bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution of antibiotic resistance genes in chicken gut microbiota commensals
Authors: Juricova Helena , Matiasovicova Jitka , Kubasova Tereza , Cejkova Darina , Rychlik Ivan 
Published: February 2021

AbstractAntibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.
Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context
Authors: Fujimoto Kayo , Bahl Justin , Wertheim Joel O. , Del Vecchio Natascha , Hicks Joseph T. , Damodaran Lambodhar , Hallmark Camden J. , Lavingia Richa , Mora Ricardo , Carr Michelle , Yang Biru , Schneider John A. , Hwang Lu-Yu , McNeese Marlene 
Published: February 2021

AbstractThis study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010–2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.
The effect of particle shape on discharge and clogging
Authors: Hafez Ahmed , Liu Qi , Finkbeiner Thomas , Alouhali Raed A. , Moellendick Timothy E. , Santamarina J. Carlos 
Published: February 2021

AbstractGranular flow is common across different fields from energy resource recovery and mineral processing to grain transport and traffic flow. Migrating particles may jam and form arches that span constrictions and hinder particle flow. Most studies have investigated the migration and clogging of spherical particles, however, natural particles are rarely spherical, but exhibit eccentricity, angularity and roughness. New experiments explore the discharge of cubes, 2D crosses, 3D crosses and spheres under dry conditions and during particle-laden fluid flow. Variables include orifice-to-particle size ratio and solidity. Cubes and 3D crosses are the most prone to clogging because of their ability to interlock or the development of face-to-face contacts that can resist torque and enhance bridging. Spheres arriving to the orifice must be correctly positioned to create stable bridges, while flat 2D crosses orient their longest axes in the direction of flowlines across the orifice and favor flow. Intermittent clogging causes kinetic retardation in particle-laden flow even in the absence of inertial effects; the gradual increase in the local particle solidity above the constriction enhances particle interactions and the probability of clogging. The discharge volume before clogging is a Poisson process for small orifice-to-particle size ratio; however, the clogging probability becomes history-dependent for non-spherical particles at large orifice-to-particle size ratio and high solidities, i.e., when particle–particle interactions and interlocking gain significance.
A CRISPR-Cas9 based shuffle system for endogenous histone H3 and H4 combinatorial mutagenesis
Authors: Fu Yu , Zhu Zhenglin , Meng Geng , Zhang Rijun , Zhang Yueping 
Published: February 2021

AbstractPost-translational modifications of histone proteins greatly impact gene expression and cell fate decisions in eukaryotes. To study these, it is important to develop a convenient, multiplex, and efficient method to precisely introduce mutations to histones. Because eukaryotic cells usually contain multiple copies of histone genes, it is a challenge to mutate all histones at the same time by the traditional homologous recombination method. Here, we developed a CRISPR-Cas9 based shuffle system in Saccharomyces cerevisiae, to generate point mutations on both endogenous histone H3 and H4 genes in a rapid, seamless and multiplex fashion. Using this method, we generated yeast strains containing histone triple H3–K4R–K36R–K79R mutants and histone combinatorial H3–K56Q–H4–K59A double mutants with high efficiencies (70–80%). This CRISPR-Cas9 based mutagenesis system could be an invaluable tool to the epigenetics field.
Automated quantification of posterior vitreous inflammation: optical coherence tomography scan number requirements
Authors: Terheyden Jan Henrik , Ometto Giovanni , Montesano Giovanni , Wintergerst Maximilian W. M. , Langner Magdalena , Liu Xiaoxuan , Keane Pearse A. , Crabb David P. , Denniston Alastair K. , Finger Robert P. 
Published: February 2021

AbstractQuantifying intraocular inflammation is crucial in managing uveitis patients. We assessed the minimum B-scan density for reliable automated vitreous intensity (VI) assessment, using a novel approach based on optical coherence tomography (OCT). OCT volume scans centered on the macula were retrospectively collected in patients with uveitis. Nine B-scans per volume scan at fixed locations were automatically analyzed. The following B-scan selections were compared against the average score of 9 B-scans per volume scan as a reference standard: 1/3/5/7 central scans (1c/3c/5c/7c), 3 widely distributed scans (3w). Image data of 49 patients (31 females) were included. The median VI was 0.029 (IQR: 0.032). The intra-class-correlation coefficient of the VI across the 9 B-scans was 0.923. The median difference from the reference standard ranged between 0.001 (7c) and 0.006 (1c). It was significantly lower for scan selection 3w than 5c, p(adjusted) = 0.022, and lower for selection 7c than 3w, p(adjusted) = 0.003. The scan selections 7c and 3w showed the two highest areas under the receiver operating curve (0.985 and 0.965, respectively). Three widely distributed B-scans are sufficient to quantify VI reliably. Highest reliability was achieved using 7 central B-scans. Automated quantification of VI in uveitis is reliable and requires only few OCT B-scans.
Development and first biomechanical validation of a score to predict bone implant interface stability based on clinical qCT scans
Authors: Wähnert Dirk , Frank Andre , Ueberberg Johanna , Heilmann Lukas F. , Sauzet Odile , Raschke Michael J. , Gehweiler Dominic 
Published: February 2021

