where resource managers can establish the reproductive guild of the species of interest, and then apply the specific hydraulic requirements (Fr range) of that reproductive guild, as presented herein, in the rehabilitation of the target species.
A patatin-like phospholipase mediatesRickettsia parkeriescape from host membranes
Authors: Borgo Gina M. , Burke Thomas P. , Tran Cuong J. , Lo Nicholas T. N. , Engström Patrik , Welch Matthew D. 
Published: October 2021

AbstractSpotted fever groupRickettsiaspecies are arthropod-borne obligate intracellular bacteria that can cause mild to severe human disease. These bacteria invade host cells, replicate in the cell cytosol, and then spread from cell to cell. To access the host cytosol and avoid detection by immune surveillance mechanisms, these pathogens must have evolved efficient ways to escape membrane-bound vacuoles. AlthoughRickettsiaare predicted to express factors that disrupt host membranes, little is known about how and when these proteins function during infection. Here, we investigated the role of aRickettsiapatatin-like phospholipase A2 enzyme (Pat1) during host cell infection by characterizing aRickettsia parkerimutant with a transposon insertion in thepat1gene. We show that Pat1 is important for infection in a mouse model and in host cells. We further show that Pat1 is critical for efficiently escaping from the single and double membrane-bound vacuoles into the host cytosol, and for avoiding host galectins that mark damaged membranes. In the host cytosol, Pat1 is important for avoiding host polyubiquitin, preventing recruitment of autophagy receptor p62, and promoting actin-based motility and cell-cell spread. Our results show that Pat1 plays critical roles in escaping host membranes and promoting cell-cell spread duringR. parkeriinfection and suggest diverse roles for patatin-like phospholipases in facilitating microbial infection.ImportanceSpotted fever groupRickettsiaare bacteria that reside in ticks and can be transmitted to mammalian hosts, including humans. Severe disease is characterized by high fever, headache, and rash, and results in occasional mortality despite available treatment.Rickettsiainteract with host cell membranes while invading cells, escaping into the cytosol, and evading cellular defenses. Bacterial phospholipase enzymes have been proposed as critical factors for targeting host cell membranes, however the specific roles of rickettsial phospholipases are not well defined. We investigated the contribution of one conserved patatin-like phospholipase, Pat1, inRickettsia parkeri. We observed that Pat1 is important for virulence in an animal model. Moreover, Pat1 plays critical roles in host cells by facilitating access to the cell cytosol, inhibiting detection by host defense pathways, and promoting cell-cell spread. Our study indicates that Pat1 performs several critical functions, suggesting a broad role for phospholipases throughout theRickettsialifecycle.
Use-dependent biases primarily originate from a contaminated motor plan
Authors: Tsay Jonathan S , Kim Hyosub E , Saxena Arohi , Parvin Darius E , Verstynen Timothy , Ivry Richard B 
Published: October 2021

AbstractRepetition of a specific movement biases subsequent actions towards the recently practiced movement, a phenomenon referred to as use-dependent learning (UDL). UDL has been attributed to shifts in the tuning of neurons in the motor cortex. However, recent studies employing a forced reaction time task, including the eLife article by Marinovic et al (2017), indicate that these biases may also arise from a contaminated motor plan, one that is biased towards the practiced direction. We advanced this line of inquiry, seeking to establish the relative contribution of execution and planning processes to UDL in a center-out reaching task in which participants were able to initiate movements of their own volition. On most trials, the target appeared at a designated “frequent” location; on other trials, the target appeared at one of six “rare” locations. In Experiment 1, participants exhibited a robust movement bias towards the frequent target when movements were self-initiated quickly, but a small movement bias when movements were self-initiated slowly – the signature of a contaminated motor plan. Strikingly, the heading angles were bimodally distributed, with one peak at the frequent target location and the other at the rare target location – a finding reinforced by a re-analysis of two widely cited studies on UDL. Notably, the latter peak was shifted in the frequently practiced direction, a signature of a motor execution bias. To eliminate the contribution of planning-related UDL, we imposed a delay between target onset and movement initiation in Experiment 2. As predicted, the heading angles became unimodally distributed around the rare target. The peak of this distribution was again shifted towards the location of the frequent target, indicative of a persistent bias in motor execution. Taken together, these results highlight two distinct components of UDL even when movements are self-initiated: First, the temporal dynamics underlying movement planning, in which a default plan is progressively overridden by a new plan, produces a pronounced motor planning bias. Second, there is a small, temporally stable bias that may reflect shifts in motor unit tuning.
Spatially-resolved transcriptomics analyses of invasive fronts in solid tumors
Authors: Wu Liang , Yan Jiayan , Bai Yinqi , Chen Feiyu , Xu JiangShan , Zou Xuanxuan , Huang Ao , Hou Liangzhen , Zhong Yu , Jing Zehua , Zhou Xiaorui , Sun Haixiang , Cheng Mengnan , Ji Yuan , Luo Rongkui , Li Qinqin , Wu Liang , Wang Pengxiang , Guo Dezhen , Huang Waidong , Lei Junjie , Liao Sha , Li Yuxiang , Jiang Zhifeng , Yao Na , Yu Yang , Li Yao , Liu Fengming , Zhang Mingyuan , Yang Huanming , Yang Shuang , Xu Xun , Liu Longqi , Wang Xiangdong , Wang Jian , Fan Jia , Liu Shiping , Yang Xinrong , Chen Ao , Zhou Jian 
Published: October 2021

