bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of the composition in a composite material for microelectronics application using the Ising model
Authors: Imanaka Yoshihiko , Anazawa Toshihisa , Kumasaka Fumiaki , Jippo Hideyuki
Published: February 2021

Tailored material is necessary in many industrial applications since material properties directly determine the characteristics of components. However, the conventional trial and error approach is costly and time-consuming. Therefore, materials informatics is expected to overcome these drawbacks. Here, we show a new materials informatics approach applying the Ising model for solving discrete combinatorial optimization problems. In this study, the composition of the composite, aimed at developing a heat sink with three necessary properties: high thermal dissipation, attachability to Si, and a low weight, is optimized. We formulate an energy function equation concerning three objective terms with regard to the thermal conductivity, thermal expansion and specific gravity, with the composition variable and two constrained terms with a quadratic unconstrained binary optimization style equivalent to the Ising model and calculated by a simulated annealing algorithm. The composite properties of the composition selected from ten constituents are verified by the empirical mixture rule of the composite. As a result, an optimized composition with high thermal conductivity, thermal expansion close to that of Si, and a low specific gravity is acquired.
Management alternatives for Carmenta theobromae (Busck, 1910) (Lepidoptera: Sesiidae) and Simplicivalva ampliophilobia (Lepidoptera: Cossidae), limiting pests of guava in Colombia
Authors: Pulido-Blanco Víctor Camilo , Pinzón-Sandoval Elberth Hernando , González-Chavarro Carlos Felipe , Serrano-Cely Pablo Antonio
Published: February 2021

The larval stages ofCarmenta theobromaeBusck (1910) andSimplicivalva ampliophilobiaDavis, Gentili-Poole and Mitter (2008) attack the subcortical zone and pith in guava trees, respectively, in the first productive nucleus of fruit trees in Colombia: Hoya del Río Suárez (HRS). The presence of pest insects has been reported in 98% of the farms sampled in HRS (n = 124), with up to 96 and 11 simultaneous larvae per tree, respectively. Although the aspects of the basic biology and life cycle of both pests have been resolved, there are no strategies for managing populations in the field. Therefore, the aim of this study was to evaluate different management alternatives under laboratory and field conditions in HRS. In laboratory conditions, a completely randomized design was used in two separate experiments, each with six treatments: T1: Spinosad (a mixture of Spinosad A and D); T2: S-1,2-di(ethoxycarbonyl) ethyl 0,0-dimethylphosphorodithioate (chemical control); T3:Lecanicillium lecanii; T4:Beauveria bassiana; T5: Mix ofB. bassianaandB. brongniartii, and T6: distilled water (control). The number of dead larvae per replicate per treatment was evaluated (DL), with experimental units of five and three larvae, respectively. In the field, to the two best alternatives found for each pest in the laboratory, pruning and keeping the area around the plants free of weeds were added as cultural management, in two separate additional experiments, each with three larvae as experimental unit per treatment. ForC. theobromae,the best laboratory alternatives were chemical control (DL: 3.78) andL. lecanii(DL: 2.33), followed without statistical differences byB. bassiana(DL: 1.67). In the field, the virulence ofB. bassianaimproved (DL: 3), and together with pruning and keeping the area around the plants clear of weeds (DL: 3), they stood out as the best alternatives. ForS. ampliophilobiaunder laboratory conditions, the best alternatives were Spinosad (2.74) and chemical control (DL: 2.66), without significant difference. In the field, there were no statistical differences between the alternatives, except for the control. This statistical parity of cultural practices, and biological and chemical management is an argument in favor of the use of the former to the detriment of the third, especially when the harmful effects of the molecule S-1,2 di (ethoxycarbonyl) ethyl 0, 0-dimethyl phosphorodithioate have been proven in air, water and agricultural soils, in addition to its association with thyroid cancer in humans. This is a strong argument to favor the use of synergies of cultural and biological management methods framed in IPM, as opposed to the use of chemical agents whose harmful effects are strongly documented, and whose use is becoming increasingly prohibited.
TonEBP regulates the hyperosmotic expression of aquaporin 1 and 5 in the intervertebral disc
Authors: Snuggs J. W. , Tessier S. , Bunning R. A. B. , Shapiro I. M. , Risbud M. V. , Le Maitre C. L.
Published: February 2021

The central region of the intervertebral disc (IVD) is rich in proteoglycans, leading to a hyperosmotic environment, which fluctuates with daily loading. The cells of the nucleus pulposus (NP cells) have adapted to this environment via the function of tonicity enhancer binding protein (TonEBP), and NP cells have been shown to express several water channels known as aquaporins (AQP). We have previously shown that AQP1 and 5 decrease during IVD degeneration. Here, the regulation of AQP1 and 5 by hyperosmotic conditions and the role of TonEBP in this regulation was investigated. AQP1 and 5 gene expression was upregulated by hyperosmotic conditions mimicking the osmolality of the healthy IVD, which was abrogated by TonEBP knockdown. Furthermore, AQP1 and 5 immunopositivity was significantly reduced in TonEBPΔ/ΔE17.5 mice when compared with wildtype controls, indicating in vivo expression of AQP1 and 5 is controlled at least in part by TonEBP. This hyperosmotic regulation of AQP1 and 5 could help to explain the decreased AQP1 and 5 expression during degeneration, when the osmolality of the NP decreases. Together this data suggests that TonEBP-regulated osmo-adaptation may be disrupted during IVD degeneration when the expression of both AQPs is reduced.
Effect of gestational age and postnatal age on the endothelial glycocalyx in neonates
Authors: Puchwein-Schwepcke Alexandra , Artmann Stefanie , Rajwich Lea , Genzel-Boroviczény Orsolya , Nussbaum Claudia
Published: February 2021

