bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hamiltonian simulation algorithms for near-term quantum hardware
Authors: Clinton Laura , Bausch Johannes , Cubitt Toby 
Published: August 2021

AbstractThe quantum circuit model is the de-facto way of designing quantum algorithms. Yet any level of abstraction away from the underlying hardware incurs overhead. In this work, we develop quantum algorithms for Hamiltonian simulation "one level below” the circuit model, exploiting the underlying control over qubit interactions available in most quantum hardware and deriving analytic circuit identities for synthesising multi-qubit evolutions from two-qubit interactions. We then analyse the impact of these techniques under the standard error model where errors occur per gate, and an error model with a constant error rate per unit time. To quantify the benefits of this approach, we apply it to time-dynamics simulation of the 2D spin Fermi-Hubbard model. Combined with new error bounds for Trotter product formulas tailored to the non-asymptotic regime and an analysis of error propagation, we find that e.g. for a 5 × 5 Fermi-Hubbard lattice we reduce the circuit depth from 1, 243, 586 using the best previous fermion encoding and error bounds in the literature, to 3, 209 in the per-gate error model, or the circuit-depth-equivalent to 259 in the per-time error model. This brings Hamiltonian simulation, previously beyond reach of current hardware for non-trivial examples, significantly closer to being feasible in the NISQ era.
Complete and efficient conversion of plant cell wall hemicellulose into high-value bioproducts by engineered yeast
Authors: Sun Liang , Lee Jae Won , Yook Sangdo , Lane Stephan , Sun Ziqiao , Kim Soo Rin , Jin Yong-Su 
Published: August 2021

AbstractPlant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae. The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an enginered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.
The potential of chemical bonding to design crystallization and vitrification kinetics
Authors: Persch Christoph , Müller Maximilian J. , Yadav Aakash , Pries Julian , Honné Natalie , Kerres Peter , Wei Shuai , Tanaka Hajime , Fantini Paolo , Varesi Enrico , Pellizzer Fabio , Wuttig Matthias 
Published: August 2021

AbstractControlling a state of material between its crystalline and glassy phase has fostered many real-world applications. Nevertheless, design rules for crystallization and vitrification kinetics still lack predictive power. Here, we identify stoichiometry trends for these processes in phase change materials, i.e. along the GeTe-GeSe, GeTe-SnTe, and GeTe-Sb2Te3 pseudo-binary lines employing a pump-probe laser setup and calorimetry. We discover a clear stoichiometry dependence of crystallization speed along a line connecting regions characterized by two fundamental bonding types, metallic and covalent bonding. Increasing covalency slows down crystallization by six orders of magnitude and promotes vitrification. The stoichiometry dependence is correlated with material properties, such as the optical properties of the crystalline phase and a bond indicator, the number of electrons shared between adjacent atoms. A quantum-chemical map explains these trends and provides a blueprint to design crystallization kinetics.
En route to dynamic life processes by SNARE-mediated fusion of polymer and hybrid membranes
Authors: Otrin Lado , Witkowska Agata , Marušič Nika , Zhao Ziliang , Lira Rafael B. , Kyrilis Fotis L. , Hamdi Farzad , Ivanov Ivan , Lipowsky Reinhard , Kastritis Panagiotis L. , Dimova Rumiana , Sundmacher Kai , Jahn Reinhard , Vidaković-Koch Tanja 
Published: August 2021

AbstractA variety of artificial cells springs from the functionalization of liposomes with proteins. However, these models suffer from low durability without repair and replenishment mechanisms, which can be partly addressed by replacing the lipids with polymers. Yet natural membranes are also dynamically remodeled in multiple cellular processes. Here, we show that synthetic amphiphile membranes also undergo fusion, mediated by the protein machinery for synaptic secretion. We integrated fusogenic SNAREs in polymer and hybrid vesicles and observed efficient membrane and content mixing. We determined bending rigidity and pore edge tension as key parameters for fusion and described its plausible progression through cryo-EM snapshots. These findings demonstrate that dynamic membrane phenomena can be reconstituted in synthetic materials, thereby providing new tools for the assembly of synthetic protocells.
Interplay of diverse adjuvants and nanoparticle presentation of native-like HIV-1 envelope trimers
Authors: Sliepen Kwinten , Schermer Edith , Bontjer Ilja , Burger Judith A. , Lévai Réka Felfödiné , Mundsperger Philipp , Brouwer Philip J. M. , Tolazzi Monica , Farsang Attila , Katinger Dietmar , Moore John P. , Scarlatti Gabriella , Shattock Robin J. , Sattentau Quentin J. , Sanders Rogier W. 
Published: August 2021

