bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease
Authors: Tran Ngan K. , Lea Rodney A. , Holland Samuel , Nguyen Quan , Raghubar Arti M. , Sutherland Heidi G. , Benton Miles C. , Haupt Larisa M. , Blackburn Nicholas B. , Curran Joanne E. , Blangero John , Mallett Andrew J. , Griffiths Lyn R. 
Published: September 2021

AbstractChronic kidney disease (CKD) is a persistent impairment of kidney function. Genome-wide association studies (GWAS) have revealed multiple genetic loci associated with CKD susceptibility but the complete genetic basis is not yet clear. Since CKD shares risk factors with cardiovascular diseases and diabetes, there may be pleiotropic loci at play but may go undetected when using single phenotype GWAS. Here, we used multi-phenotype GWAS in the Norfolk Island isolate (n = 380) to identify new loci associated with CKD. We performed a principal components analysis on different combinations of 29 quantitative traits to extract principal components (PCs) representative of multiple correlated phenotypes. GWAS of a PC derived from glomerular filtration rate, serum creatinine, and serum urea identified a suggestive peak (pmin = 1.67 × 10–7) that mapped to KCNIP4. Inclusion of other secondary CKD measurements with these three kidney function traits identified the KCNIP4 locus with GWAS significance (pmin = 1.59 × 10–9). Finally, we identified a group of two SNPs with increased minor allele frequencies as potential functional variants. With the use of genetic isolate and the PCA-based multi-phenotype GWAS approach, we have revealed a potential pleotropic effect locus for CKD. Further studies are required to assess functional relevance of this locus.
Three-dimensional morphology of bacterial community developed on the index-matched materials
Authors: Okano Chigusa , Takabe Kyosuke , Hirayama Tomohiro , Nomura Nobuhiko , Yawata Yutaka 
Published: September 2021

AbstractHerein, we demonstrate that the use of index-matching materials (IMMs) allows direct visualization of microbial cells maintained at a solid–liquid interface through confocal reflection microscopy (CRM). The refractive index mismatch induces a background reflection at the solid–liquid interface that dwarfs the reflection signals from the cells and results in low-contrast images. We found that the IMMs sufficiently suppressed the background reflection at the solid–liquid interface, facilitating the imaging of microbes at the solid surface using CRM. The use of IMMs allowed quantitative analysis of the morphology of the mesh-like structure of Pseudomonas aeruginosa biofilms formed under denitrifying conditions, which led us to propose a novel structural model of the highly porous biofilm structure. These results indicate that the use of CRM coupled with an IMM offers a unique and promising tool for probing the dynamics of biofilm formation, along with visualization of environmental organisms and newly isolated bacteria, for which transformation methods are difficult to establish.
Promoting physical distancing during COVID-19: a systematic approach to compare behavioral interventions
Authors: Blanken Tessa F. , Tanis Charlotte C. , Nauta Floor H. , Dablander Fabian , Zijlstra Bonne J. H. , Bouten Rick R. M. , Oostvogel Quinten H. , Boersma Meier J. , van der Steenhoven Maya V. , van Harreveld Frenk , de Wit Sanne , Borsboom Denny 
Published: September 2021

AbstractIn the wake of the COVID-19 pandemic, physical distancing behavior turned out to be key to mitigating the virus spread. Therefore, it is crucial that we understand how we can successfully alter our behavior and promote physical distancing. We present a framework to systematically assess the effectiveness of behavioral interventions to stimulate physical distancing. In addition, we demonstrate the feasibility of this framework in a large-scale natural experiment (N = 639) conducted during an art fair. In an experimental design, we varied interventions to evaluate the effect of face masks, walking directions, and immediate feedback on visitors’ contacts. We represent visitors as nodes, and their contacts as links in a contact network. Subsequently, we used network modelling to test for differences in these contact networks. We find no evidence that face masks influence physical distancing, while unidirectional walking directions and buzzer feedback do positively impact physical distancing. This study offers a feasible way to optimize physical distancing interventions through scientific research. As such, the presented framework provides society with the means to directly evaluate interventions, so that policy can be based on evidence rather than conjecture.
Optimized design parameters for CRISPR Cas9 and Cas12a homology-directed repair
Authors: Schubert Mollie S. , Thommandru Bernice , Woodley Jessica , Turk Rolf , Yan Shuqi , Kurgan Gavin , McNeill Matthew S. , Rettig Garrett R. 
Published: September 2021