Prematurity predisposes to cardiovascular disease; however the underlying mechanisms remain elusive. Disturbance of the endothelial glycocalyx (EG), an important regulator of vessel function, is thought to contribute to vascular pathology. Here, we studied the EG with respect to gestational and postnatal age in preterm and term neonates. The Perfused Boundary Region (PBR), an inverse measure of glycocalyx thickness, was measured postnatally in 85 term and 39 preterm neonates. Preterm neonates were further analyzed in two subgroups i.e., neonates born < 30 weeks gestational age (group A) and neonates born ≥ 30 weeks (group B). In preterm neonates, weekly follow-up measurements were performed if possible. PBR differed significantly between preterm and term neonates with lowest values representing largest EG dimension in extremely premature infants possibly reflecting its importance in fetal vascular development. Linear regression revealed a dependence of PBR on both, gestational age and postnatal age. Furthermore, hematocrit predicted longitudinal PBR changes. PBR measured in group A at a corrected age of > 30 weeks was significantly higher than in group B at birth, pointing towards an alteration of intrinsic maturational effects by extrinsic factors. These changes might contribute to the increased cardiovascular risk associated with extreme prematurity.
CRISPR/Cas9-based targeting of fluorescent reporters to human iPSCs to isolate atrial and ventricular-specific cardiomyocytes
Authors: Chirikian Orlando , Goodyer William R. , Dzilic Elda , Serpooshan Vahid , Buikema Jan W. , McKeithan Wesley , Wu HaoDi , Li Guang , Lee Soah , Merk Markus , Galdos Francisco , Beck Aimee , Ribeiro Alexandre J. S. , Paige Sharon , Mercola Mark , Wu Joseph C. , Pruitt Beth L. , Wu Sean M.
Published: February 2021

Generating cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) has represented a significant advance in our ability to model cardiac disease. Current differentiation protocols, however, have limited use due to their production of heterogenous cell populations, primarily consisting of ventricular-like CMs. Here we describe the creation of two chamber-specific reporter hiPSC lines by site-directed genomic integration using CRISPR-Cas9 technology. In the MYL2-tdTomato reporter, the red fluorescent tdTomato was inserted upstream of the 3′ untranslated region of the Myosin Light Chain 2 (MYL2) gene in order faithfully label hiPSC-derived ventricular-like CMs while avoiding disruption of endogenous gene expression. Similarly, in the SLN-CFP reporter, Cyan Fluorescent Protein (CFP) was integrated downstream of the coding region of the atrial-specific gene, Sarcolipin (SLN). Purification of tdTomato+ and CFP+ CMs using flow cytometry coupled with transcriptional and functional characterization validated these genetic tools for their use in the isolation of bona fide ventricular-like and atrial-like CMs, respectively. Finally, we successfully generated a double reporter system allowing for the isolation of both ventricular and atrial CM subtypes within a single hiPSC line. These tools provide a platform for chamber-specific hiPSC-derived CM purification and analysis in the context of atrial- or ventricular-specific disease and therapeutic opportunities.
Daytime nap and nighttime breastfeeding are associated with toddlers’ nighttime sleep
Authors: Nakagawa Machiko , Ohta Hidenobu , Shimabukuro Rinshu , Asaka Yoko , Nakazawa Takayo , Oishi Yoshihisa , Hirata Michio , Ando Akiko , Ikeda Takashi , Yoshimura Yuko , Mitani Yusuke , Kaneshi Yousuke , Morioka Keita , Fukutomi Rika , Kobayashi Kyoko , Ozawa Miwa , Takeshima Masahiro , Mishima Kazuo , Kikuchi Mitsuru , Cho Kazutoshi , Yoda Hitoshi , Kusakawa Isao
Published: February 2021

The purpose of the present study is to examine the association between toddlers' sleep arrangements and their nighttime sleep duration and other sleep variables. For this investigation, we performed a study in which child activity and sleep levels were recorded using actigraphy. The parents of 1.5-year-old toddlers (n = 106) were asked to attach an actigraphy unit to their child’s waist with an adjustable elastic belt and complete a sleep diary for 7 consecutive days. Questionnaires were used to assess the sleep arrangements of the toddlers. There was a significant negative correlation between nap duration and nighttime sleep duration, suggesting that longer nap sleep induces shorter nighttime sleep duration. Among the sleep arrangements, such as nighttime breastfeeding or co-sleeping, only nighttime breastfeeding predicted shorter nighttime sleep duration. Our findings indicate that shorter naps induce a longer nighttime sleep in 1.5-year-old toddlers while nighttime breastfeeding decreases their nighttime sleep duration.
Skyrmion ratchet propagation: utilizing the skyrmion Hall effect in AC racetrack storage devices
Authors: Göbel Börge , Mertig Ingrid
Published: February 2021