AbstractThe immunogenicity of HIV-1 envelope (Env) trimers is generally poor. We used the clinically relevant ConM SOSIP trimer to compare the ability of different adjuvants (squalene emulsion, ISCOMATRIX, GLA-LSQ, and MPLA liposomes) to support neutralizing antibody (NAb) responses in rabbits. The trimers were administered as free proteins or on nanoparticles. The rank order for the adjuvants was ISCOMATRIX > SE > GLA-LSQ ~ MPLA liposomes > no adjuvant. Stronger NAb responses were elicited when the ConM SOSIP trimers were presented on ferritin nanoparticles. We also found that the GLA-LSQ adjuvant induced an unexpectedly strong antibody response to the ferritin core of the nanoparticles. This “off-target” effect may have compromised its ability to induce the more desired antitrimer antibodies. In summary, both adjuvants and nanoparticle display can improve the magnitude of the antibody response to SOSIP trimers but the best combination of trimer presentation and adjuvant can only be identified experimentally.
European primary forest database v2.0
Authors: Sabatini Francesco Maria , Bluhm Hendrik , Kun Zoltan , Aksenov Dmitry , Atauri José A. , Buchwald Erik , Burrascano Sabina , Cateau Eugénie , Diku Abdulla , Duarte Inês Marques , Fernández López Ángel B. , Garbarino Matteo , Grigoriadis Nikolaos , Horváth Ferenc , Keren Srđan , Kitenberga Mara , Kiš Alen , Kraut Ann , Ibisch Pierre L. , Larrieu Laurent , Lombardi Fabio , Matovic Bratislav , Melu Radu Nicolae , Meyer Peter , Midteng Rein , Mikac Stjepan , Mikoláš Martin , Mozgeris Gintautas , Panayotov Momchil , Pisek Rok , Nunes Leónia , Ruete Alejandro , Schickhofer Matthias , Simovski Bojan , Stillhard Jonas , Stojanovic Dejan , Szwagrzyk Jerzy , Tikkanen Olli-Pekka , Toromani Elvin , Volosyanchuk Roman , Vrška Tomáš , Waldherr Marcus , Yermokhin Maxim , Zlatanov Tzvetan , Zagidullina Asiya , Kuemmerle Tobias 
Published: August 2021

AbstractPrimary forests, defined here as forests where the signs of human impacts, if any, are strongly blurred due to decades without forest management, are scarce in Europe and continue to disappear. Despite these losses, we know little about where these forests occur. Here, we present a comprehensive geodatabase and map of Europe’s known primary forests. Our geodatabase harmonizes 48 different, mostly field-based datasets of primary forests, and contains 18,411 individual patches (41.1 Mha) spread across 33 countries. When available, we provide information on each patch (name, location, naturalness, extent and dominant tree species) and the surrounding landscape (biogeographical regions, protection status, potential natural vegetation, current forest extent). Using Landsat satellite-image time series (1985–2018) we checked each patch for possible disturbance events since primary forests were identified, resulting in 94% of patches free of significant disturbances in the last 30 years. Although knowledge gaps remain, ours is the most comprehensive dataset on primary forests in Europe, and will be useful for ecological studies, and conservation planning to safeguard these unique forests.
Fibrinogen–Albumin-Ratio is an independent predictor of thromboembolic complications in patients undergoing VA-ECMO
Authors: Roth Sebastian , Jansen Catrin , M’Pembele René , Stroda Alexandra , Boeken Udo , Akhyari Payam , Lichtenberg Artur , Hollmann Markus W. , Huhn Ragnar , Lurati Buse Giovanna , Aubin Hug 
Published: August 2021

