bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast
Authors: Zhang Ying , De Laurentiis Evelina , Bohnsack Katherine E. , Wahlig Mascha , Ranjan Namit , Gruseck Simon , Hackert Philipp , Wölfle Tina , Rodnina Marina V. , Schwappach Blanche , Rospert Sabine 
Published: February 2021

AbstractThe guided entry of tail-anchored proteins (GET) pathway assists in the posttranslational delivery of tail-anchored proteins, containing a single C-terminal transmembrane domain, to the ER. Here we uncover how the yeast GET pathway component Get4/5 facilitates capture of tail-anchored proteins by Sgt2, which interacts with tail-anchors and hands them over to the targeting component Get3. Get4/5 binds directly and with high affinity to ribosomes, positions Sgt2 close to the ribosomal tunnel exit, and facilitates the capture of tail-anchored proteins by Sgt2. The contact sites of Get4/5 on the ribosome overlap with those of SRP, the factor mediating cotranslational ER-targeting. Exposure of internal transmembrane domains at the tunnel exit induces high-affinity ribosome binding of SRP, which in turn prevents ribosome binding of Get4/5. In this way, the position of a transmembrane domain within nascent ER-targeted proteins mediates partitioning into either the GET or SRP pathway directly at the ribosomal tunnel exit.
Internal constraints and arrested relaxation in main-chain nematic elastomers
Authors: Ohzono Takuya , Katoh Kaoru , Minamikawa Hiroyuki , Saed Mohand O. , Terentjev Eugene M. 
Published: February 2021

AbstractNematic liquid crystal elastomers (N-LCE) exhibit intriguing mechanical properties, such as reversible actuation and soft elasticity, which manifests as a wide plateau of low nearly-constant stress upon stretching. N-LCE also have a characteristically slow stress relaxation, which sometimes prevents their shape recovery. To understand how the inherent nematic order retards and arrests the equilibration, here we examine hysteretic stress-strain characteristics in a series of specifically designed main-chain N-LCE, investigating both macroscopic mechanical properties and the microscopic nematic director distribution under applied strains. The hysteretic features are attributed to the dynamics of thermodynamically unfavoured hairpins, the sharp folds on anisotropic polymer strands, the creation and transition of which are restricted by the nematic order. These findings provide a new avenue for tuning the hysteretic nature of N-LCE at both macro- and microscopic levels via different designs of polymer networks, toward materials with highly nonlinear mechanical properties and shape-memory applications.
SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation
Authors: Li Jingting , Xu Xiaojun , Tiwari Manisha , Chen Yifang , Fuller Mackenzie , Bansal Varun , Tamayo Pablo , Das Soumita , Ghosh Pradipta , Sen George L. 
Published: February 2021

AbstractIn adult tissue, stem and progenitor cells must tightly regulate the balance between proliferation and differentiation to sustain homeostasis. How this exquisite balance is achieved is an area of active investigation. Here, we show that epidermal genes, including ~30% of induced differentiation genes already contain stalled Pol II at the promoters in epidermal stem and progenitor cells which is then released into productive transcription elongation upon differentiation. Central to this process are SPT6 and PAF1 which are necessary for the elongation of these differentiation genes. Upon SPT6 or PAF1 depletion there is a loss of human skin differentiation and stratification. Unexpectedly, loss of SPT6 also causes the spontaneous transdifferentiation of epidermal cells into an intestinal-like phenotype due to the stalled transcription of the master regulator of epidermal fate P63. Our findings suggest that control of transcription elongation through SPT6 plays a prominent role in adult somatic tissue differentiation and the inhibition of alternative cell fate choices.
Machine learning aided carrier recovery in continuous-variable quantum key distribution
Authors: Chin Hou-Man , Jain Nitin , Zibar Darko , Andersen Ulrik L. , Gehring Tobias 
Published: February 2021