AbstractCRISPR–Cas proteins are RNA-guided nucleases used to introduce double-stranded breaks (DSBs) at targeted genomic loci. DSBs are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Providing an exogenous DNA template during repair allows for the intentional, precise incorporation of a desired mutation via the HDR pathway. However, rates of repair by HDR are often slow compared to the more rapid but less accurate NHEJ-mediated repair. Here, we describe comprehensive design considerations and optimized methods for highly efficient HDR using single-stranded oligodeoxynucleotide (ssODN) donor templates for several CRISPR–Cas systems including S.p. Cas9, S.p. Cas9 D10A nickase, and A.s. Cas12a delivered as ribonucleoprotein (RNP) complexes. Features relating to guide RNA selection, donor strand preference, and incorporation of blocking mutations in the donor template to prevent re-cleavage were investigated and were implemented in a novel online tool for HDR donor template design. These findings allow for high frequencies of precise repair utilizing HDR in multiple mammalian cell lines. Tool availability: https://www.idtdna.com/HDR
A comparative shape analysis of the cervical spine between individuals with cervicogenic headaches and asymptomatic controls
Authors: Masharawi Youssef , Mansour Aumayma Murad , Peled Natan , Weisman Asaf 
Published: September 2021

AbstractAs some researchers theorized that cervicogenic headache (CEH) might be related to bony and discal features of the cervical spine, this retrospective study examined the shapes of the cervical vertebrae and intervertebral discs (IVDs) of individuals with CEH and compared them to asymptomatic controls. Scans of 40 subjects in their late 20’s–mid 30’s affected with CEH and 40 asymptomatic controls were obtained (overall = 19,040 measurements, age-sex matched, 20 males and 20 females in each group). The following cervical spine variables were measured: Supine lordosis, vertebral body-heights, A-P lengths, mediolateral widths and sagittal-wedging; IVDs heights and sagittal-wedging; pedicle heights, widths and transverse angles; laminar widths and transverse angles; articular facet angles, spinal canal, and transverse foramen lengths, widths, and areas. Both groups had similar shape variation along the cervical in all the measured parameters. There were no significant left–right differences in all measured parameters and no significant differences between the CEH and control groups concerning sex and age. Cervical IVDs were lordotic in shape, whereas their adjacent vertebral bodies were kyphotic in shape except for C2. In conclusion, the shape of the cervical spine and IVDs in subjects in their late 20’s–mid 30’s affected with CEH is identical to asymptomatic controls.
Real-time particle size analysis using focused beam reflectance measurement as a process analytical technology tool for continuous microencapsulation process
Authors: Muhaimin Muhaimin , Chaerunisaa Anis Yohana , Bodmeier Roland 
Published: September 2021

AbstractThe online real-time particle size analysis of the microencapsules manufacturing process using the continuous solvent evaporation method was performed using focused beam reflectance measurement (FBRM). In this paper, we use FBRM measurements to investigate the effects of polymer type and compare the size distributions to those obtained using other sizing methods such as optical microscope and laser diffraction. FBRM was also utilized to measure the length-weighted chord length distribution (CLD) and particle size distribution (PSD) online during particle solidification, which could not be done with laser diffraction or nested sieve analysis. The chord lengths and CLD data were taken at specific times using an online FBRM probe mounted below the microparticle. The timing of the FBRM determinations was coordinated with the selection of microparticle samples for particle size analysis by optical microscope and laser diffraction calculation as a reference. For all three produced batches tested, FBRM, laser diffraction, and sieve analysis yielded similar results. Hardening time for the transformation of emulsion droplets into solid microparticles occurred within the first 10.5, 19, 25, 30, and 55 min, according to FBRM results. The FBRM CLDs revealed that a larger particle size mean resulted in a longer CLD and a lower peak of particle number. The FBRM data revealed that the polymer type had a significant impact on microparticle CLD and the transformation process.
Spatiotemporal development of coexisting wave domains of Rho activity in the cell cortex
Authors: Hladyshau Siarhei , Kho Mary , Nie Shuyi , Tsygankov Denis 
Published: September 2021