Magnetic skyrmions are whirl-like nano-objects with topological protection. When driven by direct currents, skyrmions move but experience a transverse deflection. This so-called skyrmion Hall effect is often regarded a drawback for memory applications. Herein, we show that this unique effect can also be favorable for spintronic applications: We show that in a racetrack with a broken inversion symmetry, the skyrmion Hall effect allows to translate an alternating current into a directed motion along the track, like in a ratchet. We analyze several modes of the ratchet mechanism and show that it is unique for topological magnetic whirls. We elaborate on the fundamental differences compared to the motion of topologically trivial magnetic objects, as well as classical particles driven by periodic forces. Depending on the exact racetrack geometry, the ratchet mechanism can be soft or strict. In the latter case, the skyrmion propagates close to the efficiency maximum.
Early life dietary intervention in dairy calves results in a long-term reduction in methane emissions
Authors: Meale S. J. , Popova M. , Saro C. , Martin C. , Bernard A. , Lagree M. , Yáñez-Ruiz D. R. , Boudra H. , Duval S. , Morgavi D. P.
Published: February 2021

Recent evidence suggests that changes in microbial colonization of the rumen prior to weaning may imprint the rumen microbiome and impact phenotypes later in life. We investigated how dietary manipulation from birth influences growth, methane production, and gastrointestinal microbial ecology. At birth, 18 female Holstein and Montbéliarde calves were randomly assigned to either treatment or control (CONT). Treatment was 3-nitrooxypropanol (3-NOP), an investigational anti-methanogenic compound that was administered daily from birth until three weeks post-weaning (week 14). Samples of rumen fluid and faecal content were collected at weeks 1, 4, 11, 14, 23, and 60 of life. Calves were tested for methane emissions using the GreenFeed system during the post-weaning period (week 11–23 and week 56–60 of life). Calf physiological parameters (BW, ADG and individual VFA) were similar across groups throughout the trial. Treated calves showed a persistent reduction in methane emissions (g CH4/d) throughout the post-weaning period up to at least 1 year of life, despite treatment ceasing three weeks post-weaning. Similarly, despite variability in the abundance of individual taxa across weeks, the rumen bacterial, archaeal and fungal structure differed between CONT and 3-NOP calves across all weeks, as visualised using sparse-PLS-DA. Similar separation was also observed in the faecal bacterial community. Interestingly, despite modest modifications to the abundance of rumen microbes, the reductive effect of 3-NOP on methane production persisted following cessation of the treatment period, perhaps indicating a differentiation of the ruminal microbial ecosystem or a host response triggered by the treatment in the early development phase.
Mechanisms for mutual support in motor interactions
Authors: Sacheli Lucia Maria , Musco Margherita Adelaide , Zazzera Elisa , Paulesu Eraldo
Published: February 2021

What is the key to successful interaction? Is it sufficient to represent a common goal, or does the way our partner achieves that goal count as well? How do we react when our partner misbehaves? We used a turn-taking music-like task requiring participants to play sequences of notes together with a partner, and we investigated how people adapt to a partner’s error that violates their expectations. Errors consisted of either playing a wrong note of a sequence that the agents were playing together (thus preventing the achievement of the joint goal) or playing the expected note with an unexpected action. In both cases, we found post-error slowing and inaccuracy suggesting the participants’ implicit tendency to correct the partner’s error and produce the action that the partner should have done. We argue that these “joint” monitoring processes depend on the motor predictions made within a (dyadic) motor plan and may represent a basic mechanism for mutual support in motor interactions.
Liquid level sensor based on dynamic Fabry–Perot interferometers in processed capillary fiber
Authors: Roldán-Varona Pablo , Pérez-Herrera Rosa Ana , Rodríguez-Cobo Luis , Reyes-González Luis , López-Amo Manuel , López-Higuera José Miguel
Published: February 2021

In this work, a novel optical fiber sensor capable of measuring both the liquid level and its refractive index is designed, manufactured and demonstrated through simulations and experimentally. For this, a silica capillary hollow-core fiber is used. The fiber, with a sensing length of 1.55 mm, has been processed with a femtosecond laser, so that it incorporates four holes in its structure. In this way, the liquid enters the air core, and it is possible to perform the sensing through the Fabry–Perot cavities that the liquid generates. The detection mode is in reflection. With a resolution of 4 μm (liquid level), it is in the state of the art of this type of sensor. The system is designed so that in the future it will be capable of measuring the level of immiscible liquids, that is, liquids that form stratified layers. It can be useful to determine the presence of impurities in tanks.
Classification of paediatric brain tumours by diffusion weighted imaging and machine learning
Authors: Novak Jan , Zarinabad Niloufar , Rose Heather , Arvanitis Theodoros , MacPherson Lesley , Pinkey Benjamin , Oates Adam , Hales Patrick , Grundy Richard , Auer Dorothee , Gutierrez Daniel Rodriguez , Jaspan Tim , Avula Shivaram , Abernethy Laurence , Kaur Ramneek , Hargrave Darren , Mitra Dipayan , Bailey Simon , Davies Nigel , Clark Christopher , Peet Andrew
Published: February 2021