AbstractSufficient implant anchoring in osteoporotic bone is one major challenge in trauma and orthopedic surgery. In these cases, preoperative planning of osteosynthesis is becoming increasingly important. This study presents the development and first biomechanical validation of a bone-implant-anchorage score based on clinical routine quantitative computer tomography (qCT) scans. 10 pairs of fresh frozen femora (mean age 77.4 years) underwent clinical qCT scans after placing 3 referential screws (for matching with the second scan). Afterwards, three 4.5 mm cortical screws (DePuy Synthes, Zuchwil, Switzerland) were placed in each distal femur in the dia-metaphyseal transition followed by the second CT scan. The femur was segmented using thresholding and its outer shape was visualized as a surface model. A 3D model of the cortex screw in STL format was used to model the screw surface precisely. For each femur, the 3 cortex screw models were exactly positioned at the locations previously determined using the second CT scan. The BMD value was calculated at the center of each triangle as an interpolation from the measured values at the three vertices (triangle corners) in the CT. Scores are based on the sum of all the triangles’ areas multiplied by their BMD values. Four different scores were calculated. A screw pull-out test was performed until loss of resistance. A quadratic model adequately describes the relation between all the scores and pull-out values. The square of the best score explains just fewer than 70% of the total variance of the pull-out values and the standardized residual which were approximately normally distributed. In addition, there was a significant correlation between this score and the peak pull-out force (p < 0.001). The coefficient of determination was 0.82. The presented score has the potential to improve preoperative planning by adding the mechanical to the anatomical dimension when planning screw placement.
Assessment of common housekeeping genes as reference for gene expression studies using RT-qPCR in mouse choroid plexus
Authors: Ho Kim Hoa , Patrizi Annarita 
Published: February 2021

AbstractChoroid plexus (ChP), a vascularized secretory epithelium located in all brain ventricles, plays critical roles in development, homeostasis and brain repair. Reverse transcription quantitative real-time PCR (RT-qPCR) is a popular and useful technique for measuring gene expression changes and also widely used in ChP studies. However, the reliability of RT-qPCR data is strongly dependent on the choice of reference genes, which are supposed to be stable across all samples. In this study, we validated the expression of 12 well established housekeeping genes in ChP in 2 independent experimental paradigms by using popular stability testing algorithms: BestKeeper, DeltaCq, geNorm and NormFinder. Rer1 and Rpl13a were identified as the most stable genes throughout mouse ChP development, while Hprt1 and Rpl27 were the most stable genes across conditions in a mouse sensory deprivation experiment. In addition, Rpl13a, Rpl27 and Tbp were mutually among the top five most stable genes in both experiments. Normalisation of Ttr and Otx2 expression levels using different housekeeping gene combinations demonstrated the profound effect of reference gene choice on target gene expression. Our study emphasized the importance of validating and selecting stable housekeeping genes under specific experimental conditions.
A new FTIR method for estimating the firing temperature of ceramic bronze-casting moulds from early China
Authors: Yan Bichen , Liu Siran , Chastain Matthew L. , Yang Shugang , Chen Jianli 
Published: February 2021

AbstractIntricate ceramic bronze-casting moulds are among the most significant archaeological remains found at Bronze Age metallurgical workshops in China. Firing temperature was presumably one of the most important technical factors in mould making. However, it has proven difficult to determine the firing temperatures of excavated moulds using existing analytical methods. This study establishes an innovative new method for using Fourier-transform infrared spectroscopy (FTIR) to estimate the firing temperature of clay-containing remains. The method is based on the finding that the infrared absorptivity of fired clay minerals, measured at the Si–O–Si stretching resonance band, is negatively correlated with firing temperature. Moulds and mould cores dating to the Early Shang period (sixteenth to fourteenth century BCE) are found to have been fired at extremely low temperatures—as low as 200–300 °C in many instances. These results provide critical new data for understanding the metallurgical technology of ancient China.
Enhancement of elastin expression by transdermal administration of sialidase isozyme Neu2
Authors: Minami Akira , Fujita Yuka , Goto Jun , Iuchi Ayano , Fujita Kosei , Mikami Yasuyo , Shiratori Mako , Ishii Ami , Mitragotri Samir , Iwao Yasunori , Kanazawa Hiroaki , Kurebayashi Yuuki , Takahashi Tadanobu , Otsubo Tadamune , Ikeda Kiyoshi , Suzuki Takashi 
Published: February 2021

