bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production
Authors: Greenhalgh Jonathan C. , Fahlberg Sarah A. , Pfleger Brian F. , Romero Philip A. 
Published: October 2021

AbstractAlcohol-forming fatty acyl reductases (FARs) catalyze the reduction of thioesters to alcohols and are key enzymes for microbial production of fatty alcohols. Many metabolic engineering strategies utilize FARs to produce fatty alcohols from intracellular acyl-CoA and acyl-ACP pools; however, enzyme activity, especially on acyl-ACPs, remains a significant bottleneck to high-flux production. Here, we engineer FARs with enhanced activity on acyl-ACP substrates by implementing a machine learning (ML)-driven approach to iteratively search the protein fitness landscape. Over the course of ten design-test-learn rounds, we engineer enzymes that produce over twofold more fatty alcohols than the starting natural sequences. We characterize the top sequence and show that it has an enhanced catalytic rate on palmitoyl-ACP. Finally, we analyze the sequence-function data to identify features, like the net charge near the substrate-binding site, that correlate with in vivo activity. This work demonstrates the power of ML to navigate the fitness landscape of traditionally difficult-to-engineer proteins.
Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe
Authors: Sharma Mrinank , Mindermann Sören , Rogers-Smith Charlie , Leech Gavin , Snodin Benedict , Ahuja Janvi , Sandbrink Jonas B. , Monrad Joshua Teperowski , Altman George , Dhaliwal Gurpreet , Finnveden Lukas , Norman Alexander John , Oehm Sebastian B. , Sandkühler Julia Fabienne , Aitchison Laurence , Gavenčiak Tomáš , Mellan Thomas , Kulveit Jan , Chindelevitch Leonid , Flaxman Seth , Gal Yarin , Mishra Swapnil , Bhatt Samir , Brauner Jan Markus 
Published: October 2021

AbstractEuropean governments use non-pharmaceutical interventions (NPIs) to control resurging waves of COVID-19. However, they only have outdated estimates for how effective individual NPIs were in the first wave. We estimate the effectiveness of 17 NPIs in Europe’s second wave from subnational case and death data by introducing a flexible hierarchical Bayesian transmission model and collecting the largest dataset of NPI implementation dates across Europe. Business closures, educational institution closures, and gathering bans reduced transmission, but reduced it less than they did in the first wave. This difference is likely due to organisational safety measures and individual protective behaviours—such as distancing—which made various areas of public life safer and thereby reduced the effect of closing them. Specifically, we find smaller effects for closing educational institutions, suggesting that stringent safety measures made schools safer compared to the first wave. Second-wave estimates outperform previous estimates at predicting transmission in Europe’s third wave.
Stabilizing indium sulfide for CO2 electroreduction to formate at high rate by zinc incorporation
Authors: Chi Li-Ping , Niu Zhuang-Zhuang , Zhang Xiao-Long , Yang Peng-Peng , Liao Jie , Gao Fei-Yue , Wu Zhi-Zheng , Tang Kai-Bin , Gao Min-Rui 
Published: October 2021

AbstractRecently developed solid-state catalysts can mediate carbon dioxide (CO2) electroreduction to valuable products at high rates and selectivities. However, under commercially relevant current densities of > 200 milliamperes per square centimeter (mA cm−2), catalysts often undergo particle agglomeration, active-phase change, and/or element dissolution, making the long-term operational stability a considerable challenge. Here we report an indium sulfide catalyst that is stabilized by adding zinc in the structure and shows dramatically improved stability. The obtained ZnIn2S4 catalyst can reduce CO2 to formate with 99.3% Faradaic efficiency at 300 mA cm−2 over 60 h of continuous operation without decay. By contrast, similarly synthesized indium sulfide without zinc participation deteriorates quickly under the same conditions. Combining experimental and theoretical studies, we unveil that the introduction of zinc largely enhances the covalency of In-S bonds, which “locks” sulfur—a catalytic site that can activate H2O to react with CO2, yielding HCOO* intermediates—from being dissolved during high-rate electrolysis.
A light tunable differentiation system for the creation and control of consortia in yeast
Authors: Aditya Chetan , Bertaux François , Batt Gregory , Ruess Jakob 
Published: October 2021

AbstractArtificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.
Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio
Authors: Jannesar Masoomeh , Seyedi Seyed Mahdi , Botanga Christopher 
Published: October 2021

AbstractWe developed novel miRNA-based markers based on salt responsive miRNA sequences to detect polymorphisms in miRNA sequences and locations. The validation of 76 combined miRNA + miRNA and miRNA + ISSR markers in the three extreme pistachio populations led to the identification of three selected markers that could link salt tolerance phenotype to genotype and divided pistachio genotypes and Pistacia species into three clusters. This novel functional marker system, in addition to more efficient performance, has higher polymorphisms than previous miRNA-based marker systems. The functional importance of the target gene of five miRNAs in the structure of the three selected markers in regulation of different genes such as ECA2, ALA10, PFK, PHT1;4, PTR3, KUP2, GRAS, TCP, bHLH, PHD finger, PLATZ and genes involved in developmental, signaling and biosynthetic processes shows that the polymorphism associated with these selected miRNAs can make a significant phenotypic difference between salt sensitive and tolerant pistachio genotypes. The sequencing results of selected bands showed the presence of conserved miRNAs in the structure of the mitochondrial genome. Further notable findings of this study are that the sequences of PCR products of two selected markers were annotated as Gypsy and Copia retrotransposable elements. The transposition of retrotransposons with related miRNAs by increasing the number of miRNA copies and changing their location between nuclear and organellar genomes can affect the regulatory activity of these molecules. These findings show the crucial role of retrotransposon-derived miRNAs as mobile epigenetic regulators between intracellular genomes in regulating salt stress responses as well as creating new and tolerant phenotypes for adaptation to environmental conditions.
Population pharmacokinetic model of cefazolin in total hip arthroplasty
Authors: Lanoiselée J. , Chaux R. , Hodin S. , Bourayou S. , Gibert A. , Philippot R. , Molliex S. , Zufferey P. J. , Delavenne X. , Ollier E. 
Published: October 2021

AbstractCefazolin is an antibiotic recommended for infection prevention in total hip arthroplasty (THA). However, the dosing regimen necessary to achieve therapeutic concentrations in obese patients remains unclear. The aim of this study was to conduct a population analysis of cefazolin pharmacokinetics (PK) and assess whether cefazolin administration should be weight adapted in THA. Adult patients undergoing THA surgery received an injection of 2000 mg of cefazolin, doubled in the case of BMI > 35 kg/m2 and total body weight > 100 kg. A population PK study was conducted to quantify cefazolin exposure over time compared to the therapeutic concentration threshold. A total of 484 cefazolin measurements were acquired in 100 patients, of whom 29% were obese. A 2-compartment model best fitted the data, and creatinine clearance determined interpatient variability in elimination clearance. Our PK simulations using a 2000 mg cefazolin bolus showed that cefazolin concentrations remained above the threshold throughout surgery, regardless of weight or renal function. A 2000 mg cefazolin single injection without adaptation to weight or renal function and without intraoperative reinjection was efficient in maintaining therapeutic concentrations throughout surgery. The optimal target concentration and necessary duration of its maintenance remain unclear.
Changes in elbow joint contact area in symptomatic valgus instability of the elbow in baseball players
Authors: Numaguchi Kyosuke , Momma Daisuke , Matsui Yuki , Oohinata Jun , Yamaguchi Takayoshi , Inoue Nozomu , Kondo Eiji , Iwasaki Norimasa 
Published: October 2021