To determine if apparent diffusion coefficients (ADC) can discriminate between posterior fossa brain tumours on a multicentre basis. A total of 124 paediatric patients with posterior fossa tumours (including 55 Medulloblastomas, 36 Pilocytic Astrocytomas and 26 Ependymomas) were scanned using diffusion weighted imaging across 12 different hospitals using a total of 18 different scanners. Apparent diffusion coefficient maps were produced and histogram data was extracted from tumour regions of interest. Total histograms and histogram metrics (mean, variance, skew, kurtosis and 10th, 20th and 50th quantiles) were used as data input for classifiers with accuracy determined by tenfold cross validation. Mean ADC values from the tumour regions of interest differed between tumour types, (ANOVA P < 0.001). A cut off value for mean ADC between Ependymomas and Medulloblastomas was found to be of 0.984 × 10−3 mm2 s−1 with sensitivity 80.8% and specificity 80.0%. Overall classification for the ADC histogram metrics were 85% using Naïve Bayes and 84% for Random Forest classifiers. The most commonly occurring posterior fossa paediatric brain tumours can be classified using Apparent Diffusion Coefficient histogram values to a high accuracy on a multicentre basis.
Influence of lesion and disease subsets on the diagnostic performance of the quantitative flow ratio in real-world patients
Authors: Lee Kwan Yong , Hwang Byung-Hee , Kim Moo Jun , Choo Eun-Ho , Choi Ik Jun , Kim Chan Jun , Lee Sang-Wook , Lee Joo Myung , Kim Mi-Jeong , Jeon Doo Soo , Chung Wook Sung , Youn Ho-Joong , Kim Ki Jun , Yoon Myeong-Ho , Chang Kiyuk
Published: February 2021

The quantitative flow ratio (QFR) is a novel angiography-based computational method assessing functional ischemia caused by coronary stenosis. This study aimed to evaluate the diagnostic performance of quantitative flow ratio (QFR) in patients with angina and acute myocardial infarction (AMI) and to identify the conditions with low diagnostic performance. We assessed the QFR for 1077 vessels under fractional flow ratio (FFR) evaluation in 915 patients with angina and AMI. The diagnostic accuracies of the QFR for identifying an FFR ≤ 0.8 were 95.98% (95% confidence interval [CI] 94.52 to 97.14%) for the angina group and 92.42% (95% CI 86.51 to 96.31%) for the AMI group. The diagnostic accuracy of the QFR in the borderline FFR zones (> 0.75, ≤ 0.85) (91.23% [95% CI 88.25 to 93.66%]) was significantly lower than that in others (difference: 4.32; p = 0.001). The condition accompanying both AMI and the borderline FFR zone showed the lowest QFR diagnostic accuracy in our data (83.93% [95% CI 71.67 to 92.38]). The diagnostic accuracy was reduced for tandem lesions (p = 0.04, not correcting for multiple testing). Our study found that the QFR method yielded a high overall diagnostic performance in real-world patients. However, low diagnostic accuracy has been observed in borderline FFR zones with AMI, and the hybrid FFR approach needs to be considered.
Effects of salicylic acid, zinc and glycine betaine on morpho-physiological growth and yield of maize under drought stress
Authors: Shemi Ramadan , Wang Rui , Gheith El-Sayed M. S. , Hussain Hafiz Athar , Hussain Saddam , Irfan Muhammad , Cholidah Linna , Zhang Kangping , Zhang Sai , Wang Longchang
Published: February 2021

Drought is one of the major environmental stresses that negatively affect the maize (Zea mays L.) growth and production throughout the world. Foliar applications of plant growth regulators, micronutrients or osmoprotectants for stimulating drought-tolerance in plants have been intensively reported. A controlled pot experiment was conducted to study the relative efficacy of salicylic acid (SA), zinc (Zn), and glycine betaine (GB) foliar applications on morphology, chlorophyll contents, relative water content (RWC), gas-exchange attributes, activities of antioxidant enzymes, accumulations of reactive oxygen species (ROS) and osmolytes, and yield attributes of maize plants exposed to two soil water conditions (85% field capacity: well-watered, 50% field capacity: drought stress) during critical growth stages. Drought stress significantly reduced the morphological parameters, yield and its components, RWC, chlorophyll contents, and gas-exchange parameters except for intercellular CO2 concentration, compared with well water conditions. However, the foliar applications considerably enhanced all the above parameters under drought. Drought stress significantly (p < 0.05) increased the hydrogen peroxide and superoxide anion contents, and enhanced the lipid peroxidation rate measured in terms of malonaldehyde (MDA) content. However, ROS and MDA contents were substantially decreased by foliar applications under drought stress. Antioxidant enzymes activity, proline content, and the soluble sugar were increased by foliar treatments under both well-watered and drought-stressed conditions. Overall, the application of GB was the most effective among all compounds to enhance the drought tolerance in maize through reduced levels of ROS, increased activities of antioxidant enzymes and higher accumulation of osmolytes contents.
Effect of heat treatments on superconducting properties and connectivity in K-doped BaFe2As2
Authors: Tarantini Chiara , Pak Chongin , Su Yi-Feng , Hellstrom Eric E. , Larbalestier David C. , Kametani Fumitake
Published: February 2021

