bluuebunny/crossref_metadata_2025 huggingface dataset:
A method for autonomous collision-free navigation of a quadrotor UAV in unknown tunnel-like environments
Authors: Elmokadem Taha , Savkin Andrey V.
Published: June 2021

Unmanned aerial vehicles (UAVs) have become essential tools for exploring, mapping and inspection of unknown three-dimensional (3D) tunnel-like environments which is a very challenging problem. A computationally light navigation algorithm is developed in this paper for quadrotor UAVs to autonomously guide the vehicle through such environments. It uses sensors observations to safely guide the UAV along the tunnel axis while avoiding collisions with its walls. The approach is evaluated using several computer simulations with realistic sensing models and practical implementation with a quadrotor UAV. The proposed method is also applicable to other UAV types and autonomous underwater vehicles.
New challenges and solutions for information retrieval: information specialists as “bricklayers” in the health technology assessment framework
Authors: Waffenschmidt Siw , Kaunelis David , Harboe Ingrid
Published: June 2021

We are pleased to present this information retrieval issue. Our goal is to highlight the variety of tasks and organizational structures of information retrieval within heath technology assessment (HTA). This special issue was planned and organized by the HTAi Information Retrieval Group (IRG). The choice of publications in this issue reflects the versatility and high competence in information retrieval methodology that is needed as an information specialist. Furthermore, it provides insights into the daily challenges faced by information specialists.
Powder X-ray diffraction of varenicline hydrogen tartrate Form B (Chantix®), (C13H14N3)(HC4H4O6)
Authors: Kaduk James A. , Gindhart Amy M. , Blanton Thomas N.
Published: June 2021

The crystal structure of varenicline hydrogen tartrate Form B (Chantix®) has been refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Varenicline hydrogen tartrate Form B crystallizes in space group P212121 (#19) with a = 7.07616(2), b = 7.78357(2), c = 29.86149(7) Å, V = 1644.706(6) Å3, and Z = 4. The hydrogen bonds were identified and quantified. Hydrogen bonds link the cations and anions in zig-zag chains along the b-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).
State of the science and future research directions in palliative and end-of-life care in paediatric cardiology: a report from the Harvard Radcliffe Accelerator Workshop
Authors: Cousino Melissa K. , Lord Blyth T. , Blume Elizabeth D.
Published: June 2021

Workshop proceedings, priorities, and recommendations from the “State of the Science and Future Directions in Palliative and End-of-Life Care in Pediatric Cardiology,” a Harvard Radcliffe Accelerator Workshop, are detailed. Eight priorities for research were identified, including patient and family decision making, communication, patient and family experience, patient symptom measurement and management, training and curriculum development, teamwork, family hardships and bereavement, and ethical considerations. Barriers to research in this area were also identified: lack of outcome/measurement tools, lack of research funding, small population sizes, lack of effort/protected time for research, undervalued research topic by field and colleagues, and heterogeneous research participant diversity. Priorities and barriers were mostly consistent with those reported by the field of paediatric palliative care at large. These collective, consensus-based findings from diverse, multidisciplinary leaders in the field, as well as parent representatives, provide a catalyst for scientific advancement specific to paediatric and end-of-life care in paediatric cardiology.
Family caregiver grief and post-loss adjustment: A longitudinal cohort study
Authors: Coelho Alexandra , Roberto Magda , Barros Luísa , Barbosa António
Published: June 2021

Objective

In order to better understand the different grieving trajectories of the family caregivers (FCs), this study aims to examine the evolution of prolonged grief disorder (PGD) symptoms and the predictive role of the caregiving-related factors in the FCs' grieving trajectory from pre- to post-death.

Method

A prospective cohort study was carried out with advanced cancer FCs evaluated before death (T1) and 6–12 months post-loss (T2).

Results

Participants in T1 (n= 156) were mostly female, adult child, or spouse of the care recipient, with a mean age of 51.78 (SD = 13.29). At T2, 87 FCs participated in the survey. PGD prevalence was higher pre-death (38.6%) than in bereavement (33.7%). Of those who met the PGD criteria before death, most also met these criteria after death (n= 26, 61.9%). Psychological distress and caregiver burden were highly correlated with pre-death grief, which in turn played a critical role in mediating the link between psychological distress and bereavement outcome. Great emotional closeness in the relationship was predictive of PGD symptoms persistence. In contrast, the long-term consequences of caregiver burden were not confirmed.