AbstractThe aim of this study was to evaluate the joint contact area of the dominant side and that of the non-dominant side without valgus instability in symptomatic pitchers. Ten symptomatic elbow medial ulnar collateral ligament (UCL) deficient baseball pitchers participated in this study. Computed tomography (CT) data from the dominant and non-dominant elbows were obtained with and without elbow valgus stress. The CT imaging data of each elbow joint were reconstructed using a 3D reconstruction software package, and the radiocapitellar and ulnohumeral joint contact areas were calculated. The center of the contact area and the translation from the position without stress to the position with valgus stress were also calculated. With elbow valgus stress, the contact area changed, and the center of the radiocapitellar joint contact area translated significantly more laterally in the dominant elbow than in the non-dominant elbow (p = 0.0361). In addition, the center of the ulnohumeral joint contact area translated significantly more posteriorly in the dominant elbow than in the non-dominant elbow (p = 0.0413). These changes in contact areas could be the reason for cartilage injury at the posterior trochlea in pitchers with UCL deficiency.
A pilot study of novel duodenal covered self-expandable metal stent fixation
Authors: Hori Yasuki , Hayashi Kazuki , Naitoh Itaru , Miyabe Katsuyuki , Natsume Makoto , Yoshida Michihiro , Kataoka Hiromi 
Published: October 2021

AbstractMigration of duodenal covered self-expandable metal stents (C-SEMSs) is the main cause of stent dysfunction in patients with malignant gastric outlet obstruction (mGOO). Because endoscopic SEMS placement is frequently selected in patients with poor performance status, we concurrently focused on the safety of the treatment. This pilot study included 15 consecutive patients with mGOO who underwent duodenal partially covered SEMS (PC-SEMS) placement with fixation using an over-the-scope-clip (OTSC). Technical feasibility, clinical success for oral intake estimated by the Gastric Outlet Obstruction Scoring System (GOOSS) score, and adverse events including stent migration were retrospectively assessed. All procedures were successful, and clinical success was achieved in 86.7% (13/15). Mean GOOSS scores were improved from 0.07 to 2.53 after the procedure (P < 0.001). Median survival time was 84 days, and all patients were followed up until death. Stent migration occurred in one case (6.7%) at day 17, which was successfully treated by removal of the migrated PC-SEMS using an enteroscope. For fixation using an OTSC, additional time required for the procedure was 8.9 ± 4.1 min and we did not observe OTSC-associated adverse events. Poor performance status was associated with clinical success (P = 0.03), but we could provide the treatment safely and reduce mGOO symptoms even in patients with poor performance status. In conclusion, duodenal PC-SEMS fixation using an OTSC is feasible for preventing stent migration in patients with mGOO including those with poor performance status.
Simultaneous transcranial and transcutaneous spinal direct current stimulation to enhance athletic performance outcome in experienced boxers
Authors: Kamali Ali-Mohammad , Kazemiha Milad , Keshtkarhesamabadi Behnam , Daneshvari Mohsan , Zarifkar Asadollah , Chakrabarti Prasun , Kateb Babak , Nami Mohammad 
Published: October 2021

AbstractTranscranial direct current stimulation (tDCS) is among the rapidly growing experimental approaches to enhance athletic performance. Likewise, novel investigations have recently addressed the effects of transcutaneous spinal Direct Current Stimulation (tsDCS) on motor functions such as reduced reaction time. The impact of tDCS, and tsDCS might be attributed to altered spontaneous neural activity and membrane potentials of cortical and corticomotoneuronal cells, respectively. Given the paucity of empirical research in non-invasive brain stimulation in sports neuroscience, especially in boxing, the present investigation studied the effects of neuromodulation on motor and cognitive functions of professional boxers. The study sample comprised 14 experienced male boxers who received random sequential real or sham direct current stimulation over the primary motor cortex (M1) and paraspinal region (corresponding to the hand area) in two sessions with a 72-h interval. Unlike sham stimulation, real stimulation improved selective attention and reaction time of the experienced boxers [enhanced selective attention (p < 0.0003), diminished right hand (p < 0.0001) and left hand reaction time (p < 0.0006)]. Meanwhile, the intervention left no impact on the participants’ cognitive functions (p > 0.05). We demonstrated that simultaneous stimulation of the spinal cord and M1 can improve the performance of experienced boxers through neuromodulation. The present study design may be extended to examine the role of neurostimulation in other sport fields.
Evaluating posterior vitreous detachment by widefield 23-mm swept-source optical coherence tomography imaging in healthy subjects
Authors: Chiku Yoshiaki , Hirano Takao , Takahashi Yoshiaki , Tuchiya Ayako , Nakamura Marie , Murata Toshinori 
Published: October 2021