Fe-based superconductors and in particular K-doped BaFe2As2 (K-Ba122) are materials of interest for possible future high-field applications. However the critical current density (Jc) in polycrystalline Ba122 is still quite low and connectivity issues are suspected to be responsible. In this work we investigated the properties of high-purity, carefully processed, K-Ba122 samples synthesized with two separate heat treatments at various temperatures between 600 and 825 °C. We performed specific heat characterization and Tc-distribution analysis up to 16 T and we compared them with magnetic Tc and Jc characterizations, and transmission-electron-microscopy (TEM) microstructures. We found no direct correlation between the magnetic Tc and Jc, whereas the specific heat Tc-distributions did provide valuable insights. In fact the best Jc-performing sample, heat treated first at 750 °C and then at 600 °C, has the peak of the Tc-distributions at the highest temperatures and the least field sensitivity, thus maximizing Hc2. We also observed that the magnetic Tc onset was always significantly lower than the specific heat Tc: although we partially ascribe the lower magnetization Tc to the small grain size (< λ, the penetration depth) of the K-Ba122 phase, this behaviour also implies the presence of some grain-boundary barriers to current flow. Comparing the Tc-distribution with Jc, our systematic synthesis study reveals that increasing the first heat treatment above 750 °C or the second one above 600 °C significantly compromises the connectivity and suppresses the vortex pinning properties. We conclude that high-purity precursors and clean processing are not yet enough to overcome all Jc limitations. However, our study suggests that a higher temperature Tc-distribution, a larger Hc2 and a better connectivity could be achieved by lowering the second heat treatment temperature below 600 °C thus enhancing, as a consequence, Jc.
Systematic review and meta-analysis of the efficacy of prophylactic abdominal drainage in major liver resections
Authors: Dezfouli Sepehr Abbasi , Ünal Umut Kaan , Ghamarnejad Omid , Khajeh Elias , Ali-Hasan-Al-Saegh Sadeq , Ramouz Ali , Salehpour Roozbeh , Golriz Mohammad , Chang De-Hua , Mieth Markus , Hoffmann Katrin , Probst Pascal , Mehrabi Arianeb
Published: February 2021

Prophylactic drainage after major liver resection remains controversial. This systematic review and meta-analysis evaluate the value of prophylactic drainage after major liver resection. PubMed, Web of Science, and Cochrane Central were searched. Postoperative bile leak, bleeding, interventional drainage, wound infection, total complications, and length of hospital stay were the outcomes of interest. Dichotomous outcomes were presented as odds ratios (OR) and for continuous outcomes, weighted mean differences (MDs) were computed by the inverse variance method. Summary effect measures are presented together with their corresponding 95% confidence intervals (CI). The certainty of evidence was evaluated using the Grades of Research, Assessment, Development and Evaluation (GRADE) approach, which was mostly moderate for evaluated outcomes. Three randomized controlled trials and five non-randomized trials including 5,050 patients were included. Bile leakage rate was higher in the drain group (OR: 2.32; 95% CI 1.18–4.55; p = 0.01) and interventional drains were inserted more frequently in this group (OR: 1.53; 95% CI 1.11–2.10; p = 0.009). Total complications were higher (OR: 1.71; 95% CI 1.45–2.03; p < 0.001) and length of hospital stay was longer (MD: 1.01 days; 95% CI 0.47–1.56 days; p < 0.001) in the drain group. The use of prophylactic drainage showed no beneficial effects after major liver resection; however, the definitions and classifications used to report on postoperative complications and surgical complexity are heterogeneous among the published studies. Further well-designed RCTs with large sample sizes are required to conclusively determine the effects of drainage after major liver resection.
Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives
Authors: Nishiki Shingo , Lee Kenichi , Kanai Mizue , Nakayama Shu-ichi , Ohnishi Makoto
Published: February 2021

Japan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.
Sentiment correlation in financial news networks and associated market movements
Authors: Wan Xingchen , Yang Jie , Marinov Slavi , Calliess Jan-Peter , Zohren Stefan , Dong Xiaowen
Published: February 2021

In an increasingly connected global market, news sentiment towards one company may not only indicate its own market performance, but can also be associated with a broader movement on the sentiment and performance of other companies from the same or even different sectors. In this paper, we apply NLP techniques to understand news sentiment of 87 companies among the most reported on Reuters for a period of 7 years. We investigate the propagation of such sentiment in company networks and evaluate the associated market movements in terms of stock price and volatility. Our results suggest that, in certain sectors, strong media sentiment towards one company may indicate a significant change in media sentiment towards related companies measured as neighbours in a financial network constructed from news co-occurrence. Furthermore, there exists a weak but statistically significant association between strong media sentiment and abnormal market return as well as volatility. Such an association is more significant at the level of individual companies, but nevertheless remains visible at the level of sectors or groups of companies.
Pupillometry as a reliable metric of auditory detection and discrimination across diverse stimulus paradigms in animal models
Authors: Montes-Lourido Pilar , Kar Manaswini , Kumbam Isha , Sadagopan Srivatsun
Published: February 2021