AbstractReduction of elastin in the skin causes various skin diseases as well as wrinkles and sagging with aging. Sialidase is a hydrolase that cleaves a sialic acid residue from sialoglycoconjugate. Cleavage of sialic acid from microfibrils by the sialidase isozyme Neu1 facilitates elastic fiber assembly. In the present study, we showed that a lower layer of the dermis and muscle showed relatively intense sialidase activity. The sialidase activity in the skin decreased with aging. Choline and geranate (CAGE), one of the ionic liquids, can deliver the sialidase subcutaneously while maintaining the enzymatic activity. The elastin level in the dermis was increased by applying sialidase from Arthrobacter ureafaciens (AUSA) with CAGE on the skin for 5 days in rats and senescence-accelerated mice prone 1 and 8. Sialidase activity in the dermis was considered to be mainly due to Neu2 based on the expression level of sialidase isozyme mRNA. Transdermal administration of Neu2 with CAGE also increased the level of elastin in the dermis. Therefore, not only Neu1 but also Neu2 would be involved in elastic fiber assembly. Transdermal administration of sialidase is expected to be useful for improvement of wrinkles and skin disorders due to the loss of elastic fibers.
Structural degradation of tungsten sandwiched in hafnia layers determined by in-situ XRD up to 1520 °C
Authors: Krishnamurthy Gnanavel Vaidhyanathan , Chirumamilla Manohar , Rout Surya Snata , Furlan Kaline P. , Krekeler Tobias , Ritter Martin , Becker Hans-Werner , Petrov Alexander Yu , Eich Manfred , Störmer Michael 
Published: February 2021

AbstractThe high-temperature stability of thermal emitters is one of the critical properties of thermophotovoltaic (TPV) systems to obtain high radiative power and conversion efficiencies. W and HfO2 are ideal due to their high melting points and low vapor pressures. At high temperatures and given vacuum conditions, W is prone to oxidation resulting in instantaneous sublimation of volatile W oxides. Herein, we present a detailed in-situ XRD analysis of the morphological changes of a 3-layer-system: HfO2/W/HfO2 layers, in a high-temperature environment, up to 1520 °C. These samples were annealed between 300 °C and 1520 °C for 6 h, 20 h, and 40 h at a vacuum pressure below 3 × 10–6 mbar using an in-situ high-temperature X-ray diffractometer, which allows investigation of crucial alterations in HfO2 and W layers. HfO2 exhibits polymorphic behavior, phase transformations and anisotropy of thermal expansion leads to formation of voids above 800 °C. These voids serve as transport channels for the residual O2 present in the annealing chamber to access W, react with it and form volatile tungsten oxides. An activation energy of 1.2 eV is calculated. This study clarifies the limits for the operation of W-HfO2 spectrally selective emitters for TPV in high-temperature applications.
Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody
Authors: Valenzuela Nieto Guillermo , Jara Ronald , Watterson Daniel , Modhiran Naphak , Amarilla Alberto A. , Himelreichs Johanna , Khromykh Alexander A. , Salinas-Rebolledo Constanza , Pinto Teresa , Cheuquemilla Yorka , Margolles Yago , López González del Rey Natalia , Miranda-Chacon Zaray , Cuevas Alexei , Berking Anne , Deride Camila , González-Moraga Sebastián , Mancilla Héctor , Maturana Daniel , Langer Andreas , Toledo Juan Pablo , Müller Ananda , Uberti Benjamín , Krall Paola , Ehrenfeld Pamela , Blesa Javier , Chana-Cuevas Pedro , Rehren German , Schwefel David , Fernandez Luis Ángel , Rojas-Fernandez Alejandro 
Published: February 2021

AbstractDespite unprecedented global efforts to rapidly develop SARS-CoV-2 treatments, in order to reduce the burden placed on health systems, the situation remains critical. Effective diagnosis, treatment, and prophylactic measures are urgently required to meet global demand: recombinant antibodies fulfill these requirements and have marked clinical potential. Here, we describe the fast-tracked development of an alpaca Nanobody specific for the receptor-binding-domain (RBD) of the SARS-CoV-2 Spike protein with potential therapeutic applicability. We present a rapid method for nanobody isolation that includes an optimized immunization regimen coupled with VHH libraryE. colisurface display, which allows single-step selection of Nanobodies using a simple density gradient centrifugation of the bacterial library. The selected single and monomeric Nanobody, W25, binds to the SARS-CoV-2 S RBD with sub-nanomolar affinity and efficiently competes with ACE-2 receptor binding. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent.
Study of the fluorescence and interaction between cyclodextrins and neochlorogenic acid, in comparison with chlorogenic acid
Authors: Navarro-Orcajada Silvia , Matencio Adrián , Vicente-Herrero Cristina , García-Carmona Francisco , López-Nicolás José Manuel 
Published: February 2021

