bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monomeric streptavidin phage display allows efficient immobilization of bacteriophages on magnetic particles for the capture, separation, and detection of bacteria
Authors: Carmody Caitlin M. , Nugen Sam R. 
Published: September 2023

AbstractImmobilization of bacteriophages onto solid supports such as magnetic particles has demonstrated ultralow detection limits as biosensors for the separation and detection of their host bacteria. While the potential impact of magnetized phages is high, the current methods of immobilization are either weak, costly, inefficient, or laborious making them less viable for commercialization. In order to bridge this gap, we have developed a highly efficient, site-specific, and low-cost method to immobilize bacteriophages onto solid supports. While streptavidin–biotin represents an ideal conjugation method, the functionalization of magnetic particles with streptavidin requires square meters of coverage and therefore is not amenable to a low-cost assay. Here, we genetically engineered bacteriophages to allow synthesis of a monomeric streptavidin during infection of the bacterial host. The monomeric streptavidin was fused to a capsid protein (Hoc) to allow site-specific self-assembly of up to 155 fusion proteins per capsid. Biotin coated magnetic nanoparticles were functionalized with mSA-Hoc T4 phage demonstrated in an E. coli detection assay with a limit of detection of < 10 CFU in 100 mLs of water. This work highlights the creation of genetically modified bacteriophages with a novel capsid modification, expanding the potential for bacteriophage functionalized biotechnologies.
The Dictyostelium discoideum FimA protein, unlike yeast and plant fimbrins, is regulated by calcium similar to mammalian plastins
Authors: Ishida Hiroaki , Woodman Andrew G. , Kitada Naoya , Aizawa Tomoyasu , Vogel Hans J. 
Published: September 2023

AbstractPlastins, also known as fimbrins, are highly conserved eukaryotic multidomain proteins that are involved in actin-bundling. They all contain four independently folded Calponin Homology-domains and an N-terminal headpiece that is comprised of two calcium-binding EF-hand motifs. Since calcium-binding has been shown to be integral to regulating the activity of the three mammalian plastin proteins, we decided to study the properties of the headpiece regions of fimbrins from the model plant Arabidopsis thaliana, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe and the amoeba Dictyostelium discoideum. Of these protein domains only the FimA headpiece from the amoeba protein possesses calcium binding properties. Structural characterization of this protein domain by multidimensional NMR and site-directed mutagenesis studies indicates that this EF-hand region of FimA also contains a regulatory ‘switch helix’ that is essential to regulating the activity of the human L-plastin protein. Interestingly this regulatory helical region seems to be lacking in the plant and yeast proteins and in fimbrins from all other nonmotile systems. Typical calmodulin antagonists can displace the switch-helix from the FimA headpiece, suggesting that such drugs can deregulate the Ca2+-regulation of the actin-bunding in the amoeba, thereby making it a useful organism for drug screening against mammalian plastins.
The hydrodynamic performance of duck feet for submerged swimming resembles oars rather than delta-wings
Authors: Ribak Gal , Gurka Roi 
Published: September 2023

AbstractWaterfowl use webbed feet to swim underwater. It has been suggested that the triangular shape of the webbed foot functions as a lift-generating delta wing rather than a drag-generating oar. To test this idea, we studied the hydrodynamic characteristics of a diving duck’s (Aythya nyroca) foot. The foot’s time varying angles-of-attack (AoAs) during paddling were extracted from movies of ducks diving vertically in a water tank. Lift and drag coefficients of 3D-printed duck-foot models were measured as a function of AoA in a wind-tunnel; and the near-wake flow dynamics behind the foot model was characterized using particle image velocimetry (PIV) in a flume. Drag provided forward thrust during the first 80% of the power phase, whereas lift dominated thrust production at the end of the power stroke. In steady flow, the transfer of momentum from foot to water peaked at 45° < AoA < 60°, due to an organized wake flow pattern (vortex street), whereas at AoAs > 60° the flow behind the foot was fully separated, generating high drag levels. The flow characteristics do not constitute the vortex lift typical of delta wings. Rather, duck feet seem to be an adaptation for propulsion at a wide range of AoAs, on and below the water surface.
Classification of cancer cells at the sub-cellular level by phonon microscopy using deep learning
Authors: Pérez-Cota Fernando , Martínez-Arellano Giovanna , La Cavera Salvatore , Hardiman William , Thornton Luke , Fuentes-Domínguez Rafael , Smith Richard J. , McIntyre Alan , Clark Matt 
Published: September 2023