AbstractVeno-arterial extracorporeal membrane oxygenation (VA-ECMO) supports patients suffering from refractory cardiogenic shock. Thromboembolic complications (TeC) are common in VA-ECMO patients and are associated with increased morbidity and mortality. Valid markers to predict TeC in VA-ECMO patients are lacking. The present study investigated the predictive value of baseline Fibrinogen–Albumin-Ratio (FAR) for in-hospital TeC in patients undergoing VA-ECMO. This retrospective cohort study included patients who underwent VA-ECMO therapy due to cardiogenic shock at the University Hospital Duesseldorf, Germany between 2011 and 2018. Main exposure was baseline FAR measured at initiation of VA-ECMO therapy. The primary endpoint was the in-hospital incidence of TeC. In total, 344 patients were included into analysis (74.7% male, mean age 59 ± 14 years). The in-hospital incidence of TeC was 34%. Receiver operating characteristics (ROC) curve of FAR for in-hospital TeC revealed an area under the curve of 0.67 [95% confidence interval (CI) 0.61–0.74]. Youden index determined a cutoff of 130 for baseline FAR. Multivariate logistic regression revealed an adjusted odds-ratio of 3.72 [95% CI 2.26–6.14] for the association between FAR and TeC. Baseline FAR is independently associated with in-hospital TeC in patients undergoing VA-ECMO. Thus, FAR might contribute to the prediction of TeC in this cohort.
The role and value of science in shark conservation advocacy
Authors: Shiffman David S. , Macdonald Catherine C. , Wallace S. Scott , Dulvy Nicholas K. 
Published: August 2021

AbstractMany species of sharks are threatened with extinction, and there has been a longstanding debate in scientific and environmental circles over the most effective and appropriate strategy to conserve and protect them. Should we allow for sustainable fisheries exploitation of species which can withstand fishing pressure, or ban all fisheries for sharks and trade in shark products? In the developing world, exploitation of fisheries resources can be essential to food security and poverty alleviation, and global management efforts are typically focused on sustainably maximizing economic benefits. This approach aligns with traditional fisheries management and the perspectives of most surveyed scientific researchers who study sharks. However, in Europe and North America, sharks are increasingly venerated as wildlife to be preserved irrespective of conservation status, resulting in growing pressure to prohibit exploitation of sharks and trade in shark products. To understand the causes and significance of this divergence in goals, we surveyed 155 shark conservation focused environmental advocates from 78 environmental non-profits, and asked three key questions: (1) where do advocates get scientific information? (2) Does all policy-relevant scientific information reach advocates? and (3) Do advocates work towards the same policy goals identified by scientific researchers? Findings suggest many environmental advocates are aware of key scientific results and use science-based arguments in their advocacy, but a small but vocal subset of advocates report that they never read the scientific literature or speak to scientists. Engagement with science appears to be a key predictor of whether advocates support sustainable management of shark fisheries or bans on shark fishing and trade in shark products. Conservation is a normative discipline, and this analysis more clearly articulates two distinct perspectives in shark conservation. Most advocates support the same evidence-based policies as academic and government scientists, while a smaller percentage are driven more by moral and ethical beliefs and may not find scientific research relevant or persuasive. We also find possible evidence that a small group of non-profits may be misrepresenting the state of the science while claiming to use science-based arguments, a concern that has been raised by surveyed scientists about the environmental community. This analysis suggests possible alternative avenues for engaging diverse stakeholders in productive discussions about shark conservation.
Population affinity and variation of sexual dimorphism in three-dimensional facial forms: comparisons between Turkish and Japanese populations
Authors: Tanikawa Chihiro , Akcam M. Okan , Gokalp Hatice , Zere Edlira , Takada Kenji 
Published: August 2021