AbstractPosterior vitreous detachment (PVD) is a separation between the posterior vitreous cortex and internal limiting membrane. Although PVD was historically considered an acute event, recent studies using spectral-domain optical coherence tomography (SD-OCT) revealed a gradual progression of PVD in healthy subjects. Although SD-OCT improved PVD studies, the narrow imaging angle and long examination time were problematic to allow wide angle capture. The Xephilio OCT-S1 (Canon), a swept-source OCT (SS-OCT) device, can obtain up to 23-mm of widefield B-scan images in a single acquisition. We used this widefield SS-OCT to quantitatively evaluate the PVD stage in 214 healthy subjects aged 4–89 years and determine whether PVD stages differ between the bilateral eyes of each patient. Age was significantly positively correlated with the overall PVD stage (ρ = 0.7520, P < 0.001). Interestingly, partial PVD occurred in children as young as 5 years, indicating that initial PVD onset may occur much earlier than previously reported. Furthermore, PVD stages of the bilateral eyes were highly consistent in 183 subjects (85.5%). Widefield 23-mm SS-OCT thus revealed that PVD started earlier than anticipated, and age was correlated with the symmetry of PVD stage. Widefield 23-mm SS-OCT may also be clinically useful for the evaluation of diseased eyes.
Design of frequency selective surface based on Minkowski fractal and interdigital capacitance
Authors: Khajevandi Amir , Oraizi Homayoon 
Published: October 2021

AbstractIn this paper, the Minkowski fractal is used to design the geometry of a frequency selective surface (FSS) unit cell, which resembles the shapes found in nature. The proposed FSS unit cell has both angular and polarization stabilities of incident wave. For the miniaturization of FSS and decrease of resonance frequency, interdigital capacitances (IDCs) are devised in the FSS structure, which do not eliminate angular and polarization stabilities. The dimensions of the unit cell are 5 mm × 5 mm and miniaturized 0.095λ0×0.095λ0. The resonance frequency is specified as 5.75 GHz with 155 MHz bandwidth. An equivalent circuit is derived for the unit cell to evaluate its frequency responses. The effects of variations of the geometrical dimensions of the FSS unit cell on its performance are studied. A prototype model of proposed FSS is fabricated and measured. The performance of its full‐wave computer simulation results and measured data are compared and are shown to be in good agreement.
Shazam for bats: Internet of Things for continuous real‐time biodiversity monitoring
Authors: Gallacher Sarah , Wilson Duncan , Fairbrass Alison , Turmukhambetov Daniyar , Firman Michael , Kreitmayer Stefan , Mac Aodha Oisin , Brostow Gabriel , Jones Kate 
Published: October 2021

AbstractBiodiversity surveys are often required for development projects in cities that could affect protected species such as bats. Bats are important biodiversity indicators of the wider health of the environment and activity surveys of bat species are used to report on the performance of mitigation actions. Typically, sensors are used in the field to listen to the ultrasonic echolocation calls of bats or the audio data is recorded for post‐processing to calculate the activity levels. Current methods rely on significant human input and therefore present an opportunity for continuous monitoring and in situ machine learning detection of bat calls in the field. Here, we show the results from a longitudinal study of 15 novel Internet connected bat sensors—Echo Boxes—in a large urban park. The study provided empirical evidence of how edge processing can reduce network traffic and storage demands by several orders of magnitude, making it possible to run continuous monitoring activities for many months including periods which traditionally would not be monitored. Our results demonstrate how the combination of artificial intelligence techniques and low‐cost sensor networks can be used to create novel insights for ecologists and conservation decision‐makers.
STEPARSYN: A Bayesian code to infer stellar atmospheric parameters using spectral synthesis
Authors: Tabernero H. M. , Marfil E. , Montes D. , González Hernández J. I. 
Published: October 2021

