bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alteration of coastal productivity and artisanal fisheries interact to affect a marine food web
Authors: Ávila-Thieme M. Isidora , Corcoran Derek , Pérez-Matus Alejandro , Wieters Evie A. , Navarrete Sergio A. , Marquet Pablo A. , Valdovinos Fernanda S. 
Published: January 2021

AbstractTop-down and bottom-up forces determine ecosystem function and dynamics. Fisheries as a top-down force can shorten and destabilize food webs, while effects driven by climate change can alter the bottom-up forces of primary productivity. We assessed the response of a highly-resolved intertidal food web to these two global change drivers, using network analysis and bioenergetic modelling. We quantified the relative importance of artisanal fisheries as another predator species, and evaluated the independent and combined effects of fisheries and changes in plankton productivity on food web dynamics. The food web was robust to the loss of all harvested species but sensitive to the decline in plankton productivity. Interestingly, fisheries dampened the negative impacts of decreasing plankton productivity on non-harvested species by reducing the predation pressure of harvested consumers on non-harvested resources, and reducing the interspecific competition between harvested and non-harvested basal species. In contrast, the decline in plankton productivity increased the sensitivity of harvested species to fishing by reducing the total productivity of the food web. Our results show that strategies for new scenarios caused by climate change are needed to protect marine ecosystems and the wellbeing of local communities dependent on their resources.
Antimicrobial effects of syndiotactic polypeptides
Authors: Hazam Prakash Kishore , Phukan Chimanjita , Akhil R. , Singh Anjali , Ramakrishnan Vibin 
Published: January 2021

AbstractWe present design and antibacterial studies of stereochemically diversified antimicrobial peptides against multidrug-resistant bacterial pathogens. Syndiotactic polypeptides are polymers of alternating L and D amino acids with LDLD or DLDL backbone stereochemical sequence, which can form stable gramicidin like helical conformations. We designed, synthesized and characterized eight model molecular systems with varied electrostatic fingerprints, modulated through calibrated sequence positioning. Six out of eight model systems showed very impressive antimicrobial activity against three difficult to treat bacterial species, Gentamicin resistant MRSA, E. coli and Mycobacterium. More importantly, the designed LDLD peptides were equally potent in serum, an important drawback of poly L peptide sequences due to enzyme mediated degradation and ion sensitivity. Further, we tested the activity of the designed peptides against drug-resistant clinical isolates of Staphylococcus aureus and Escherichia coli. Molecular dynamics simulation studies suggest formation of an assembly of individual peptides, preceding the membrane interaction and deformation. The activity estimates are comparable with the available peptide based antimicrobials, and are also highly specific and less toxic as per standard estimates. Incorporation of D amino-acids can significantly expand the peptide design space, which can in turn manifest in future biomaterial designs, especially antimicrobials.
Transperineal ultrasound as a reliable tool in the assessment of membranous urethra length in radical prostatectomy patients
Authors: Piotr Kania , Rafał Mieleszko , Marcin Kuligowski , Karol Dudka , Monika Kuca , Jakub Biedrzycki , Bartosz Zwolan , Tadeusz Dmowski , Maciej Salagierski 
Published: January 2021

AbstractTo evaluate the usefulness of transperineal ultrasound (TPUS) as a method of membranous urethra length (MUL) measurement and investigate whether preoperative (MULpre) and postoperative (MULpost) would be associated with the degree and time of urinary continence recovery after laparoscopic radical prostatectomy (LRP). 84 patients who underwent LRP between January 2017 and December 2018 were selected for final analysis. All patients had preoperative and postoperative measurement of MUL in TPUS. Urinary continence was defined as no pad or a safety pad. Recovery of continence was assessed at 1, 3, 6 and 12 months after catheter removal. We prospectively analyzed correlation of MULpre, MULpost and a percent change in membranous urethral length (MULratio) with the urinary continence status. 69 (82%) patients regained continence in the follow-up of 12 months. MULpre, MULpost and MULratio assessed in TPUS were larger in subgroups of patients who regained continence earlier and in the entire continent group. Spearman rank test showed strong correlations between MULpost and MULratio (R—0.6 and R—0.56, respectively, p < 0.0001) with the time to continence recovery in the cumulative 12 months follow-up. TPUS allowed a reliable measurement of MUL before and after LRP. MULpre, MULpost as well as MULratio are related with time to regain continence and recovery rate after LRP. Sparing longest possible sphincteric urethra, with respect to oncological outcomes is a key factor in recovering continence after prostate cancer surgery.
A finite element analysis of relationship between fracture, implant and tibial tunnel
Authors: Wang Yiqun , Qi Erpeng , Zhang Xiaojun , Xue Lu , Wang Lianyou , Tian Jiahe 
Published: January 2021