AbstractNeochlorogenic acid, a less-studied isomer of chlorogenic acid, has been seen to posses antioxidant, antifungal, anti-inflammatory and anticarcinogenic effects, which makes it an interesting candidate for incorporation in functional foods. However, its poor solubility in water and susceptibility to oxidation make such a task difficult. To overcome that, its encapsulation in cyclodextrins (CDs) is proposed. The fluorescence of neochlorogenic acid in different pH conditions was analyzed, and caffeic acid was proved to be the fluorescent moiety in the molecule. An encapsulation model whereby the ligand poses two potential complexation sites (caffeic and D-(-)-quinic moieties), showed that α-CD and HP-β-CD formed the best inclusion complexes with neochlorogenic acid, followed by M-β-CD, β-CD and γ-CD. Molecular docking with the two best CDs gave better scores for α-CD, despite HP-β-CD providing stabilization through H-bonds. The encapsulation of chlorogenic acid led to a similar CD order and scores, although constants were higher for α-CD, β-CD and M-β-CD, lower for HP-β-CD, and negligible for γ-CD. The protonation state affected these results leading to a different order of CD preference. The solubility and the susceptibility to oxidation of neochlorogenic acid improved after complexation with α-CD and HP-β-CD, while the antioxidant activity of both isomers was maintained.
Integrated analysis identifies oxidative stress genes associated with progression and prognosis in gastric cancer
Authors: Wu Zhengyuan , Wang Lin , Wen Zhenpei , Yao Jun 
Published: February 2021

AbstractOxidative stress (OS) reactions are reported to be associated with oncogenesis and tumor progression. However, little is known about the potential diagnostic value of OS in gastric cancer (GC). This study identified hub OS genes associated with the prognosis and progression of GC and illustrated the underlying mechanisms. The transcriptome data and corresponding GC clinical information were collected from The Cancer Genome Atlas (TCGA) database. Aberrantly expressed OS genes between tumors and adjacent normal tissues were screened, and 11 prognosis-associated genes were identified with a series of bioinformatic analyses and used to construct a prognostic model. These genes were validated in the Gene Expression Omnibus (GEO) database. Furthermore, weighted gene co-expression network analysis (WGCNA) was subsequently conducted to identify the most significant hub genes for the prediction of GC progression. Analysis revealed that a good prognostic model was constructed with a better diagnostic accuracy than other clinicopathological characteristics in both TCGA and GEO cohorts. The model was also significantly associated with the overall survival of patients with GC. Meanwhile, a nomogram based on the risk score was established, which displayed a favorable discriminating ability for GC. In the WGCNA analysis, 13 progression-associated hub OS genes were identified that were also significantly associated with the progression of GC. Furthermore, functional and gene ontology (GO) analyses were performed to reveal potential pathways enriched with these genes. These results provide novel insights into the potential applications of OS-associated genes in patients with GC.
Effectiveness of a stand-alone, smartphone-based virtual reality exposure app to reduce fear of heights in real-life: a randomized trial
Authors: Bentz Dorothée , Wang Nan , Ibach Merle K. , Schicktanz Nathalie S. , Zimmer Anja , Papassotiropoulos Andreas , de Quervain Dominique J. F. 
Published: February 2021

AbstractSmartphone-based virtual reality (VR) applications (apps) might help to counter low utilization rates of available treatments for fear of heights. Demonstration of effectiveness in real-life situations of such apps is crucial, but lacking so far. Objective of this study was to develop a stand-alone, smartphone-based VR exposure app—Easy Heights—and to test its effectiveness in a real-life situation. We performed a single-blind, parallel group, randomized controlled trial. We recruited 70 participants with fear of heights, aged 18–60 years. Primary outcome was performance in a real-life Behavioral Avoidance Test (BAT) on a lookout tower after a single 1-h app use (phase 1) and after additional repeated (6 × 30 min) app use at home (phase 2). After phase 2, but not phase 1, participants in theEasy Heightscondition showed significantly higher BAT scores compared to participants in the control condition (Cohen’s d = 1.3,p = 0.0001). Repeated use of our stand-alone, smartphone-based VR exposure app reduces avoidance behavior and fear, providing a low-threshold treatment for fear of heights.