bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of alternative untranslated regions within the mRNA of the CELF1 splicing factor affects its expression
Authors: Kajdasz Arkadiusz , Niewiadomska Daria , Sekrecki Michal , Sobczak Krzysztof 
Published: January 2022

AbstractCUG-binding protein, ELAV-like Family Member 1 (CELF1) plays an important role during the development of different tissues, such as striated muscle and brain tissue. CELF1 is an RNA-binding protein that regulates RNA metabolism processes, e.g., alternative splicing, and antagonizes other RNA-binding proteins, such as Muscleblind-like proteins (MBNLs). Abnormal activity of both classes of proteins plays a crucial role in the pathogenesis of myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults. In this work, we show that alternative splicing of exons forming both the 5′ and 3′ untranslated regions (UTRs) of CELF1 mRNA is efficiently regulated during development and tissue differentiation and is disrupted in skeletal muscles in the context of DM1. Alternative splicing of the CELF1 5′UTR leads to translation of two potential protein isoforms that differ in the lengths of their N-terminal domains. We also show that the MBNL and CELF proteins regulate the distribution of mRNA splicing isoforms with different 5′UTRs and 3′UTRs and affect the CELF1 expression by changing its sensitivity to specific microRNAs or RNA-binding proteins. Together, our findings show the existence of different mechanisms of regulation of CELF1 expression through the distribution of various 5′ and 3′ UTR isoforms within CELF1 mRNA.
Tunable circular dichroism through absorption in coupled optical modes of twisted triskelia nanostructures
Authors: Rodríguez-Álvarez Javier , García-Martín Antonio , Fraile Rodríguez Arantxa , Batlle Xavier , Labarta Amílcar 
Published: January 2022

AbstractWe present a system consisting of two stacked chiral plasmonic nanoelements, so-called triskelia, that exhibits a high degree of circular dichroism. The optical modes arising from the interactions between the two elements are the main responsible for the dichroic signal. Their excitation in the absorption cross section is favored when the circular polarization of the light is opposite to the helicity of the system, so that an intense near-field distribution with 3D character is excited between the two triskelia, which in turn causes the dichroic response. Therefore, the stacking, in itself, provides a simple way to tune both the value of the circular dichroism, up to 60%, and its spectral distribution in the visible and near infrared range. We show how these interaction-driven modes can be controlled by finely tuning the distance and the relative twist angle between the triskelia, yielding maximum values of the dichroism at 20° and 100° for left- and right-handed circularly polarized light, respectively. Despite the three-fold symmetry of the elements, these two situations are not completely equivalent since the interplay between the handedness of the stack and the chirality of each single element breaks the symmetry between clockwise and anticlockwise rotation angles around 0°. This reveals the occurrence of clear helicity-dependent resonances. The proposed structure can be thus finely tuned to tailor the dichroic signal for applications at will, such as highly efficient helicity-sensitive surface spectroscopies or single-photon polarization detectors, among others.
The identification, logic and enlightenments of intra-urban place communities in China
Authors: Yang Xie , Jie Zhang , Xiao Chen 
Published: January 2022

AbstractSpatial agglomeration phenomena on the earth permeate in various fields of the natural and human world, yet their researches in human society are relatively few with the focus mainly on the economic concept of “industrial clusters”. Precise quantitative descriptions, in-depth logical analyses and proper application approaches for urban planning are lacked in various intra-urban spatial agglomeration phenomena. By using over 10 million POIs in the mainland China, 18 grid network models with two varieties of spatial relationships (co-location/adjacent) are constructed in this article. 23 typical place communities are extracted based on complex network analysis, and four types of agglomeration driving forces are summarized. A comprehensive demonstration displaying the application process of co-location/adjacent place matrices in auxiliary decision of the implanted place types is carried out with the example of the revitalization project of Taoxichuan Area in the city of Jingdezhen.
In vivo electrical conductivity measurement of muscle, cartilage, and peripheral nerve around knee joint using MR-electrical properties tomography
Authors: Lee Ji Hyun , Yoon Young Cheol , Kim Hyun Su , Lee Jiyeong , Kim Eunju , Findeklee Christian , Katscher Ulrich 
Published: January 2022