AbstractThere is a consensus about the strong correlation between the elasticity of cells and tissue and their normal, dysplastic, and cancerous states. However, developments in cell mechanics have not seen significant progress in clinical applications. In this work, we explore the possibility of using phonon acoustics for this purpose. We used phonon microscopy to obtain a measure of the elastic properties between cancerous and normal breast cells. Utilising the raw time-resolved phonon-derived data (300 k individual inputs), we employed a deep learning technique to differentiate between MDA-MB-231 and MCF10a cell lines. We achieved a 93% accuracy using a single phonon measurement in a volume of approximately 2.5 μm3. We also investigated means for classification based on a physical model that suggest the presence of unidentified mechanical markers. We have successfully created a compact sensor design as a proof of principle, demonstrating its compatibility for use with needles and endoscopes, opening up exciting possibilities for future applications.
A pancancer analysis of the oncogenic role of cyclin B1 (CCNB1) in human tumors
Authors: Dai Peng , Xiong Lecai , Wei Yanhong , Wei Xiaoyan , Zhou Xuefeng , Zhao Jinping , Tang Hexiao 
Published: September 2023

AbstractAberrant levels of the G2/M cyclin cyclin B1 (gene CCNB1) have been associated with multiple cancers; however, the literature lacks a focused and comprehensive analysis of the regulation of this important regulator of cell proliferation in cancer. Through this work, we performed a pancancer analysis of the levels of CCNB1 and dissected aspects of regulation and how this correlates with cancer prognosis. We comprehensively evaluated the expression and promoter methylation of CCNB1 across 38 cancers based on RNA sequencing data obtained from the Cancer Genome Atlas (TCGA). The correlation of CCNB1 with prognosis and the tumor microenvironment was explored. Using lung adenocarcinoma data, we studied the potential upstream noncoding RNAs involved in the regulation of CCNB1 and validated the protein levels and prognostic value of CCNB1 for this disease site. CCNB1 was highly expressed, and promoter methylation was reduced in most cancers. Gene expression of CCNB1 correlated positively with poor prognosis of tumor patients, and these results were confirmed at the protein level using lung adenocarcinoma. CCNB1 expression was associated with the infiltration of T helper cells, and this further correlated with poor prognosis for certain cancers, including renal clear cell carcinoma and lung adenocarcinoma. Subsequently, we identified a specific upstream noncoding RNA contributing to CCNB1 overexpression in lung adenocarcinoma through correlation analysis, expression analysis and survival analysis. This study provides a comprehensive analysis of the expression and methylation status of CCNB1 across several forms of cancer and provides further insight into the mechanistic pathways regulating Cyclin B1 in the tumorigenesis process.
Permeability evolution of Bentheim Sandstone at simulated georeservoir conditions
Authors: Fazio Marco , Chandler Michael R. , Sauter Martin 
Published: September 2023

AbstractBentheim Sandstone is considered a suitable conventional georeservoir rock even at great depth because of its mineral composition, homogeneity, micro- and macrostructure, and is also used as a reference material in rock deformation tests. However, a full characterization of the permeability at representative depths has never been performed. Here we report new experimental data where the permeability of Bentheim Sandstone is measured both with a simultaneous variation and with a sequential variation of three different variables to simulate georeservoir conditions. The results indicate a decrease in permeability with simulated increasing depth until 2–3 km, followed by a partial permeability recovery until 4–5 km depth. During the exhumation path, initially, permeability is unaffected, but at shallow depths, a sharp increase in permeability is observed, likely due to microcracking. These variations are a consequence of a complex interaction between stress, pore pressure and temperature, highlighting the importance of experiments considering all three variables when studying the evolution of permeability at depth. These results will aid with the accurate estimation of permeability at different georeservoir conditions.
Validating virtual administration of neuropsychological testing in Parkinson disease: a pilot study
Authors: Gallagher Julia , Mamikonyan Eugenia , Xie Sharon X. , Tran Baochan , Shaw Sarah , Weintraub Daniel 
Published: September 2023