AbstractSolid tumors are complex ecosystems, and heterogeneity is the major challenge for overcoming tumor relapse and metastasis. Uncovering the spatial heterogeneity of cell types and functional states in tumors is essential for developing effective treatment, especially in invasive fronts of tumor, the most active region for tumor cells infiltration and invasion. We firstly used SpaTial Enhanced REsolution Omics-sequencing (Stereo-seq) with a nanoscale resolution to characterize the tumor microenvironment of intrahepatic cholangiocarcinoma (ICC). Enrichment of distinctive immune cells, suppressive immune microenvironment and metabolic reprogramming of tumor cells were identified in the 500µm-wide zone centered bilaterally on the tumor boundary, namely invasive fronts of tumor. Furthermore, we found the damaged states of hepatocytes with overexpression of Serum Amyloid A (SAA) in invasive fronts, recruiting macrophages for facilitating further tumor invasion, and thus resulting in a worse prognosis. We also confirmed these findings in hepatocellular carcinoma and other liver metastatic cancers. Our work highlights the remarkable potential of high-resolution-spatially resolved transcriptomic approaches to provide meaningful biological insights for comprehensively dissecting the tumor ecosystem and guiding the development of novel therapeutic strategies for solid tumors.
Microbial stowaways – waterbirds as dispersal vectors of aquatic pro- and microeukaryotic communities
Authors: Szabó Beáta , Szabó Attila , Vad Csaba F. , Boros Emil , Lukić Dunja , Ptacnik Robert , Márton Zsuzsanna , Horváth Zsófia 
Published: October 2021

AbstractAimWaterbirds are important dispersal vectors of multicellular organisms such as macrophytes, aquatic macroinvertebrates, and zooplankton. However, no study to date has focused on their potential role in dispersing aquatic microbial communities (i.a., bacteria, algae, protozoa). Here, we explicitly studied passive transport (endozoochory) of prokaryotes and unicellular microeukaryotes by waterbirds based on DNA metabarcoding approaches. By directly comparing the dispersed set of organisms to the source pool of a natural metacommunity, we aimed for a realistic estimate of the overall importance of waterbird zoochory for natural microbial communities.LocationShallow saline temporary ponds (soda pans) in the cross-border region of Austria and Hungary.TaxonProkaryotes and unicellular microeukaryotes.MethodsIn 2017 and 2018, water samples from 25 natural aquatic habitats along with fresh droppings of the dominant greylag goose (Anser anser) and four other waterbird species were collected in a habitat network of temporary ponds. Their prokaryotic and microeukaryotic communities were identified via 16S and 18S rRNA gene amplicon sequencing. Sequence reads were analysed using mothur. After quality filtering of the reads, pro- and microeukaryotic amplicon sequencing variant (ASV) compositions were compared between the aquatic and dropping samples, across years and waterbird species.ResultsWe found that 28% of the dominant aquatic prokaryotic and 19% of the microeukaryotic ASVs were transported byA. anser. ASV richness inA. anserdroppings was lower, but compositional variation was higher compared to the aquatic communities, probably resulting from stochastic pick-up of microbes from multiple aquatic habitats. We furthermore found that the composition of prokaryotic ASVs in bird droppings were different among the two years and reflected the actual aquatic communities. The dispersed set of microbes were largely similar among the different waterbird species except for the planktivore filter-feeder northern shoveler (Spatula clypeata) which was outstanding by dispersing a more species-rich subset of microeukaryotes than shorebirds or geese.Main conclusionsBy using a combined amplicon-sequencing approach to characterize microorganisms in waterbird droppings and in the associated environment, our study provides strong evidence for endozoochory of natural aquatic microorganism communities. These results imply that waterbirds may be crucial in maintaining ecological connectivity between discrete aquatic habitats at the level of microbial communities.
Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome
Authors: Martinez-Ara Miguel , Comoglio Federico , van Arensbergen Joris , van Steensel Bas 
Published: October 2021

AbstractGene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter need to be biochemically compatible for promoter regulation to occur, but this compatibility has remained poorly characterised in mammalian cells. We used high-throughput combinatorial reporter assays to test thousands of CRE – promoter pairs from three Mb-sized genomic regions in mouse cells. This revealed that CREs vary substantially in their promoter compatibility, ranging from striking specificity for a single promoter to quantitative differences in activation across a broad set of promoters. More than half of the tested CREs exhibit significant promoter selectivity. Housekeeping promoters tend to have similar CRE preferences, but other promoters exhibit a wide diversity of compatibilities. Higher-order TF motif combinations may account for compatibility. CRE–promoter selectivity does not correlate with looping interactions in the native genomic context, suggesting that chromatin folding and compatibility are two orthogonal mechanisms that confer specificity to gene regulation.