AbstractThe secret key rate of a continuous-variable quantum key distribution (CV-QKD) system is limited by excess noise. A key issue typical to all modern CV-QKD systems implemented with a reference or pilot signal and an independent local oscillator is controlling the excess noise generated from the frequency and phase noise accrued by the transmitter and receiver. Therefore accurate phase estimation and compensation, so-called carrier recovery, is a critical subsystem of CV-QKD. Here, we explore the implementation of a machine learning framework based on Bayesian inference, namely an unscented Kalman filter (UKF), for estimation of phase noise and compare it to a standard reference method and a previously demonstrated machine learning method. Experimental results obtained over a 20-km fibre-optic link indicate that the UKF can ensure very low excess noise even at low pilot powers. The measurements exhibited low variance and high stability in excess noise over a wide range of pilot signal to noise ratios. This may enable CV-QKD systems with low hardware implementation complexity which can seamlessly work on diverse transmission lines.
Directional excitation of surface plasmon using multi-mode interference in an aperture
Authors: Alam M. Z. , Yang Z. , Sheik-Bahae M. , Aitchison J. S. , Mojahedi M. 
Published: February 2021

AbstractPlasmonics is a promising technology that can find many applications in nanophotonics and biosensing. Local excitation of surface plasmons with high directionality is required for many of these applications. We demonstrate that by controlling the interference of light in a metal slot with the adjustment of the angle of incidence, it is possible to achieve highly directional surface plasmon excitation. Our numerical analysis of the structure showing a strong directionality of excited surface plasmon is confirmed by near field scanning measurements. The proposed structure can be useful for many applications including excitation of plasmonic waveguides, nanolithography, and optical sensing. To illustrate its usefulness, we experimentally demonstrate that it can be used for highly directional excitation of a dielectric loaded plasmonic waveguide. We also propose a simple structure for surface plasmon interference lithography capable of providing high image contrast using this scheme.
Thiourea and hydrogen peroxide priming improved K+ retention and source-sink relationship for mitigating salt stress in rice
Authors: Pandey Manish , Paladi Radha Krishna , Srivastava Ashish Kumar , Suprasanna Penna 
Published: February 2021

AbstractPlant bioregulators (PBRs) represent low-cost chemicals for boosting plant defense, especially under stress conditions. In the present study, redox based PBRs such as thiourea (TU; a non-physiological thiol-based ROS scavenger) and hydrogen peroxide (H2O2; a prevalent biological ROS) were assessed for their ability to mitigate NaCl stress in rice variety IR 64. Despite their contrasting redox chemistry, TU or H2O2 supplementation under NaCl [NaCl + TU (NT) or NaCl + H2O2 (NH)] generated a reducing redox environment in planta, which improved the plant growth compared with those of NaCl alone treatment. This was concomitant with better K+ retention and upregulated expression of NaCl defense related genes including HAK21, LEA1, TSPO and EN20 in both NT and NH treated seedlings. Under field conditions, foliar applications of TU and H2O2, at vegetative growth, pre-flowering and grain filling stages, increased growth and yield attributes under both control and NaCl stress conditions. Principal component analysis revealed glutathione reductase dependent reduced ROS accumulation in source (flag leaves) and sucrose synthase mediated sucrose catabolism in sink (developing inflorescence), as the key variables associated with NT and NH mediated effects, respectively. In addition, photosystem-II efficiency, K+ retention and source-sink relationship were also improved in TU and H2O2 treated plants. Taken together, our study highlights that reducing redox environment acts as a central regulator of plant’s tolerance responses to salt stress. In addition, TU and H2O2 are proposed as potential redox-based PBRs for boosting rice productivity under the realistic field conditions.
Assessment of corneal biomechanics, tonometry and pachymetry with the Corvis ST in myopia
Authors: Wang Xiaorui , McAlinden Colm , Zhang Hongbing , Yan Jie , Wang Dan , Wei Wei , Mi Shengjian 
Published: February 2021