AbstractCOVID-19 has highlighted the need for remote cognitive testing, but the reliability and validity of virtual cognitive testing in Parkinson disease (PD) is unknown. Therefore, we assessed PD participants enrolled in an observational, cognition-focused study with an extensive cognitive battery completed both in-person and via video conference close in time. Data for 35 PD participants with normal cognition to mild dementia were analyzed. Only one test (semantic verbal fluency) demonstrated a difference in score by administration type, with a significantly better score virtually. Only three tests demonstrated good reliability for in-person versus virtual testing, but reliability values for visit 1 versus visit 2 were similarly low overall. Trail Making Test B was successfully administered virtually to only 18 participants due to technical issues. Virtual and in-person cognitive testing generate similar scores at the group level, but with poor to moderate reliability for most tests. Mode of test administration, learning effects, and technical difficulties explained little of the low test–retest reliability, indicating possible significant short-term variability in cognitive performance in PD in general, which has implications for clinical care and research. In-person cognitive testing with a neuropsychologist remains the gold standard, and it remains to be determined if virtual cognitive testing is feasible in PD.
Palaeoenvironments and hominin evolutionary dynamics in southeast Asia
Authors: Bacon Anne-Marie , Bourgon Nicolas , Dufour Elise , Demeter Fabrice , Zanolli Clément , Westaway Kira E. , Joannes-Boyau Renaud , Duringer Philippe , Ponche Jean-Luc , Morley Mike W. , Suzzoni Eric , Frangeul Sébastien , Boesch Quentin , Antoine Pierre-Olivier , Boualaphane Souliphane , Sichanthongtip Phonephanh , Sihanam Daovee , Huong Nguyen Thi Mai , Tuan Nguyen Anh , Fiorillo Denis , Tombret Olivier , Patole-Edoumba Elise , Zachwieja Alexandra , Luangkhoth Thonglith , Souksavatdy Viengkeo , Dunn Tyler E. , Shackelford Laura , Hublin Jean-Jacques 
Published: September 2023

AbstractSecure environmental contexts are crucial for hominin interpretation and comparison. The discovery of a Denisovan individual and associated fauna at Tam Ngu Hao 2 (Cobra) Cave, Laos, dating back to 164–131 ka, allows for environmental comparisons between this (sub)tropical site and the Palearctic Denisovan sites of Denisova Cave (Russia) and Baishiya Karst Cave (China). Denisovans from northern latitudes foraged in a mix of forested and open landscapes, including tundra and steppe. Using stable isotope values from the Cobra Cave assemblage, we demonstrate that, despite the presence of nearby canopy forests, the Denisovan individual from Cobra Cave primarily consumed plants and/or animals from open forests and savannah. Using faunal evidence and proxy indicators of climates, results herein highlight a local expansion of rainforest at ~ 130 ka, raising questions about how Denisovans responded to this local climate change. Comparing the diet and habitat of the archaic hominin from Cobra Cave with those of earlyHomo sapiensfrom Tam Pà Ling Cave (46–43 ka), Laos, it appears that only our species was able to exploit rainforest resources.
Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria
Authors: Jawaharraj Kalimuthu , Peta Vincent , Dhiman Saurabh Sudha , Gnimpieba Etienne Z. , Gadhamshetty Venkataramana 
Published: September 2023

AbstractSulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz.,transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes ofDesulfovibriospp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures ofOleidesulfovibrio alaskensis(OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.
Biomechanical performance evaluation of a modified proximal humerus locking plate for distal humerus shaft fracture using finite element analysis
Authors: Lee Jung-Soo , Kim Kwang Gi , Yoon Yong-Cheol 
Published: September 2023