AbstractThis study aimed to investigate whether in vivo MR-electrical properties tomography (MR-EPT) is feasible in musculoskeletal tissues by evaluating the conductivity of muscle, cartilage, and peripheral nerve around the knee joint, and to explore whether these measurements change after exercise. This prospective study was approved by the institutional review board. On February 2020, ten healthy volunteers provided written informed consent and underwent MRI of the right knee using a three-dimensional balanced steady-state free precession (bSSFP) sequence. To test the effect of loading, the subjects performed 60 squatting exercises after baseline MRI, immediately followed by post-exercise MRI with the same sequences. After reconstruction of conductivity map based on the bSSFP sequence, conductivity of muscles, cartilages, and nerves were measured. Measurements between the baseline and post-exercise MRI were compared using the paired t-test. Test–retest reliability for baseline conductivity was evaluated using the intraclass correlation coefficient. The baseline and post-exercise conductivity values (mean ± standard deviation) [S/m] of muscles, cartilages, and nerves were 1.73 ± 0.40 and 1.82 ± 0.50 (p = 0.048), 2.29 ± 0.47 and 2.51 ± 0.37 (p = 0.006), and 2.35 ± 0.57 and 2.36 ± 0.57 (p = 0.927), respectively. Intraclass correlation coefficient for the baseline conductivity of muscles, cartilages, and nerves were 0.89, 0.67, and 0.89, respectively. In conclusion, in vivo conductivity measurement of musculoskeletal tissues is feasible using MR-EPT. Conductivity of muscles and cartilages significantly changed with an overall increase after exercise.
Stent grafts improved patency of ruptured hemodialysis vascular accesses
Authors: Liao Min-Tsun , Luo Chien-Ming , Hsieh Ming-Chien , Hsieh Mu-Yang , Lin Chih-Ching , Chie Wei-Chu , Yang Ten-Fang , Wu Chih-Cheng 
Published: January 2022

AbstractThis study aimed to compare stent graft with balloon tamponade for ruptured dialysis access during percutaneous transluminal angioplasty. Patients over an 8-year period (2010–2018) were identified from a database of 11,609 procedures. The primary endpoint was target lesion primary patency at 12 months. A total of 143 patients who had rupture dialysis access were enrolled, of whom 52 were salvaged by stent grafts and 91 were salvaged by balloon tamponade. The 6-month target lesion primary patency was greater in the stent graft group than in the balloon tamponade group (66.7% vs. 29.5%, P < 0.001). The benefit of stent grafts was sustained for 12 months (52.5% vs. 9.0%, P < 0.001). The stent grafts increased the median time from the index procedure to the next intervention in the ruptured area by 171 days (260 vs. 89 days) at 12 months. There was no significant difference in the access circuit patency rates at 6 months (25.5% vs. 19.8%, P = 0.203) and 12 months (12.0% vs. 5.8%, P = 0.052). The patency results of the stent grafts remained after the multivariable adjustment analysis. Compared to balloon tamponade alone, stent grafts provided superior target lesion primary patency at 6 and 12 months. The access circuit patency rates were similar.
Ti/TiO2/SiO2 multilayer thin films with enhanced spectral selectivity for optical narrow bandpass filters
Authors: Kim Dongju , Kim Kang Min , Han Hyuksu , Lee Junho , Ko Deahyeon , Park Kyoung Ryeol , Jang Kyu-bong , Kim Dongwon , Forrester Jennifer Sue , Lee Seung Hwan , Kim Jong Cheol , Mhin Sungwook 
Published: January 2022