Context. STEPARSYN is an automatic code written in Python 3.X designed to infer the stellar atmospheric parameters Teff, log g, and [Fe/H] of FGKM-type stars following the spectral synthesis method.
Aims. We present a description of the STEPARSYN code and test its performance against a sample of late-type stars that were observed with the HERMES spectrograph mounted at the 1.2-m Mercator Telescope. This sample contains 35 late-type targets with well-known stellar parameters determined independently from spectroscopy. The code is available to the astronomical community in a GitHub repository.
Methods. STEPARSYN uses a Markov chain Monte Carlo sampler to explore the parameter space by comparing synthetic model spectra generated on the fly to the observations. The synthetic spectra are generated with an spectral emulator.
Results. We computed Teff, log g, and [Fe/H] for our sample stars and discussed the performance of the code. We calculated an internal scatter for these targets of −12 ± 117 K in Teff, 0.04 ± 0.14 dex in log g, and 0.05 ± 0.09 dex in [Fe/H]. In addition, we find that the log g values obtained with STEPARSYN are consistent with the trigonometric surface gravities to the 0.1 dex level. Finally, STEPARSYN can compute stellar parameters that are accurate down to 50 K, 0.1 dex, and 0.05 dex for Teff, log g, and [Fe/H] for stars with v sin i ≤ 30 km s−1.
Post-Soviet Agricultural Restructuring: A Success Story After All?
Authors: Petrick Martin 
Published: October 2021

AbstractChallenging the initial expectation that all post-Soviet economies will evolve from collective toward fully individualized farming, I argue that they separated into two different reform paths. In the European successor countries and Kazakhstan, corporate and family farms coexist, labor exited agriculture, and capital inflow boosted labor productivity (a “Westernization”). In the Transcaucasian and the other Central Asian countries, complete farm individualization did not increase labor productivity much, in turn keeping rural incomes depressed (a “Southernization” akin to the Global South). Future policies should promote income alternatives to agriculture and improve the flexibility and transparency of farm consolidation processes.
The Spectrum of Reality
Authors: Singh Anirudh 
Published: October 2021

While the subjective normally exists in the mind, it is possible to transform it into the objective through the process of experimental measurement. The existence of the semiconductor hole as a real particle that determines the measurable properties of semiconductors demonstrates that a missing electron can acquire all the properties of a real particle. This analogy can be used to explain how the initially imaginary massless and elusive particle proposed by Pauli in 1930 to explain nuclear beta decay was eventually made real through experimental verification by Cowan and Reines in 1956. The act of measurement is thus able to create reality. This process is dubbed “the spectrum of reality.”
While not all physical entities are directly accessible to experimental measurement, all experiments of physics always happen in the “here and now.”
The design and implementation of physical experiments are often concatenations of hypotheses and measurement.
Humans act as animate observers at the interface of the physical realms, and are able to create theories, and design and conduct experiments, as well as interpret their outcomes.
Emerging Issues
Authors: Singh Anirudh 
Published: October 2021

In Part 3 of this book we consider some of the issues of physics that have emerged due to the historical nature of its development. These range from issues of physics due to inconsistencies in its structure, to the dichotomous nature of its framework and issues of unification. This chapter begins by examining the matter particle–force particle duality of the particle physics framework. This is a divergent development from the reductionist concepts of the General Theory of Relativity, which attempts to unify matter with space–time, making the unification of gravity with the other three fundamental forces difficult. A method of contending with these two developments within the same framework is suggested.
Quasiparticles are entities that share some, but not all, of the intrinsic properties of particles, and are found in abundance within the confined limits of the solid state. It is suggested that the concept of quasiparticles may be extensible to the internal nuclear and particle environments, where quarks also exist in confined dimensions.
The possibility of the existence of particles with variable intrinsic properties is speculated upon, after critically analyzing the relation between symmetry and conserved intrinsic properties postulated by Noether's Theorem.