AbstractThe Rho family GTPases are molecular switches that regulate cytoskeletal dynamics and cell movement through a complex spatiotemporal organization of their activity. In Patiria miniata (starfish) oocytes under in vitro experimental conditions (with overexpressed Ect2, induced expression of Δ90 cyclin B, and roscovitine treatment), such activity generates multiple co-existing regions of coherent propagation of actin waves. Here we use computational modeling to investigate the development and properties of such wave domains. The model reveals that the formation of wave domains requires a balance between the activation and inhibition in the Rho signaling motif. Intriguingly, the development of the wave domains is preceded by a stage of low-activity quasi-static patterns, which may not be readily observed in experiments. Spatiotemporal patterns of this stage and the different paths of their destabilization define the behavior of the system in the later high-activity (observable) stage. Accounting for a strong intrinsic noise allowed us to achieve good quantitative agreement between simulated dynamics in different parameter regimes of the model and different wave dynamics in Patiria miniata and wild type Xenopus laevis (frog) data. For quantitative comparison of simulated and experimental results, we developed an automated method of wave domain detection, which revealed a sharp reversal in the process of pattern formation in starfish oocytes. Overall, our findings provide an insight into spatiotemporal regulation of complex and diverse but still computationally reproducible cell-level actin dynamics.
An improved data-free surrogate model for solving partial differential equations using deep neural networks
Authors: Chen Xinhai , Chen Rongliang , Wan Qian , Xu Rui , Liu Jie 
Published: September 2021

AbstractPartial differential equations (PDEs) are ubiquitous in natural science and engineering problems. Traditional discrete methods for solving PDEs are usually time-consuming and labor-intensive due to the need for tedious mesh generation and numerical iterations. Recently, deep neural networks have shown new promise in cost-effective surrogate modeling because of their universal function approximation abilities. In this paper, we borrow the idea from physics-informed neural networks (PINNs) and propose an improved data-free surrogate model, DFS-Net. Specifically, we devise an attention-based neural structure containing a weighting mechanism to alleviate the problem of unstable or inaccurate predictions by PINNs. The proposed DFS-Net takes expanded spatial and temporal coordinates as the input and directly outputs the observables (quantities of interest). It approximates the PDE solution by minimizing the weighted residuals of the governing equations and data-fit terms, where no simulation or measured data are needed. The experimental results demonstrate that DFS-Net offers a good trade-off between accuracy and efficiency. It outperforms the widely used surrogate models in terms of prediction performance on different numerical benchmarks, including the Helmholtz, Klein–Gordon, and Navier–Stokes equations.
BAP1 methylation: a prognostic marker of uveal melanoma metastasis
Authors: Bakhoum Mathieu F. , Curtis Ellis J. , Goldbaum Michael H. , Mischel Paul S. 
Published: September 2021

AbstractUveal melanoma, the most common intraocular primary cancer in adults, is characterized by striking variability in metastatic tendencies. BAP1 deletion in the primary tumor is associated with uveal melanoma metastasis, but it cannot always be resolved by bulk DNA sequencing of heterogeneous tumors. Here, we show that assessment of BAP1 methylation is an accurate and readily clinically actionable assay to accurately identify high-risk uveal melanoma patients.
A pH, thermal and light triple-stimuli responsive micellar solution formed by a cationic surfactant and trans-o-hydroxycinnamic acid
Authors: Lv Dongmei , Liu Qi , Wu Huijun , Cheng Yiyao , Wang Chenyong , Yin Baolin , Wei Xilian , Li Jing 
Published: September 2021

A multi-stimuli responsive wormlike micellar solution (pH, temperature and light irradiation) was constructed by mixing a cationic surfactant R16HTAB and trans-o-hydroxycinnamic acid OHCA in aqueous solution.
Super-resolution imaging to reveal the nanostructure of tripartite synapses
Authors: Aleksejenko Natalija , Heller Janosch P. 
Published: September 2021