AbstractThin film-based optical sensors have been attracting increasing interest for use in developing technologies such as biometrics. Multilayered dielectric thin films with different refractive indices have been utilized to modulate the optical properties in specific wavelength bands for spectral selectivity of Thin Film Narrow Bandpass Filters (TFNBFs). Progress in TFNBF design has been made with the incorporation of metallic thin films. Narrower bandwidths with higher transmittance have been achieved in specific spectral bands. In this work, Ti/TiO2/SiO2 based multilayer thin films were prepared using pulsed-DC reactive sputtering. Computer simulations using the Essential Macleod Program allowed the optimal number of layers and thickness of the multilayer thin films to be determined to efficiently tailor the optical path transmitting specific wavelength bands. The addition of Ti metal layers within dielectric (TiO2/SiO2) multilayer thin films significantly changes the cutoff frequency of transmittance at specific wavelengths. Representative 26 multilayer films consisting of Ti, TiO2, and SiO2 show lower transmittance of 10.29% at 400 nm and 10.48% at 680 nm. High transmittance of 80.42% at 485 nm was observed, which is expected to improve the spectral selectivity of the TFNBF. This work provides a contribution to future simulation based design strategy based on experimental thin film engineering for potential industrial development opportunities such as optical biometrics.
Distinct soil bacterial patterns along narrow and broad elevational gradients in the grassland of Mt. Tianshan, China
Authors: Li Rui , Liu Yunhua , Cheng Junhui , Xue Nana , Sun Zongjiu , Zhang Pan , Li Ning , Di Xiaoshuang , Fan Weihua , Deng Jiang , Ma Yucheng , Li Minfei , Sheng Jiandong 
Published: January 2022

AbstractBacteria are essential regulators of soil biogeochemical cycles. While several studies of bacterial elevational patterns have been performed in recent years, the drivers of these patterns remain incompletely understood. To clarify bacterial distribution patterns and diversity across narrow- and broad-scale elevational gradients, we collected soil samples from 22 sites in the grasslands of Mt. Tianshan in China along three elevational transects and the overall elevation transect: (1) 6 sites at elevations of 1047–1587 m, (2) 8 sites at 876–3070 m, and (3) 8 sites at 1602–2110 m. The bacterial community diversity across the overall elevation transects exhibited a hump-like pattern, whereas consistent patterns were not observed in the separate elevational transects. The bacterial community composition at the phylum level differed across the transects and elevation sites. The Actinobacteria was the most abundant phylum overall (41.76%) but showed clear variations in the different transects. Furthermore, heatmap analyses revealed that both pH and mean annual temperature (MAT) were significantly (P < 0.05) correlated with bacterial community composition as well as the dominant bacterial phyla, classes, and genera. These findings provide an inclusive view of bacterial community structures in relation to the environmental factors of the different elevational patterns.
Hyperrealistic neural decoding for reconstructing faces from fMRI activations via the GAN latent space
Authors: Dado Thirza , Güçlütürk Yağmur , Ambrogioni Luca , Ras Gabriëlle , Bosch Sander , van Gerven Marcel , Güçlü Umut 
Published: January 2022

AbstractNeural decoding can be conceptualized as the problem of mapping brain responses back to sensory stimuli via a feature space. We introduce (i) a novel experimental paradigm that uses well-controlled yet highly naturalistic stimuli with a priori known feature representations and (ii) an implementation thereof for HYPerrealistic reconstruction of PERception (HYPER) of faces from brain recordings. To this end, we embrace the use of generative adversarial networks (GANs) at the earliest step of our neural decoding pipeline by acquiring fMRI data as participants perceive face images synthesized by the generator network of a GAN. We show that the latent vectors used for generation effectively capture the same defining stimulus properties as the fMRI measurements. As such, these latents (conditioned on the GAN) are used as the in-between feature representations underlying the perceived images that can be predicted in neural decoding for (re-)generation of the originally perceived stimuli, leading to the most accurate reconstructions of perception to date.
Holotoxin disassembly by protein disulfide isomerase is less efficient for Escherichia coli heat-labile enterotoxin than cholera toxin
Authors: Serrano Albert , Guyette Jessica L. , Heim Joel B. , Taylor Michael , Cherubin Patrick , Krengel Ute , Teter Ken , Tatulian Suren A. 
Published: January 2022

AbstractCholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) are structurally similar AB5-type protein toxins. They move from the cell surface to the endoplasmic reticulum where the A1 catalytic subunit is separated from its holotoxin by protein disulfide isomerase (PDI), thus allowing the dissociated A1 subunit to enter the cytosol for a toxic effect. Despite similar mechanisms of toxicity, CT is more potent than LT. The difference has been attributed to a more stable domain assembly for CT as compared to LT, but this explanation has not been directly tested and is arguable as toxin disassembly is an indispensable step in the cellular action of these toxins. We show here that PDI disassembles CT more efficiently than LT, which provides a possible explanation for the greater potency of the former toxin. Furthermore, direct examination of CT and LT domain assemblies found no difference in toxin stability. Using novel analytic geometry approaches, we provide a detailed characterization of the positioning of the A subunit with respect to the B pentamer and demonstrate significant differences in the interdomain architecture of CT and LT. Protein docking analysis further suggests that these global structural differences result in distinct modes of PDI-toxin interactions. Our results highlight previously overlooked structural differences between CT and LT that provide a new model for the PDI-assisted disassembly and differential potency of these toxins.
Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality
Authors: Custodio María , Espinoza Ciro , Peñaloza Richard , Peralta-Ortiz Tessy , Sánchez-Suárez Héctor , Ordinola-Zapata Alberto , Vieyra-Peña Enedia 
Published: January 2022

AbstractThe cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.
Combinations of deletion and missense variations of the dynein-2 DYNC2LI1 subunit found in skeletal ciliopathies cause ciliary defects
Authors: Qiu Hantian , Tsurumi Yuta , Katoh Yohei , Nakayama Kazuhisa 
Published: January 2022

AbstractCilia play crucial roles in sensing and transducing extracellular signals. Bidirectional protein trafficking within cilia is mediated by the intraflagellar transport (IFT) machinery containing IFT-A and IFT-B complexes, with the aid of kinesin-2 and dynein-2 motors. The dynein-2 complex drives retrograde trafficking of the IFT machinery after its transportation to the ciliary tip as an IFT cargo. Mutations in genes encoding the dynein-2-specific subunits (DYNC2H1, WDR60, WDR34, DYNC2LI1, and TCTEX1D2) are known to cause skeletal ciliopathies. We here demonstrate that several pathogenic variants of DYNC2LI1 are compromised regarding their ability to interact with DYNC2H1 and WDR60. When expressed in DYNC2LI1-knockout cells, deletion variants of DYNC2LI1 were unable to rescue the ciliary defects of these cells, whereas missense variants, as well as wild-type DYNC2LI1, restored the normal phenotype. DYNC2LI1-knockout cells coexpressing one pathogenic deletion variant together with wild-type DYNC2LI1 demonstrated a normal phenotype. In striking contrast, DYNC2LI1-knockout cells coexpressing the deletion variant in combination with a missense variant, which mimics the situation of cells of compound heterozygous ciliopathy individuals, demonstrated ciliary defects. Thus, DYNC2LI1 deletion variants found in individuals with skeletal ciliopathies cause ciliary defects when combined with a missense variant, which expressed on its own does not cause substantial defects.
Mechanical power normalized to lung-thorax compliance indicates weaning readiness in prolonged ventilated patients
Authors: Ghiani Alessandro , Paderewska Joanna , Walcher Swenja , Tsitouras Konstantinos , Neurohr Claus , Kneidinger Nikolaus 
Published: January 2022