AbstractThe extra-articular distal humerus plate (EADHP) has been widely used for surgical treatment of distal humerus shaft fracture (DHSF). However, the surgical approach, fixation methods, and implant positions of the EADHP remain controversial owing to iatrogenic radial nerve injury and complaints such as skin irritation related to the plate. Anterior plating with a modified (upside-down application) proximal humerus locking plate (PHILOS) has been proposed as an alternative, However, research on its biomechanical performance remain insufficient and were mostly based on retrospective studies. This study quantitatively compared and evaluated the biomechanical performance between posterior plating with the EADHP and anterior plating with a modified PHILOS using finite element analysis (FEA). The FEA simulation results that both the EADHP and PHILOS had adequate biomechanical performance and stability under axial, bending, and varus force load conditions. The PHILOS has a fixed stability comparable to that of the EADHP, and fixation was achieved using only four locking screws within a fixed range of 30 mm just above the olecranon fossa. The results show that the PHILOS could be an option for the fixation of a DHSF when considering the dissection range and complaints (e.g. skin irritation) associated with the EADHP.
CSE1L is a negative regulator of the RB-DREAM pathway in p53 wild-type NSCLC and can be targeted using an HDAC1/2 inhibitor
Authors: Duan Lei , Tadi Mehrdad Jafari , Maki Carl G. 
Published: September 2023

AbstractP53 represses transcription by activating p21 expression and promoting formation of RB1-E2F1 and RBL1/RBL2-DREAM transcription repressor complexes. The DREAM complex is composed of DP1, RB-family proteins RBL1 or RBL2 (p107/p130), E2F4/5, and MuvB. We recently reported RBL2-DREAM contributes to improved therapy responses in p53 wild-type NSCLC cells and improved outcomes in NSCLC patients whose tumors express wild-type p53. In the current study we identified CSE1L as a novel inhibitor of the RBL2-DREAM pathway and target to activate RBL2-DREAM in NSCLC cells. CSE1L is an oncoprotein that maintains repression of genes that can be reactivated by HDAC inhibitors. Mocetinostat is a HDAC inhibitor in clinical trials with selectivity against HDACs 1 and 2. Knockdown of CSE1L in NSCLC cells or treatment with mocetinostat increased p21, activated RB1 and RBL2, repressed DREAM target genes, and induced toxicity in a manner that required wild-type p53. Lastly, we found high levels of CSE1L and specific DREAM-target genes are candidate markers to identify p53 wild-type NSCLCs most responsive to mocetinostat. Thus, we identified CSE1L as a critical negative regulator of the RB-DREAM pathway in p53 wild-type NSCLC that can be indirectly targeted with HDAC1/2 inhibitors (mocetinostat) in current clinical trials. High expression of CSE1L and DREAM target genes could serve as a biomarker to identify p53 wild-type NSCLCs most responsive to this HDAC1/2 inhibitor.
Overuse of the psychoactive analgesics’ opioids and gabapentinoid drugs in patients having surgery for nerve entrapment disorders
Authors: Dahlin Lars B. , Perez Raquel , Nyman Erika , Zimmerman Malin , Merlo Juan 
Published: September 2023

AbstractKnowledge about risks for overuse of psychoactive analgesics in patients having primary surgery for carpal tunnel syndrome (CTS) or ulnar nerve entrapment (UNE), or both, is limited. We investigated if patients with those nerve entrapment disorders have a higher risk of overuse of psychoactive analgesics (i.e., opioids and gabapentinoid drugs) before, after, and both before and after surgery than observed in the general population after accounting for demographical and socioeconomic factors. Using a large record linkage database, we analysed 5,966,444 individuals (25–80 years), residing in Sweden December 31st, 2010–2014, of which 31,380 underwent surgery 2011–2013 for CTS, UNE, or both, applying logistic regression to estimate relative risk (RR) and 95% confidence interval (CI). Overall, overuse of the psychoactive analgesics was low in the general population. Compared to those individuals, unadjusted RR (95% CI) of overuse ranged in patients between 2.77 (2.57–3.00) with CTS after surgery and 6.21 (4.27–9.02) with both UNE and CTS after surgery. These risks were only slightly reduced after adjustment for demographical and socioeconomic factors. Patients undergoing surgery for CTS, UNE, or both, have a high risk of overuse of psychoactive analgesics before, after, and both before and after surgery.
Associations between physical size and space are strongly asymmetrical
Authors: Richter Melanie , Wühr Peter 
Published: September 2023