AbstractThe purpose of this article was to use finite element analysis (FEA) to study the relationship of tibial tunnel (TT) with fracture pattern and implants. A computed tomography scan of full-length tibia and fibula was obtained. Models were built after three-dimensional reconstruction. The corresponding plates and screws were constructed and assembled together with fracture models. FEA was performed and contourplots were output. The Von Mises stresses of nodes and displacements of elements were extracted. Student’s t test was used to compare the values of Von Mises stresses and displacements between corresponding models. Differences in Von Mises stresses and displacements of fragments and implants between models with and without TT were nearly all statistically significant. However, the displacements of fragments and implants for all models were < 2 mm. TT in fracture models had larger Von Mises stresses than TT in intact tibial model. However, displacements of TT in fracture models showed similar or even smaller results to those in intact tibial model. Although almost all the tested parameters were statistically significant, differences were small and values were all below the clinical threshold. This study could promote open reduction and internal fixation with one-stage reconstruction for treatment of tibial plateau fractures associated with anterior cruciate ligament (ACL) ruptures.
Enzyme and lateral flow monoclonal antibody-based immunoassays to simultaneously determine spirotetramat and spirotetramat-enol in foodstuffs
Authors: Cevallos-Cedeño Ramón E. , Agulló Consuelo , Abad-Fuentes Antonio , Abad-Somovilla Antonio , Mercader Josep V. 
Published: January 2021

AbstractSpirotetramat is employed worldwide to fight insect pests due to its high efficiency. This chemical is quickly metabolized by plants into spirotetramat-enol, so current regulations establish that both compounds must be determined in foodstuffs for monitoring purposes. Nowadays, immunochemical methods constitute rapid and cost-effective strategies for chemical contaminant analysis at trace levels. However, high-affinity binders and suitable bioconjugates are required. In this study, haptens with opposite functionalisation sites were synthesized in order to generate high-affinity monoclonal antibodies. A direct competitive enzyme-linked immunosorbent assay with an IC50 value for the sum of spirotetramat and spirotetramat-enol of 0.1 μg/L was developed using selected antibodies and a novel heterologous bioconjugate carrying a rationally-designed hapten. Studies with fortified grape, grape juice, and wine samples showed good precision and accuracy values, with limits of quantification well below the maximum residue limits. Excellent correlation of results was observed with a standard reference chromatographic method. As a step forward, a lateral flow immunoassay was developed for onsite screening analysis of spirotetramat in wine. This assay was successfully validated according to Regulation 519/2014/EU for semi-quantitative methods at concentrations in line with the legal levels of spirotetramat and spirotetramat-enol in grapes, with a satisfactory false suspect rate below 2%.
TNFα promotes oral cancer growth, pain, and Schwann cell activation
Authors: Salvo Elizabeth , Tu Nguyen H. , Scheff Nicole N. , Dubeykovskaya Zinaida A. , Chavan Shruti A. , Aouizerat Bradley E. , Ye Yi 
Published: January 2021