AbstractExamining the extent to which sex differences in three-dimensional (3D) facial soft tissue configurations are similar across diverse populations could suggest the source of the indirect evolutionary benefits of facial sexual dimorphism traits. To explore this idea, we selected two geographically distinct populations. Three-dimensional model faces were derived from 272 Turkish and Japanese men and women; their facial morphologies were evaluated using landmark and surface-based analyses. We found four common facial features related to sexual dimorphism. Both Turkish and Japanese females had a shorter lower face height, a flatter forehead, greater sagittal cheek protrusion in the infraorbital region but less prominence of the cheek in the parotid-masseteric region, and an antero-posteriorly smaller nose when compared with their male counterparts. The results indicated the possible phylogenetic contribution of the masticatory organ function and morphogenesis on sexual dimorphism of the human face in addition to previously reported biological and psychological characteristics, including sexual maturity, reproductive potential, mating success, general health, immune response, age, and personality.
Improved functional properties of meat analogs by laccase catalyzed protein and pectin crosslinks
Authors: Sakai Kiyota , Sato Yukihide , Okada Masamichi , Yamaguchi Shotaro 
Published: August 2021

AbstractThe gap between the current supply and future demand of meat has increased the need to produce plant-based meat analogs. Methylcellulose (MC) is used in most commercial products. Consumers and manufacturers require the development of other novel binding systems, as MC is not chemical-free. We aimed to develop a novel chemical-free binding system for meat analogs. First, we found that laccase (LC) synergistically crosslinks proteins and sugar beet pectin (SBP). To investigate the ability of these SBP-protein crosslinks, textured vegetable protein (TVP) was used. The presence of LC and SBP improved the moldability and binding ability of patties, regardless of the type, shape, and size of TVPs. The hardness of LC-treated patties with SBP reached 32.2 N, which was 1.7- and 7.9-fold higher than that of patties with MC and transglutaminase-treated patties. Additionally, the cooking loss and water/oil-holding capacity of LC-treated patties with SBP improved by up to 8.9–9.4% and 5.8–11.3%, compared with patties with MC. Moreover, after gastrointestinal digestion, free amino nitrogen released from LC-treated patties with SBP was 2.3-fold higher than that released from patties with MC. This is the first study to report protein-SBP crosslinks by LC as chemical-free novel binding systems for meat analogs.
Efficacy and safety of primary, early and late needle-knife fistulotomy for biliary access
Authors: Canena Jorge , Lopes Luís , Fernandes João , Alexandrino Gonçalo , Figueiredo Luísa , Moreira Marta , Araújo Tarcísio , Lourenço Luís , Horta David , Familiari Pietro , Dinis-Ribeiro Mário 
Published: August 2021

AbstractEuropean Society of Gastrointestinal Endoscopy recommends needle-knife fistulotomy (NKF) as the preferred precut technique. However, there is little information on whether NKF performed at different times is associated with different success and adverse event rates. We compared the outcomes of 3 different timings of NKF. This was an observational study conducted at 4 institutions and this was a retrospective analysis of prospectively collected data. We included 330 consecutive patients submitted to NKF attempt for biliary access. Patients were divided into three groups: NKF as an initial procedure for biliary access (group A, n = 121); early NKF defined as after 5 min, 5 attempts, or 2 pancreatic passages (group B, n = 99); and late NKF: after at least 10 min of unsuccessful standard biliary cannulation (group C, n = 110). We assessed the success rate of biliary cannulation at initial ERCP, time to perform NKF until biliary cannulation, overall biliary cannulation rate (second ERCP when initial failure), adverse event rate, and predictors of post-ERCP pancreatitis (PEP). The initial cannulation rate was 98%, 91% and 94% for groups A, B and C respectively, p = 0.08, whereas overall biliary cannulation rate was 100%, 95% and 98%, p = 0.115. The adverse event rate/PEP was 4.1%/2.5%, 7.1%/4% and 10.9%/8.2%, for groups A, B and C respectively, (p = 0.197 and p = 0.190). Median time for creating the fistula was A = 4.0 min, B = 3.2 min, and C = 5.6 min, p < 000.1. Each additional minute spent attempting cannulation increased the odds ratio (OR) for PEP by 1.072, and patients with 3 or more risk factors for pancreatitis had a higher chance of PEP. In conclusion, the timing of NFK does not appear to influence success rates but late NFK is associated with a higher time to create a fistula and an increased risk of pancreatitis. Primary NFK is associated with a high rate of success and a low rate of PEP and deserves additional investigation.
Cholinesterase activity in serum during general anesthesia in patients with or without vascular disease
Authors: Brzezinski-Sinai Yitzhak , Zwang Ester , Plotnikova Elena , Halizov Ester , Shapira Itzhak , Zeltser David , Rogowski Ori , Berliner Shlomo , Matot Idit , Shenhar-Tsarfaty Shani 
Published: August 2021