AbstractThe spatial–size association of response codes (SSARC) effect describes the phenomenon that left responses are faster and more accurate to small stimuli whereas right responses are faster and more accurate to large stimuli, as compared to the opposite mapping. The effect indicates associations between the mental representations of physical size and space. Importantly, the theoretical accounts of SSARC effects make different predictions about the reciprocity and/or symmetry of spatial–size associations. To investigate the reciprocity of SSARC effects, we compared compatibility effects in two verbal choice-response tasks: a size–location (typical SSARC) task and a location–size (reciprocal SSARC) task. In the size–location task, participants responded verbally to a small/large stimulus by saying “left”/“right”. In the location–size task, participants responded verbally to a left-/right-side stimulus by saying “small”/“large”. Participants completed both tasks with a compatible (small–left, large–right; left–small, right–large) and an incompatible (small–right, large–left; left–large, right–small) mapping. A regular SSARC effect emerged in the size–location task. However, no reciprocal SSARC effect emerged in the location–size task if outliers were excluded. If outliers were not excluded, small reciprocal SSARC effects occurred. Associations underlying the SSARC effect are thus strongly asymmetrical: Physical (stimulus) size can prime spatial responses much more strongly than spatial (stimulus) position can prime size-related responses. The finding of asymmetrical associations between size and space is in line with some theoretical accounts of the SSARC effect but at odds with others.
Prevalence of low trabecular bone score and its association with disease severity and activity in patients with axial spondyloarthritis
Authors: Saisirivechakun Pannarat , Mahakkanukrauh Ajanee , Pongchaiyakul Chatlert , Boonya-ussadorn Trirat , Narongroeknawin Pongthorn , Pakchotanon Rattapol , Assavatanabodee Paijit , Chaiamnuay Sumapa 
Published: September 2023

AbstractAxial spondyloarthritis (axSpA) increases the risk of osteoporosis and vertebral fractures. Bone mineral density (BMD) measured by dual X-ray absorptiometry (DXA) has limitations in axSpA patients. Trabecular bone score (TBS) indirectly assesses bone microarchitecture and can be used to predict fracture risk. However, few studies have investigated the role of TBS in axSpA patients. The objective of this study were to compare TBS between axSpA patients and 1:1 sex- and age-matched healthy volunteers and determine factors associated with low TBS in axSpA patients. A cross-sectional study was conducted in two tertiary-care hospitals. A total of 137 axSpA patients and healthy volunteers were enrolled. Demographics, disease characteristics, and risk factors for osteoporosis were recorded. TBS, BMD at the lumbar spine, hip, and vertebral fractures were assessed by DXA. Low TBS was defined as a TBS value < 1.230. Factors associated with low TBS were examined by logistic regression. Most patients were male (75.9%) and tested positive for HLA-B27 (88.3%). The mean (SD) age was 42.8 (12.0) years. The mean (SD) of TBS in the axSpA patients was lower than those in the healthy volunteers [1.402 (0.107) vs 1.440 (0.086), respectively; p = 0.002]. The mean (SD) of lumbar BMD in the axSpA patients was higher than in healthy volunteers [1.186 (0.212) vs 1.087 (0.124), p < 0.001], whereas the mean (SD) of femoral neck BMD in the axSpA group was lower than that in the healthy volunteers [0.867 (0.136) vs 0.904 (0.155), p = 0.038]. Disease severity as indicated by sacroiliac joint fusion and a high ASDAS score were associated with low TBS with the odds ratios (95% confidence interval) of 11.8 (1.2–115.4) and 5.2 (1.6–16.9), respectively. In conclusion, axSpA patients had a higher prevalence of low TBS than healthy volunteers. Sacroiliac joint fusion and a high ASDAS score were associated with low TBS.