Estimates of detection and discrimination thresholds are often used to explore broad perceptual similarities between human subjects and animal models. Pupillometry shows great promise as a non-invasive, easily-deployable method of comparing human and animal thresholds. Using pupillometry, previous studies in animal models have obtained threshold estimates to simple stimuli such as pure tones, but have not explored whether similar pupil responses can be evoked by complex stimuli, what other stimulus contingencies might affect stimulus-evoked pupil responses, and if pupil responses can be modulated by experience or short-term training. In this study, we used an auditory oddball paradigm to estimate detection and discrimination thresholds across a wide range of stimuli in guinea pigs. We demonstrate that pupillometry yields reliable detection and discrimination thresholds across a range of simple (tones) and complex (conspecific vocalizations) stimuli; that pupil responses can be robustly evoked using different stimulus contingencies (low-level acoustic changes, or higher level categorical changes); and that pupil responses are modulated by short-term training. These results lay the foundation for using pupillometry as a reliable method of estimating thresholds in large experimental cohorts, and unveil the full potential of using pupillometry to explore broad similarities between humans and animal models.
Chondrogenesis of human amniotic fluid stem cells in Chitosan-Xanthan scaffold for cartilage tissue engineering
Authors: Zuliani Carolina C. , Damas Ingrid I. , Andrade Kleber C. , Westin Cecília B. , Moraes Ângela M. , Coimbra Ibsen Bellini
Published: February 2021

Articular chondral lesions, caused either by trauma or chronic cartilage diseases such as osteoarthritis, present very low ability to self-regenerate. Thus, their current management is basically symptomatic, progressing very often to invasive procedures or even arthroplasties. The use of amniotic fluid stem cells (AFSCs), due to their multipotentiality and plasticity, associated with scaffolds, is a promising alternative for the reconstruction of articular cartilage. Therefore, this study aimed to investigate the chondrogenic potential of AFSCs in a micromass system (high-density cell culture) under insulin-like growth factor 1 (IGF-1) stimuli, as well as to look at their potential to differentiate directly when cultured in a porous chitosan-xanthan (CX) scaffold. The experiments were performed with a CD117 positive cell population, with expression of markers (CD117, SSEA-4, Oct-4 and NANOG), selected from AFSCs, after immunomagnetic separation. The cells were cultured in both a micromass system and directly in the scaffold, in the presence of IGF-1. Differentiation to chondrocytes was confirmed by histology and by using immunohistochemistry. The construct cell-scaffold was also analyzed by scanning electron microscopy (SEM). The results demonstrated the chondrogenic potential of AFSCs cultivated directly in CX scaffolds and also in the micromass system. Such findings support and stimulate future studies using these constructs in osteoarthritic animal models.
Elevated preoptic brain activity in zebrafish glial glycine transporter mutants is linked to lethargy-like behaviors and delayed emergence from anesthesia
Authors: Venincasa Michael J. , Randlett Owen , Sumathipala Sureni H. , Bindernagel Richard , Stark Matthew J. , Yan Qing , Sloan Steven A. , Buglo Elena , Meng Qing Cheng , Engert Florian , Züchner Stephan , Kelz Max B. , Syed Sheyum , Dallman Julia E.
Published: February 2021

Delayed emergence from anesthesia was previously reported in a case study of a child with Glycine Encephalopathy. To investigate the neural basis of this delayed emergence, we developed a zebrafish glial glycine transporter (glyt1 − / −) mutant model. We compared locomotor behaviors; dose–response curves for tricaine, ketamine, and 2,6-diisopropylphenol (propofol); time to emergence from these anesthetics; and time to emergence from propofol after craniotomy in glyt1−/− mutants and their siblings. To identify differentially active brain regions in glyt1−/− mutants, we used pERK immunohistochemistry as a proxy for brain-wide neuronal activity. We show that glyt1−/− mutants initiated normal bouts of movement less frequently indicating lethargy-like behaviors. Despite similar anesthesia dose–response curves, glyt1−/− mutants took over twice as long as their siblings to emerge from ketamine or propofol, mimicking findings from the human case study. Reducing glycine levels rescued timely emergence in glyt1−/− mutants, pointing to a causal role for elevated glycine. Brain-wide pERK staining showed elevated activity in hypnotic brain regions in glyt1−/− mutants under baseline conditions and a delay in sensorimotor integration during emergence from anesthesia. Our study links elevated activity in preoptic brain regions and reduced sensorimotor integration to lethargy-like behaviors and delayed emergence from propofol in glyt1−/− mutants.
Nanobodies mapped to cross-reactive and divergent epitopes on A(H7N9) influenza hemagglutinin using yeast display
Authors: Gaiotto Tiziano , Ramage Walter , Ball Christina , Risley Paul , Carnell George W. , Temperton Nigel , Engelhardt Othmar G. , Hufton Simon E.
Published: February 2021