AbstractTo evaluate the repeatability of Corvis ST corneal biomechanical, tonometry and pachymetry measurements, and agreement of pachymetry measures with the Pentacam HR and RTVue OCT. Three consecutive measurements of the right eye of 238 myopic subjects were acquired with the Corvis ST, Pentacam HR, and RTVue OCT. Repeatability of Corvis ST was evaluated by within-subject standard deviation [Sw] and repeatability limit [r]. The agreement of central corneal thickness (CCT) measurements were compared among the three instruments using the Bland–Altman limits of agreement. Comparisons were further stratified by CCT (Corneathin ≤ 500 µm; Corneanormal = 500–550 µm; Corneathick > 550 µm). Sw was below 1 mmHg in Corneathin, Corneanormal, and Corneathick groups for IOP and bIOP. Sw for SP-A1 were 4.880, 6.128, 7.719 mmHg/mm respectively. Sw for CBI were 0.228, 0.157, 0.076, and correspondingly Sw for TBI and SSI were 0.094 and 0.056, 0.079 and 0.053, 0.070 and 0.053. The Bland–Altman plots for CCT implied poor agreement with mean differences of 29.49 µm between Corvis and OCT, 9.33 µm between Pentacam and OCT, and 20.16 µm between Corvis and Pentacam. The Corvis ST showed good repeatability with the exception of CBI in the various CCT groups. The CCT measured by Corvis ST was not interchangeable with Pentacam HR and RTVue OCT.
Contactless analysis of heart rate variability during cold pressor test using radar interferometry and bidirectional LSTM networks
Authors: Shi Kilin , Steigleder Tobias , Schellenberger Sven , Michler Fabian , Malessa Anke , Lurz Fabian , Rohleder Nicolas , Ostgathe Christoph , Weigel Robert , Koelpin Alexander 
Published: February 2021

AbstractContactless measurement of heart rate variability (HRV), which reflects changes of the autonomic nervous system (ANS) and provides crucial information on the health status of a person, would provide great benefits for both patients and doctors during prevention and aftercare. However, gold standard devices to record the HRV, such as the electrocardiograph, have the common disadvantage that they need permanent skin contact with the patient. Being connected to a monitoring device by cable reduces the mobility, comfort, and compliance by patients. Here, we present a contactless approach using a 24 GHz Six-Port-based radar system and an LSTM network for radar heart sound segmentation. The best scores are obtained using a two-layer bidirectional LSTM architecture. To verify the performance of the proposed system not only in a static measurement scenario but also during a dynamic change of HRV parameters, a stimulation of the ANS through a cold pressor test is integrated in the study design. A total of 638 minutes of data is gathered from 25 test subjects and is analysed extensively. High F-scores of over 95% are achieved for heartbeat detection. HRV indices such as HF norm are extracted with relative errors around 5%. Our proposed approach is capable to perform contactless and convenient HRV monitoring and is therefore suitable for long-term recordings in clinical environments and home-care scenarios.
Association of HSS score and mechanical alignment after primary TKA of patients suffering from constitutional varus knee that caused by combined deformities: a retrospective study
Authors: Zhang Zhifeng , Chai Wei , Zhao Guanghui , Zhang Qida , Chen Zhenxian , Wang Xinyao , Wei Pingping , Zhang Yanwei , Jin Zhongmin , Qiu Yusheng 
Published: February 2021

AbstractFor pre-operative osteoarthritis (OA) patients with varus knee, previous studies showed inconsistent results. Therefore, we conducted this study to better identify the association of Hospital for Special Surgery (HSS) score and mechanical alignment. 44 patients (51 knees) with constitutional varus knee caused by combined deformities (LDFA (lateral distal femoral angle) > 90°and MPTA (medial proximal tibial angle) < 85°)) were selected and analyzed with a mean follow-up period of 14 months after total knee arthroplasty (TKA). From January 2015 to December 2016, patients were collected consecutively after primary TKA. After filtering, fifty-one knees (44patients) were analyzed with a mean follow-up period of 14 months. All patients were divided into two groups based on post-operative hip-knee-ankle (HKA) acute angle: varus mechanical alignment (VMA) group (HKA < − 3°) and neutral mechanical axis (NMA) group (− 3° ≤ HKA ≤ 3°). 30 knees were included in the NMA group, and 21 knees in the VMA group. Comparisons of HSS between NMA group and VMA group were performed. After adjusting for age and Body Mass Index (BMI) confounders, Compared with NMA group, the HSS score in VMA group decreased by 0.81 units (95% CI, − 3.37 to 1.75) p = 0.5370). For pre-operative constitutional varus knee caused by combined deformities in chinese populations, no significant association between post-operative lower limb mechanical alignment and HSS score was found.
Plasmodium oocysts respond with dormancy to crowding and nutritional stress
Authors: Habtewold Tibebu , Sharma Aayushi A. , Wyer Claudia A. S. , Masters Ellen K. G. , Windbichler Nikolai , Christophides George K. 
Published: February 2021