AbstractSince critical respiratory muscle workload is a significant determinant of weaning failure, applied mechanical power (MP) during artificial ventilation may serve for readiness testing before proceeding on a spontaneous breathing trial (SBT). Secondary analysis of a prospective, observational study in 130 prolonged ventilated, tracheotomized patients. Calculated MP’s predictive SBT outcome performance was determined using the area under receiver operating characteristic curve (AUROC), measures derived from k-fold cross-validation (likelihood ratios, Matthew's correlation coefficient [MCC]), and a multivariable binary logistic regression model. Thirty (23.1%) patients failed the SBT, with absolute MP presenting poor discriminatory ability (MCC 0.26; AUROC 0.68, 95%CI [0.59‒0.75], p = 0.002), considerably improved when normalized to lung-thorax compliance (LTCdyn-MP, MCC 0.37; AUROC 0.76, 95%CI [0.68‒0.83], p < 0.001) and mechanical ventilation PaCO2 (so-called power index of the respiratory system [PIrs]: MCC 0.42; AUROC 0.81 [0.73‒0.87], p < 0.001). In the logistic regression analysis, PIrs (OR 1.48 per 1000 cmH2O2/min, 95%CI [1.24‒1.76], p < 0.001) and its components LTCdyn-MP (1.25 per 1000 cmH2O2/min, [1.06‒1.46], p < 0.001) and mechanical ventilation PaCO2 (1.17 [1.06‒1.28], p < 0.001) were independently related to SBT failure. MP normalized to respiratory system compliance may help identify prolonged mechanically ventilated patients ready for spontaneous breathing.
Osteonecrosis development by tooth extraction in zoledronate treated mice is inhibited by active vitamin D analogues, anti-inflammatory agents or antibiotics
Authors: Soma Tomoya , Iwasaki Ryotaro , Sato Yuiko , Kobayashi Tami , Ito Eri , Matsumoto Tatsuaki , Kimura Atsushi , Miyamoto Kana , Matsumoto Morio , Nakamura Masaya , Morita Mayu , Asoda Seiji , Kawana Hiromasa , Nakagawa Taneaki , Miyamoto Takeshi 
Published: January 2022

AbstractInvasive dental treatment such as tooth extraction following treatment with strong anti-bone resorptive agents, including bisphosphonates and denosumab, reportedly promotes osteonecrosis of the jaw (ONJ) at the extraction site, but strategies to prevent ONJ remain unclear. Here we show that in mice, administration of either active vitamin D analogues, antibiotics or anti-inflammatory agents can prevent ONJ development induced by tooth extraction during treatment with the bisphosphonate zoledronate. Specifically, tooth extraction during treatment with zoledronate induced osteonecrosis in mice, but administration of either 1,25(OH)2D3 or ED71, both active vitamin D analogues, significantly antagonized osteonecrosis development, even under continuous zoledronate treatment. 1,25(OH)2D3 or ED71 administration also significantly inhibited osteocyte apoptosis induced by tooth extraction and bisphosphonate treatment. Administration of either active vitamin D analogue significantly inhibited elevation of serum inflammatory cytokine levels in mice in response to injection of lipopolysaccharide, an infection mimetic. Furthermore, administration of either anti-inflammatory or antibiotic reagents significantly blocked ONJ development following tooth extraction and zoledronate treatment. These findings suggest that administration of active vitamin D, anti-inflammatory agents or antibiotics could prevent ONJ development induced by tooth extraction in patients treated with zoledronate.
Study of risk factors for healthcare-associated infections in acute cardiac patients using categorical principal component analysis (CATPCA)
Authors: Renes Carreño Emilio , Escribá Bárcena Almudena , Catalán González Mercedes , Álvarez Lerma Francisco , Palomar Martínez Mercedes , Nuvials Casals Xavier , Jaén Herreros Felisa , Montejo González Juan Carlos 
Published: January 2022

AbstractUsing categorical principal component analysis, we aimed to determine the relationship between health care-associated infections (HAIs) and diagnostic categories (DCs) in patients with acute heart disease using data collected in the Spanish prospective ENVIN-HELICS intensive care registry over a 10-year period (2005–2015). A total of 69,876 admissions were included, of which 5597 developed HAIs. Two 2-component CATPCA models were developed. In the first model, all cases were included; the first component was determined by the duration of the invasive devices, the ICU stay, the APACHE II score and the HAIs; the second component was determined by the type of admission (medical or surgical) and by the DCs. No clear association between DCs and HAIs was found. Cronbach’s alpha was 0.899, and the variance accounted for (VAF) was 52.5%. The second model included only admissions that developed HAIs; the first component was determined by the duration of the invasive devices and the ICU stay; the second component was determined by the inflammatory response, the mortality in the ICU and the HAIs. Cronbach’s alpha value was 0.855, and VAF was 46.9%. These findings highlight the role of exposure to invasive devices in the development of HAIS in patients with acute heart disease.