AbstractOral cancer is very painful and impairs a patient’s ability to eat, talk, and drink. Mediators secreted from oral cancer can excite and sensitize sensory neurons inducing pain. Cancer mediators can also activate Schwann cells, the peripheral glia that regulates neuronal function and repair. The contribution of Schwann cells to oral cancer pain is unclear. We hypothesize that the oral cancer mediator TNFα activates Schwann cells, which further promotes cancer progression and pain. We demonstrate that TNFα is overexpressed in human oral cancer tissues and correlates with increased self-reported pain in patients. Antagonizing TNFα reduces oral cancer proliferation, cytokine production, and nociception in mice with oral cancer. Oral cancer or TNFα alone increases Schwann cell activation (measured by Schwann cell proliferation, migration, and activation markers), which can be inhibited by neutralizing TNFα. Cancer- or TNFα-activated Schwann cells release pro-nociceptive mediators such as TNFα and nerve growth factor (NGF). Activated Schwann cells induce nociceptive behaviors in mice, which is alleviated by blocking TNFα. Our study suggests that TNFα promotes cancer proliferation, progression, and nociception at least partially by activating Schwann cells. Inhibiting TNFα or Schwann cell activation might serve as therapeutic approaches for the treatment of oral cancer and associated pain.
Circulator function in a Josephson junction circuit and braiding of Majorana zero modes
Authors: Kim Mun Dae 
Published: January 2021

AbstractWe propose a scheme for the circulator function in a superconducting circuit consisting of a three-Josephson junction loop and a trijunction. In this study we obtain the exact Lagrangian of the system by deriving the effective potential from the fundamental boundary conditions. We subsequently show that we can selectively choose the direction of current flowing through the branches connected at the trijunction, which performs a circulator function. Further, we use this circulator function for a non-Abelian braiding of Majorana zero modes (MZMs). In the branches of the system we introduce pairs of MZMs which interact with each other through the phases of trijunction. The circulator function determines the phases of the trijunction and thus the coupling between the MZMs to gives rise to the braiding operation. We modify the system so that MZMs might be coupled to the external ones to perform qubit operations in a scalable design.
A generic approach to study the kinetics of liquid–liquid phase separation under near-native conditions
Authors: Van Lindt Joris , Bratek-Skicki Anna , Nguyen Phuong N. , Pakravan Donya , Durán-Armenta Luis F. , Tantos Agnes , Pancsa Rita , Van Den Bosch Ludo , Maes Dominique , Tompa Peter 
Published: January 2021

AbstractUnderstanding the kinetics, thermodynamics, and molecular mechanisms of liquid–liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for studying often severely aggregation-prone proteins. Frequently applied approaches for inducing LLPS, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, often lead to very different kinetic behaviors. Here we demonstrate that at carefully selected pH values proteins such as the low-complexity domain of hnRNPA2, TDP-43, and NUP98, or the stress protein ERD14, can be kept in solution and their LLPS can then be induced by a jump to native pH. This approach represents a generic method for studying the full kinetic trajectory of LLPS under near native conditions that can be easily controlled, providing a platform for the characterization of physiologically relevant phase-separation behavior of diverse proteins.
Optimal combination treatment regimens of vaccine and radiotherapy augment tumor-bearing host immunity
Authors: Zhang Fayun , Zheng Zifeng , Barman Apurba Kumar , Wang Zihao , Wang Luyao , Zeng Wenfeng , Wang Luoyang , Qin Yan , Pandey Asmita , Zhang Chunling , Liang Wei 
Published: January 2021

AbstractA major obstacle to immunotherapy is insufficient infiltration of effector immune cells into the tumor microenvironment. Radiotherapy greatly reduces tumor burden but relapses often occur. Here we show that the immunosuppressive tumor microenvironment was gradually established by recruiting Tregs after radiation. Despite tumors being controlled after depletion of Tregs in the irradiated area, improvement of mice survival remained poor. A much better antitumor effect was achieved with vaccination followed by radiation than other treatments. Vaccination followed by radiation recruited more effector T cells in tumor regions, which responded to high levels of chemokines. Sequential combination of vaccination and radiotherapy could elicit distinct host immune responses. Our study demonstrated that optimal combination of irradiation and vaccination is required to achieve effective antitumor immune responses. We propose a combination regimen that could be easily translated into the clinic and offer an opportunity for rational combination therapies design in cancer treatment.
Crowding-induced opening of the mechanosensitive Piezo1 channel in silico
Authors: Jiang Wenjuan , Del Rosario John Smith , Botello-Smith Wesley , Zhao Siyuan , Lin Yi-chun , Zhang Han , Lacroix Jérôme , Rohacs Tibor , Luo Yun Lyna 
Published: January 2021