AbstractMalaria parasites develop as oocysts in the mosquito for several days before they are able to infect a human host. During this time, mosquitoes take bloodmeals to replenish their nutrient and energy reserves needed for flight and reproduction. We hypothesized that these bloodmeals are critical for oocyst growth and that experimental infection protocols, typically involving a single bloodmeal at the time of infection, cause nutritional stress to the developing oocysts. Therefore, enumerating oocysts disregarding their growth and differentiation state may lead to erroneous conclusions about the efficacy of transmission blocking interventions. Here, we examine this hypothesis in Anopheles coluzzii mosquitoes infected with the human and rodent parasites Plasmodium falciparum and Plasmodium berghei, respectively. We show that oocyst growth and maturation rates decrease at late developmental stages as infection intensities increase; an effect exacerbated at very high infection intensities but fully restored with post infection bloodmeals. High infection intensities and starvation conditions reduce RNA Polymerase III activity in oocysts unless supplemental bloodmeals are provided. Our results suggest that oocysts respond to crowding and nutritional stress with a dormancy-like strategy, which urges the development of alternative methods to assess the efficacy of transmission blocking interventions.
The marker of alkyl DNA base damage, N7-methylguanine, is associated with semen quality in men
Authors: Altakroni B. , Nevin C. , Carroll M. , Murgatroyd C. , Horne G. , Brison D. R. , Povey A. C. 
Published: February 2021

AbstractSperm DNA contains a range of DNA base damage that can arise, in part, from exposure to methylating agents. However, the effects are not fully characterized and so the aim of this study was to investigate associations between semen quality and the levels of N7-methyldeoxyguanosine (N7-MedG), a marker of exposure to methylating agents, and other markers of DNA damage and DNA methylation. Sperm samples were collected from 105 men attending an assisted reproduction clinic as part of a couple undergoing treatment for infertility and semen quality assessed manually according to WHO guidelines. Semen levels of N7-MedG, quantified by immunoslotblot, were significantly higher in men with sperm concentration < 15 × 106/ml (p ≤ 0.01), semen volume < 1.5 ml (p ≤ 0.05) and also in men with any aspect of semen quality below WHO reference levels (p ≤ 0.001). Measures of neutral Comet DNA damage were correlated with semen quality in a univariate analysis but not after adjustment for N7-MedG levels. Sperm concentration was negatively associated with % methylation at the gene for DAZL but no other marker of global or gene-specific DNA methylation. Results support the hypothesis that the known toxic and DNA damaging properties of alkylating agent exposure may have direct deleterious consequences on semen quality.
Response differences of HepG2 and Primary Mouse Hepatocytes to morphological changes in electrospun PCL scaffolds
Authors: Bate Thomas S. R. , Gadd Victoria L. , Forbes Stuart J. , Callanan Anthony 
Published: February 2021

AbstractLiver disease cases are rapidly expanding across the globe and the only effective cure for end-stage disease is a transplant. Transplant procedures are costly and current supply of donor livers does not satisfy demand. Potential drug treatments and regenerative therapies that are being developed to tackle these pressing issues require effective in-vitro culture platforms. Electrospun scaffolds provide bio-mimetic structures upon which cells are cultured to regulate function in-vitro. This study aims to shed light on the effects of electrospun PCL morphology on the culture of an immortalised hepatic cell line and mouse primary hepatocytes. Each cell type was cultured on large 4–5 µm fibres and small 1–2 µm fibres with random, aligned and highly porous cryogenically spun configurations. Cell attachment, proliferation, morphology and functional protein and gene expression was analysed. Results show that fibre morphology has a measurable influence on cellular morphology and function, with the alteration of key functional markers such as CYP1A2 expression.
Laying hen mortality in different indoor housing systems: a meta-analysis of data from commercial farms in 16 countries
Authors: Schuck-Paim Cynthia , Negro-Calduch Elsa , Alonso Wladimir J. 
Published: February 2021