Abstract
Even though neurons are the main drivers of information processing in the brain and spinal cord, other cell types are important to mediate adequate flow of information. These include electrically passive glial cells such as microglia and astrocytes, which recently emerged as active partners facilitating proper signal transduction. In disease, these cells undergo pathophysiological changes that propel disease progression and change synaptic connections and signal transmission. In the healthy brain, astrocytic processes contact pre- and postsynaptic structures. These processes can be nanoscopic, and therefore only electron microscopy has been able to reveal their structure and morphology. However, electron microscopy is not suitable in revealing dynamic changes, and it is labour- and time-intensive. The dawn of super-resolution microscopy, techniques that ‘break’ the diffraction limit of conventional light microscopy, over the last decades has enabled researchers to reveal the nanoscopic synaptic environment. In this review, we highlight and discuss recent advances in our understanding of the nano-world of the so-called tripartite synapses, the relationship between pre- and postsynapse as well as astrocytic processes. Overall, novel super-resolution microscopy methods are needed to fully illuminate the intimate relationship between glia and neuronal cells that underlies signal transduction in the brain and that might be affected in diseases such as Alzheimer’s disease and epilepsy.
Evaluation einer Webseite zu sozialrechtlichen Fragen für Familien mit einem an Typ-1-Diabetes erkrankten Kind und für pädiatrische Diabetesteams
Authors: von Sengbusch Simone , Hiort Olaf , Frielitz Fabian Simon , Lange Karin 
Published: September 2021

Zusammenfassung
Hintergrund Nach der Manifestation eines Typ-1-Diabetes bei einem Kind benötigen viele Familien differenzierte Informationen zu spezifischen sozialrechtlichen Regelungen. In vielen Diabetesfachambulanzen oder Praxen gibt es dafür jedoch keine Sozialarbeiter, sodass sich Betroffene an das Diabetesteam wenden oder im Internet nach Hilfe suchen. Im Rahmen eines Modellprojekts unterstützte die DAMP-Stiftung von 2015 bis 2021 die Einrichtung des „Kinderdiabeteslotsen für Schleswig-Holstein“ am UKSH Lübeck. Ein zentrales Element war die Erstellung einer Webseite mit juristisch geprüften Informationen für Familien und Diabetesteams: https://www.kinderdiabeteslotse-sh.de. Die Akzeptanz der Website soll hier untersucht werden.
Methode Vom 12.04.21 bis zum 17.05.21 fand eine anonyme Erhebung der Zufriedenheit mit dem Angebot mittels eines Online-Fragebogens auf der Webseite statt. Die Daten wurden deskriptiv ausgewertet.
Ergebnisse Im genannten Zeitraum wurde der Fragebogen 228-mal aufgerufen; 179 Personen beantworteten ihn vollständig. Deren Antworten gingen in die Auswertung ein. Von den 179 Teilnehmern waren 38,6 % Eltern, 4,8 % Erwachsene mit Typ-1-Diabetes und 28,1 % Fachpersonal, mehrheitlich aus Kliniken, 28,5 % der Personen machten keine Angabe. Die Internetseite wurde von 92 % der Befragten als „wichtig“ eingestuft, 85 % beurteilten die herunterladbaren schriftlichen Informationen und Handlungsanweisungen als gut und sahen dabei keinen Verbesserungsbedarf.
Diskussion Sozialrechtliche Themen stellen einen erheblichen Anteil der ambulanten Beratung dar und erfordern vom Diabetesteam ein fundiertes sozialrechtliches Wissen. Die Sozialgesetze gelten bundesweit, aber je nach Bundesland können Ansprechpartner und Sonderregelungen zu abweichenden Antragswegen führen. Dies gilt vor allem für die Hilfen zum Thema Schule.
Schlussfolgerung Es kann diskutiert werden, ob eine solche kontinuierlich aktualisierte Internetseite über ein zentrales Organ der Diabetologie deutschlandweit Familien und Diabetesteams zugänglich gemacht werden sollte.
Effect of Antibiotic Prophylaxis on Infectious Complications in Patients with Asymptomatic Bacteriuria Undergoing Urologic Surgery
Authors: Ramos-Castaneda Jorge A. , Ruano-Ravina Alberto , Osorio-Manrique Javier , Barreto-Mora Jackeline , Segura-Cardona Angela María , Lemos-Luengas Elkin V. 
Published: September 2021