Influenza H7N9 virus continues to cause infections in humans and represents a significant pandemic risk. During the most recent 5th epidemic wave in 2016/17 two distinct lineages with increased human infections and wider geographical spread emerged. In preparation for any future adaptations, broadly reactive antibodies against H7N9 are required for surveillance, therapy and prophylaxis. In this study we have isolated a panel of nanobodies (Nbs) with broad reactivity across H7 influenza strains, including H7N9 strains between 2013 and 2017. We also describe Nbs capable of distinguishing between the most recent high and low pathogenicity Yangtze River Delta lineage H7N9 strains. Nanobodies were classified into 5 distinct groups based on their epitope footprint determined using yeast display and mutational scanning. The epitope footprint of Nbs capable of distinguishing high pathogenic (HP) A/Guangdong/17SF003/2016 from low pathogenic (LP) A/Hong Kong/125/2017 (H7N9) were correlated to natural sequence divergence in the head domain at lysine 164. Several Nbs binding to the head domain were capable of viral neutralisation. The potency of one nanobody NB7-14 could be increased over 1000-fold to 113 pM by linking two Nbs together. Nbs specific for distinct epitopes on H7N9 may be useful for surveillance or therapy in human or veterinary settings.
Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Authors: Witt Kelsey E. , Yarlagadda Karthik , Allen Julie M. , Bader Alyssa C. , Simon Mary L. , Kuehn Steven R. , Swanson Kelly S. , Cross Tzu-Wen L. , Hedman Kristin M. , Ambrose Stanley H. , Malhi Ripan S.
Published: February 2021

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600–1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.
Identifying the signature of prospective motor control in children with autism
Authors: Cavallo Andrea , Romeo Luca , Ansuini Caterina , Battaglia Francesca , Nobili Lino , Pontil Massimiliano , Panzeri Stefano , Becchio Cristina
Published: February 2021

Failure to develop prospective motor control has been proposed to be a core phenotypic marker of autism spectrum disorders (ASD). However, whether genuine differences in prospective motor control permit discriminating between ASD and non-ASD profiles over and above individual differences in motor output remains unclear. Here, we combined high precision measures of hand movement kinematics and rigorous machine learning analyses to determine the true power of prospective movement data to differentiate children with autism and typically developing children. Our results show that while movement is unique to each individual, variations in the kinematic patterning of sequential grasping movements genuinely differentiate children with autism from typically developing children. These findings provide quantitative evidence for a prospective motor control impairment in autism and indicate the potential to draw inferences about autism on the basis of movement kinematics.
County-level longitudinal clustering of COVID-19 mortality to incidence ratio in the United States
Authors: Vahabi Nasim , Salehi Masoud , Duarte Julio D. , Mollalo Abolfazl , Michailidis George
Published: February 2021

As of November 12, 2020, the mortality to incidence ratio (MIR) of COVID-19 was 5.8% in the US. A longitudinal model-based clustering system on the disease trajectories over time was used to identify “vulnerable” clusters of counties that would benefit from allocating additional resources by federal, state and county policymakers. County-level COVID-19 cases and deaths, together with a set of potential risk factors were collected for 3050 U.S. counties during the 1st wave of COVID-19 (Mar25–Jun3, 2020), followed by similar data for 1344 counties (in the “sunbelt” region of the country) during the 2nd wave (Jun4–Sep2, 2020), and finally for 1055 counties located broadly in the great plains region of the country during the 3rd wave (Sep3–Nov12, 2020). We used growth mixture models to identify clusters of counties exhibiting similar COVID-19 MIR growth trajectories and risk-factors over time. The analysis identifies “more vulnerable” clusters during the 1st, 2nd and 3rd waves of COVID-19. Further, tuberculosis (OR 1.3–2.1–3.2), drug use disorder (OR 1.1), hepatitis (OR 13.1), HIV/AIDS (OR 2.3), cardiomyopathy and myocarditis (OR 1.3), diabetes (OR 1.2), mesothelioma (OR 9.3) were significantly associated with increased odds of being in a more vulnerable cluster. Heart complications and cancer were the main risk factors increasing the COVID-19 MIR (range 0.08–0.52% MIR↑). We identified “more vulnerable” county-clusters exhibiting the highest COVID-19 MIR trajectories, indicating that enhancing the capacity and access to healthcare resources would be key to successfully manage COVID-19 in these clusters. These findings provide insights for public health policymakers on the groups of people and locations they need to pay particular attention while managing the COVID-19 epidemic.
Quasistatic transfer protocols for atomtronic superfluid circuits
Authors: Winsten Yehoshua , Cohen Doron
Published: February 2021