AbstractSocietal concern with the welfare of egg laying hens housed in conventional cages is fostering a transition towards cage-free systems in many countries. However, although cage-free facilities enable hens to move freely and express natural behaviours, concerns have also been raised over the possibility that cage-free flocks experience higher mortality, potentially compromising some aspects of their welfare. To investigate this possibility, we conducted a large meta-analysis of laying hen mortality in conventional cages, furnished cages and cage-free aviaries using data from 6040 commercial flocks and 176 million hens from 16 countries. We show that except for conventional cages, mortality gradually drops as experience with each system builds up: since 2000, each year of experience with cage-free aviaries was associated with a 0.35–0.65% average drop in cumulative mortality, with no differences in mortality between caged and cage-free systems in more recent years. As management knowledge evolves and genetics are optimized, new producers transitioning to cage-free housing may experience even faster rates of decline. Our results speak against the notion that mortality is inherently higher in cage-free production and illustrate the importance of considering the degree of maturity of production systems in any investigations of farm animal health, behaviour and welfare.
The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche
Authors: Jacchetti Emanuela , Nasehi Ramin , Boeri Lucia , Parodi Valentina , Negro Alessandro , Albani Diego , Osellame Roberto , Cerullo Giulio , Matas Jose Felix Rodriguez , Raimondi Manuela Teresa 
Published: February 2021

AbstractSmart biomaterials are increasingly being used to control stem cell fate in vitro by the recapitulation of the native niche microenvironment. By integrating experimental measurements with numerical models, we show that in mesenchymal stem cells grown inside a 3D synthetic niche both nuclear transport of a myogenic factor and the passive nuclear diffusion of a smaller inert protein are reduced. Our results also suggest that cell morphology modulates nuclear proteins import through a partition of the nuclear envelope surface, which is a thin but extremely permeable annular portion in cells cultured on 2D substrates. Therefore, our results support the hypothesis that in stem cell differentiation, the nuclear import of gene-regulating transcription factors is controlled by a strain-dependent nuclear envelope permeability, probably related to the reorganization of stretch-activated nuclear pore complexes.
Development, characterization, and applications of multi-material stereolithography bioprinting
Authors: Grigoryan Bagrat , Sazer Daniel W. , Avila Amanda , Albritton Jacob L. , Padhye Aparna , Ta Anderson H. , Greenfield Paul T. , Gibbons Don L. , Miller Jordan S. 
Published: February 2021

AbstractAs a 3D bioprinting technique, hydrogel stereolithography has historically been limited in its ability to capture the spatial heterogeneity that permeates mammalian tissues and dictates structure–function relationships. This limitation stems directly from the difficulty of preventing unwanted material mixing when switching between different liquid bioinks. Accordingly, we present the development, characterization, and application of a multi-material stereolithography bioprinter that provides controlled material selection, yields precise regional feature alignment, and minimizes bioink mixing. Fluorescent tracers were first used to highlight the broad design freedoms afforded by this fabrication strategy, complemented by morphometric image analysis to validate architectural fidelity. To evaluate the bioactivity of printed gels, 344SQ lung adenocarcinoma cells were printed in a 3D core/shell architecture. These cells exhibited native phenotypic behavior as evidenced by apparent proliferation and formation of spherical multicellular aggregates. Cells were also printed as pre-formed multicellular aggregates, which appropriately developed invasive protrusions in response to hTGF-β1. Finally, we constructed a simplified model of intratumoral heterogeneity with two separate sub-populations of 344SQ cells, which together grew over 14 days to form a dense regional interface. Together, these studies highlight the potential of multi-material stereolithography to probe heterotypic interactions between distinct cell types in tissue-specific microenvironments.