Abstract
Objectives To identify the effect of duration of surgical antibiotic prophylaxis (SAP) and other variables on infectious postsurgical complications in patients with asymptomatic bacteriuria (ASB) undergoing urological surgery.
Methods We conducted an observational study of a cohort of patients with ASB scheduled for urologic surgery at three health service providers in Colombia. The study population comprised all patients with planned urologic surgery who had ASB prior to surgery from April 2018 to January 2019. The intervention evaluated was the duration of preoperative SAP, and the outcome variable was the development of any postoperative infectious complications for up to 30 days after the procedure.
Results The present study included 184 patients with ASB scheduled for urologic surgery.The median duration of preoperative SAP (p = 0.49) or of 1 dose SAP (risk ratio [RR] = 1.24; 95% confidence interval [CI]: 0.45–3.39) were not statistically different in patients with postsurgical infectious complications. Infectious complications were more frequent among patients with benign prostatic hyperplasia (RR = 6.57; 95%CI: 1.98–21.76) and hospitalization in the preceding 3 months (RR = 8.32; 95%CI: 2.69–25.71).
Conclusion One dose of antimicrobial therapy is sufficient to avoid infectious complications in patients with ASB. There were other factors associated with postsurgical infectious complications, such as benign prostatic hyperplasia and hospitalization in the preceding 3 months.
Caracterización de la infección urinaria y resistencia antimicrobiana en receptores de trasplante renal de un centro colombiano
Authors: Castañeda-Millán David Andrés , Osorio-Iriarte Juan Carlos , Alzate-Granados Juan Pablo , Amórtegui-Rodríguez Daniel , Arbeláez-Teuzaba Juan Sebastián , Romero-Sánchez María Camila , Flórez-Barbosa Karen , Fajardo-Cediel William 
Published: September 2021

ResumenLa infección del tracto urinario (ITU) es una de las principales complicaciones postrasplante renal, los datos a nivel nacional en ese grupo poblacional son limitados.
Objetivos caracterizar la microbiología de las ITU presentadas en receptores de trasplante renal (TxR) en un centro colombiano durante el periodo 2017–2019, los factores relacionados con la resistencia antimicrobiana y el impacto de la ITU en la función del injerto renal.
Métodos estudio de corte transversal ejecutado mediante el análisis de la base de datos de ingresos hospitalarios por urgencias de pacientes receptores de TxR con sospecha clínica de ITU en una institución de cuarto nivel en Bogotá, Colombia. El análisis de datos se ejecutó en STATA 13.0.
Resultados La ITU causó 12,69% de visitas a urgencias en pacientes trasplantados. Los microorganismos aislados fueron: Escherichia coli 52,22%, Klebsiella pneumoniae 16,67%, Pseudomonas aeruginosa 4,44%, Salmonella spp 4,44%, Proteus mirabilis 3,33%, Serratia marcescens 2,22%, Klebsiella oxytoca 2,22%, Citrobacter koseri 1,11%, Enterobacter cloacae 1,11%, otros 2,22%; El urocultivo fue negativo en 10% de los casos. El 28,39% (n:23) de gérmenes aislados fue multisensible mientras que el 71,60% (n:58) expresó algún tipo de patrón de resistencia distribuido así: 68,96% productor de betalactamasa de espectro extendido (BLEE), 15,52% productor de carbapenemasas, 12,06% productor de betalactamasa tipo IRT, 3,45% fue catalogado como multirresistente. 17,78% de los pacientes presentó criterios de urosepsis, no se registró ningún caso de mortalidad asociada a la ITU. La creatinina sérica tuvo un incremento promedio de 0,46 mg/dl durante el episodio de ITU (p: <0,0001) y el antecedente de diabetes mellitus se relacionó con la ITU causada por gérmenes resistentes (p: 0,008).
Conclusiones La ITU es una causa frecuente de atención en urgencias para pacientes receptores de TxR; la Escherichia coli es el microorganismo causal más frecuente y cerca del 70% de los gérmenes aislados presentó algún patrón de resistencia antimicrobiana.