AbstractMechanosensitive Piezo1 channels are essential mechanotransduction proteins in eukaryotes. Their curved transmembrane domains, called arms, create a convex membrane deformation, or footprint, which is predicted to flatten in response to increased membrane tension. Here, using a hyperbolic tangent model, we show that, due to the intrinsic bending rigidity of the membrane, the overlap of neighboring Piezo1 footprints produces a flattening of the Piezo1 footprints and arms. Multiple all-atom molecular dynamics simulations of Piezo1 further reveal that this tension-independent flattening is accompanied by gating motions that open an activation gate in the pore. This open state recapitulates experimentally obtained ionic selectivity, unitary conductance, and mutant phenotypes. Tracking ion permeation along the open pore reveals the presence of intracellular and extracellular fenestrations acting as cation-selective sites. Simulations also reveal multiple potential binding sites for phosphatidylinositol 4,5-bisphosphate. We propose that the overlap of Piezo channel footprints may act as a cooperative mechanism to regulate channel activity.
MIND bomb 2 prevents RIPK1 kinase activity-dependent and -independent apoptosis through ubiquitylation of cFLIPL
Authors: Nakabayashi Osamu , Takahashi Hirotaka , Moriwaki Kenta , Komazawa-Sakon Sachiko , Ohtake Fumiaki , Murai Shin , Tsuchiya Yuichi , Koyahara Yuki , Saeki Yasushi , Yoshida Yukiko , Yamazaki Soh , Tokunaga Fuminori , Sawasaki Tatsuya , Nakano Hiroyasu 
Published: January 2021

AbstractMind bomb 2 (MIB2) is an E3 ligase involved in Notch signalling and attenuates TNF-induced apoptosis through ubiquitylation of receptor-interacting protein kinase 1 (RIPK1) and cylindromatosis. Here we show that MIB2 bound and conjugated K48– and K63–linked polyubiquitin chains to a long-form of cellular FLICE-inhibitory protein (cFLIPL), a catalytically inactive homologue of caspase 8. Deletion of MIB2 did not impair the TNF-induced complex I formation that mediates NF-κB activation but significantly enhanced formation of cytosolic death-inducing signalling complex II. TNF-induced RIPK1 Ser166 phosphorylation, a hallmark of RIPK1 death-inducing activity, was enhanced in MIB2 knockout cells, as was RIPK1 kinase activity-dependent and -independent apoptosis. Moreover, RIPK1 kinase activity-independent apoptosis was induced in cells expressing cFLIPL mutants lacking MIB2-dependent ubiquitylation. Together, these results suggest that MIB2 suppresses both RIPK1 kinase activity-dependent and -independent apoptosis, through suppression of RIPK1 kinase activity and ubiquitylation of cFLIPL, respectively.
Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication
Authors: Nong Wenyan , Qu Zhe , Li Yiqian , Barton-Owen Tom , Wong Annette Y. P. , Yip Ho Yin , Lee Hoi Ting , Narayana Satya , Baril Tobias , Swale Thomas , Cao Jianquan , Chan Ting Fung , Kwan Hoi Shan , Ngai Sai Ming , Panagiotou Gianni , Qian Pei-Yuan , Qiu Jian-Wen , Yip Kevin Y. , Ismail Noraznawati , Pati Siddhartha , John Akbar , Tobe Stephen S. , Bendena William G. , Cheung Siu Gin , Hayward Alexander , Hui Jerome H. L. 
Published: January 2021

AbstractWhole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.
Local structure and distortions of mixed methane-carbon dioxide hydrates
Authors: Cladek Bernadette R. , Everett S. Michelle , McDonnell Marshall T. , Tucker Matthew G. , Keffer David J. , Rawn Claudia J. 
Published: January 2021