Quasi-static protocols for systems that feature a mixed phase-space with both chaos and quasi-regular regions are beyond the standard paradigm of adiabatic processes. We focus on many-body system of atoms that are described by the Bose–Hubbard Hamiltonian, specifically a circuit that consists of bosonic sites. We consider a sweep process: slow variation of the rotation frequency of the device (time dependent Sagnac phase). The parametric variation of phase-space topology implies that the quasi-static limit is not compatible with linear response theory. Detailed analysis is essential in order to determine the outcome of such transfer protocol, and its efficiency.
New machine learning and physics-based scoring functions for drug discovery
Authors: Guedes Isabella A. , Barreto André M. S. , Marinho Diogo , Krempser Eduardo , Kuenemann Mélaine A. , Sperandio Olivier , Dardenne Laurent E. , Miteva Maria A.
Published: February 2021

Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different target classes. Scoring functions based on precise physics-based descriptors better representing protein–ligand recognition process are strongly needed. We developed a set of new empirical scoring functions, named DockTScore, by explicitly accounting for physics-based terms combined with machine learning. Target-specific scoring functions were developed for two important drug targets, proteases and protein–protein interactions, representing an original class of molecules for drug discovery. Multiple linear regression (MLR), support vector machine and random forest algorithms were employed to derive general and target-specific scoring functions involving optimized MMFF94S force-field terms, solvation and lipophilic interactions terms, and an improved term accounting for ligand torsional entropy contribution to ligand binding. DockTScore scoring functions demonstrated to be competitive with the current best-evaluated scoring functions in terms of binding energy prediction and ranking on four DUD-E datasets and will be useful for in silico drug design for diverse proteins as well as for specific targets such as proteases and protein–protein interactions. Currently, the MLR DockTScore is available at www.dockthor.lncc.br.
O antigen restricts lysogenization of non-O157 Escherichia coli strains by Stx-converting bacteriophage phi24B
Authors: Golomidova A. K. , Efimov A. D. , Kulikov E. E. , Kuznetsov A. S. , Belalov I. Sh. , Letarov A. V.
Published: February 2021

Acquisition of new prophages that are able to increase the bacterial fitness by the lysogenic conversion is believed to be an important strategy of bacterial adaptation to the changing environment. However, in contrast to the factors determining the range of bacteriophage lytic activity, little is known about the factors that define the lysogenization host range. Bacteriophage phi24B is the paradigmal model of Stx-converting phages, encoding the toxins of the Shiga-toxigenic E. coli (STEC). This virus has been shown to lysogenize a wide range of E. coli strains that is much broader than the range of the strains supporting its lytic growth. Therefore, phages produced by the STEC population colonizing the small or large intestine are potentially able to lysogenize symbiotic E. coli in the hindgut, and these secondary lysogens may contribute to the overall patient toxic load and to lead to the emergence of new pathogenic STEC strains. We demonstrate, however, that O antigen effectively limit the lysogenization of the wild E. coli strains by phi24B phage. The lysogens are formed from the spontaneous rough mutants and therefore have increased sensitivity to other bacteriophages and to the bactericidal activity of the serum if compared to their respective parental strains.
The switching mechanisms of social network densification
Authors: Kobayashi Teruyoshi , Génois Mathieu
Published: February 2021

Densification and sparsification of social networks are attributed to two fundamental mechanisms: a change in the population in the system, and/or a change in the chances that people in the system are connected. In theory, each of these mechanisms generates a distinctive type of densification scaling, but in reality both types are generally mixed. Here, we develop a Bayesian statistical method to identify the extent to which each of these mechanisms is at play at a given point in time, taking the mixed densification scaling as input. We apply the method to networks of face-to-face interactions of individuals and reveal that the main mechanism that causes densification and sparsification occasionally switches, the frequency of which depending on the social context. The proposed method uncovers an inherent regime-switching property of network dynamics, which will provide a new insight into the mechanics behind evolving social interactions.
Blood lead level and risk of hypertension in the United States National Health and Nutrition Examination Survey 1999–2016
Authors: Tsoi Man Fung , Lo Chris Wai Hang , Cheung Tommy Tsang , Cheung Bernard Man Yung
Published: February 2021

Lead is a heavy metal without a biological role. High level of lead exposure is known to be associated with hypertension, but the risk at low levels of exposure is uncertain. In this study, data from US NHANES 1999–2016 were analyzed. Adults with blood lead and blood pressure measurements, or self-reported hypertension diagnosis, were included. If not already diagnosed, hypertension was defined according to the AHA/ACC 2017 hypertension guideline. Results were analyzed using R statistics version 3.5.1 with sample weight adjustment. Logistic regression was used to study the association between blood lead level and hypertension. Odds ratio (OR) and 95% confidence interval (95% CI) were estimated. Altogether, 39,477 participants were included. Every doubling in blood lead level was associated with hypertension (OR [95%CI] 1.45 [1.40–1.50]), which remained significant after adjusting for demographics. Using quartile 1 as reference, higher blood lead levels were associated with increased adjusted odds of hypertension (Quartile 4 vs. Quartile 1: 1.22 [1.09–1.36]; Quartile 3 vs. Quartile 1: 1.15 [1.04–1.28]; Quartile 2 vs. Quartile 1: 1.14 [1.05–1.25]). In conclusion, blood lead level is associated with hypertension in the general population with blood lead levels below 5 µg/dL. Our findings suggest that reducing present levels of environmental lead exposure may bring cardiovascular benefits by reducing blood pressure.