AbstractMaintaining hemodynamic stability during the induction and maintenance of anesthesia is one of the challenges of the anesthesiologist. Patients with vascular disease are at increased risk of instability due to imbalance between the sympathetic and parasympathetic parts of the autonomic nervous system, a balance accessible by serum cholinesterase activity. We aim to characterize the dynamics of cholinesterase activity in patients undergoing general anesthesia (GA) and surgery. This was a prospective study of 57 patients undergoing ambulatory or vascular surgery under GA. Cholinesterase activity was measured before the induction of anesthesia, after 15 min and at the end of surgery by calculating the capacity of serum acetylcholinesterase (AChE) and butyrylcholinesterase to hydrolyze AcetylThioCholine. Data on atherosclerotic disease, anesthesia management were analyzed. Both AChE and total cholinergic status (CS) decreased significantly after GA induction at 15 min and even more so by the end of surgery. Vascular surgery patients had lower baseline cholinesterase activity compared to ambulatory surgery patients. Patients requiring intraoperative administration of phenylephrine for hemodynamic support (21.1%) had a significantly lower level of AChE and CS compared to untreated patients. Our findings serve as a mirror to the sympathetic/parasympathetic imbalance during GA, with a marked decrease in the parasympathetic tone. The data of a subgroup analysis show a correlation between low cholinesterase activity and an increase in the need for hemodynamic support.
Determination of the electronic transport in type separated carbon nanotubes thin films doped with gold nanocrystals
Authors: Świniarski M. , Dużyńska A. , Gertych A. P. , Czerniak-Łosiewicz K. , Judek J. , Zdrojek M. 
Published: August 2021

AbstractWe report a systematic theoretical and experimental investigation on the electronic transport evolution in metallic and semiconducting carbon nanotubes thin films enriched by gold nanocrystals. We used an ultra-clean production method of both types of single-walled carbon nanotube thin films with/without gold nanocrystals, which were uniformly dispersed in the whole volume of the thin films, causing a modification of the doping level of the films (verified by Raman spectroscopy). We propose a modification of the electronic transport model with the additional high-temperature features that allow us to interpret the transport within a broader temperature range and that are related to the conductivity type of carbon nanotubes. Moreover, we demonstrate, that the proposed model is also working for thin films with the addition of gold nanocrystals, and only a change of the conductivity level of our samples is observed caused by modification of potential barriers between carbon nanotubes. We also find unusual behavior of doped metallic carbon nanotube thin film, which lowers its conductivity due to doping.
Clinical, genetic and pharmacological data support targeting the MEK5/ERK5 module in lung cancer
Authors: Sánchez-Fdez Adrián , Re-Louhau María Florencia , Rodríguez-Núñez Pablo , Ludeña Dolores , Matilla-Almazán Sofía , Pandiella Atanasio , Esparís-Ogando Azucena 
Published: August 2021

AbstractDespite advances in its treatment, lung cancer still represents the most common and lethal tumor. Because of that, efforts to decipher the pathophysiological actors that may promote lung tumor generation/progression are being made, with the final aim of establishing new therapeutic options. Using a transgenic mouse model, we formerly demonstrated that the sole activation of the MEK5/ERK5 MAPK route had a pathophysiological role in the onset of lung adenocarcinomas. Given the prevalence of that disease and its frequent dismal prognosis, our findings opened the possibility of targeting the MEK5/ERK5 route with therapeutic purposes. Here we have explored such possibility. We found that increased levels of MEK5/ERK5 correlated with poor patient prognosis in lung cancer. Moreover, using genetic as well as pharmacological tools, we show that targeting the MEK5/ERK5 route is therapeutically effective in lung cancer. Not only genetic disruption of ERK5 by CRISPR/Cas9 caused a relevant inhibition of tumor growth in vitro and in vivo; such ERK5 deficit augmented the antitumoral effect of agents normally used in the lung cancer clinic. The clinical correlation studies together with the pharmacological and genetic results establish the basis for considering the targeting of the MEK5/ERK5 route in the therapy for lung cancer.