AbstractA vast source of methane is found in gas hydrate deposits, which form naturally dispersed throughout ocean sediments and arctic permafrost. Methane may be obtained from hydrates by exchange with hydrocarbon byproduct carbon dioxide. It is imperative for the development of safe methane extraction and carbon dioxide sequestration to understand how methane and carbon dioxide co-occupy the same hydrate structure. Pair distribution functions (PDFs) provide atomic-scale structural insight into intermolecular interactions in methane and carbon dioxide hydrates. We present experimental neutron PDFs of methane, carbon dioxide and mixed methane-carbon dioxide hydrates at 10 K analyzed with complementing classical molecular dynamics simulations and Reverse Monte Carlo fitting. Mixed hydrate, which forms during the exchange process, is more locally disordered than methane or carbon dioxide hydrates. The behavior of mixed gas species cannot be interpolated from properties of pure compounds, and PDF measurements provide important understanding of how the guest composition impacts overall order in the hydrate structure.
Single hydrogen atom manipulation for reversible deprotonation of water on a rutile TiO2 (110) surface
Authors: Adachi Yuuki , Sang Hongqian , Sugawara Yasuhiro , Li Yan Jun 
Published: January 2021

AbstractThe discovery of hydrogen atoms on the TiO2 surface is crucial for many practical applications, including photocatalytic water splitting. Electronically activating interfacial hydrogen atoms on the TiO2 surface is a common way to control their reactivity. Modulating the potential landscape is another way, but dedicated studies for such an activation are limited. Here we show the single hydrogen atom manipulation, and on-surface facilitated water deprotonation process on a rutile TiO2 (110) surface using low temperature atomic force microscopy and Kelvin probe force spectroscopy. The configuration of the hydrogen atom is manipulated on this surface step by step using the local field. Furthermore, we quantify the force needed to relocate the hydrogen atom on this surface using force spectroscopy and density functional theory. Reliable control of hydrogen atoms provides a new mechanistic insight of the water molecules on a metal oxide surface.
Extended gate field-effect-transistor for sensing cortisol stress hormone
Authors: Sheibani Shokoofeh , Capua Luca , Kamaei Sadegh , Akbari Sayedeh Shirin Afyouni , Zhang Junrui , Guerin Hoel , Ionescu Adrian M. 
Published: January 2021

AbstractCortisol is a hormone released in response to stress and is a major glucocorticoid produced by adrenal glands. Here, we report a wearable sensory electronic chip using label-free detection, based on a platinum/graphene aptamer extended gate field effect transistor (EG-FET) for the recognition of cortisol in biological buffers within the Debye screening length. The device shows promising experimental features for real-time monitoring of the circadian rhythm of cortisol in human sweat. We report a hysteresis-free EG-FET with a voltage sensitivity of the order of 14 mV/decade and current sensitivity up to 80% over the four decades of cortisol concentration. The detection limit is 0.2 nM over a wide range, between 1 nM and 10 µM, of cortisol concentrations in physiological fluid, with negligible drift over time and high selectivity. The dynamic range fully covers those in human sweat. We propose a comprehensive analysis and a unified, predictive analytical mapping of current sensitivity in all regimes of operation.
Implementing Dialogic Reading Intervention Through Community-Based Participatory Research: A Tutorial
Authors: Holt Yolanda , Asagbra Elijah 
Published: January 2021

PurposeThis work describes community-based participatory research (CBPR) to support language and literacy development with Pre-K and kindergarten African American boys.MethodThe aim and goals of the project were designed using the CBPR model. Interventionists were trained with researcher-designed videos. Interventionist fidelity to training was assessed. Pre- and posttests of child language were completed after the 12 weeks of dialogic reading intervention.ResultsThe CBPR team learned the dialogic reading protocol from the video trainings and provided the lessons with fidelity. Children's postintervention scores of sound-matching and nonword repetition increased significantly. Postintervention changes in lexical diversity and productive syntax were age graded, such that younger children's scores increased over time whereas older children's scores decreased.ConclusionsCBPR is a viable method for speech-language pathologists seeking to develop language and literacy lessons for low resource communities. Self-paced videos can effectively train interventionists to provide dialogic reading lessons with fidelity. Young children's sound-matching and nonword repetition skills can improve significantly with 12 weeks of dialogic reading lessons.