Significance of results

This study provides evidence for the diversity of individual FC responses and the complex pattern of interactions between caregiving-related factors, relationship quality, and PGD symptoms evolution from pre- to post-death.
Stratospheric Quasi Biennial Oscillation Modulations of Migrating Diurnal Tide in the Mesosphere and Lower Thermosphere Over the Low and Equatorial Latitudes
Authors: Pramitha M. , Kumar K. Kishore , Ratnam M. Venkat , Praveen M. , Bhaskara Rao S. Vijaya
Published: June 2021

Horizontal wind measurements using meteor radars located at Thumba (8.5°N, 77°E; 2006–2015) Kototabang (0.2°S, 100.3°E; 2002–2017) and Tirupati (13.63°N, 79.4°E; 2013–2017) in the mesosphere‐lower thermosphere (MLT) and Specified Dynamics Whole Atmosphere Community Climate Model (SD‐WACCM) simulations are employed for investigating the diurnal tide variability at quasi‐biennial scales. The model simulations are evaluated using the meteor radar observations at three tropical locations. WACCM simulations could reproduce the seasonal evolution of diurnal tides very well over Thumba and Tirupati but there are small discrepancies over Kototabang. In order to investigate the modulation of the diurnal tide amplitudes in the MLT region by the stratospheric quasi‐biennial oscillation (SQBO), deseasonalized perturbations of diurnal tides and stratospheric winds are analyzed. A very good correspondence is found between meridional diurnal tide perturbation amplitudes and the SQBO with positive tidal perturbations during the eastward phase of SQBO and negative perturbations during the westward phase over Thumba and Tirupati. SQBO modulations of diurnal tides at global scales exhibits a positive correlation between the meridional diurnal tide perturbation with SQBO winds at 20 hPa and a negative correlation with SQBO winds at 70 hPa within ±40° latitude, except over the equator. It is also noted that the equatorial electrojet strength, is modulated by the SQBO over the Thumba, which is a dip equatorial location. The significance of present study lies in evaluating WACCM simulations at tropical locations using meteor radar measurements and in investigating the SQBO modulations of diurnal tides at global scales.
Effect of Glacial/Interglacial Recharge Conditions on Flow of Meteoric Water Through Deep Orogenic Faults: Insights Into the Geothermal System at Grimsel Pass, Switzerland
Authors: Alt‐Epping Peter , Diamond Larryn W. , Wanner Christoph , Hammond Glenn E.
Published: June 2021

Many meteoric‐recharged, fault‐hosted geothermal systems in amagmatic orogenic belts have been active through the Pleistocene glacial/interglacial climate fluctuations. The effects of climate‐induced recharge variations on fluid flow patterns and residence times of the thermal waters are complex and may influence how the geothermal and mineralization potential of the systems are evaluated. We report systematic thermal‐hydraulic simulations designed to reveal the effects of recharge variations, using a model patterned on the orogenic geothermal system at Grimsel Pass in the Swiss Alps. Previous studies have shown that fault‐bounded circulation of meteoric water is driven to depths of ∼10 km by the high alpine topography. Simulations suggest that the current single‐pass flow is typical of interglacial periods, during which (a) meteoric recharge into the fault is high (above tens of centimeters per year), (b) conditions are at or somewhat below the critical Rayleigh number, and (c) hydraulic connectivity along the fault plane is extensive (an extent of at least 10 km into increasingly higher terrain is required to explain the 10 km penetration depth). The subcritical condition constrains the bulk fault permeability to <1e‐14 m2. In contrast, the limited recharge during the numerous Pleistocene glaciation events likely induced a layered flow system, with single‐pass flow confined to shallow depths while non‐Rayleigh convection occurred deeper in the fault. The same layering can be observed at low aspect ratios (length/depth) of the fault plane, when the available recharge area limits flux through the fault.
Environmental Controls on the Temporal Evolution of Energy and CO2 Fluxes on an Arid Mangrove of Northwestern Mexico
Authors: Granados‐Martínez K. P. , Yépez E. A. , Sánchez‐Mejía Z. M. , Gutiérrez‐Jurado H. A. , Méndez‐Barroso L. A.
Published: June 2021

This work explored the environmental factors that control the temporal dynamics of vertical energy and carbon fluxes between the atmosphere and arid mangroves located on the coastline of the Gulf of California, Mexico. Net ecosystem exchange (NEE), latent (λE) and sensible heat (H) exchange fluxes were estimated in situ using the eddy covariance technique along with meteorological and hydrological observations during the period November 2017 through November 2019. Moreover, multiyear mangrove phenology at footprint‐scale was tracked using remotely sensed vegetation greenness data from Sentinel‐2. Our results suggest that the seasonal energy partition and the magnitude of NEE is highly coupled with seasonal changes in the level of tidal flooding, vapor pressure deficit (VPD) and temperature. Low tidal levels facilitate heat transmission to the atmosphere leading the energy partition to H, while the increase in flooding and VPD facilitates the transmission of water vapor resulting in λE dominance. The lowest rate of NEE was observed during the months of highest tidal flooding (June–August) while the highest seasonal rate of NEE matched with the lowest mean flood levels (March–May). Estimated annual NEE for 2018 was −745.3 gC m−2 y−1 while for 2019 was −307.4 gC m−2 y−1. Our findings suggest a possible trend of decrease in the capacity of carbon sequestration of arid mangroves with rising sea levels and air temperature as a result of global warming.
Latitudinal Migrations of the Subtropical Front at the Agulhas Plateau Through the Mid‐Pleistocene Transition
Authors: Cartagena‐Sierra Alejandra , Berke Melissa A. , Robinson Rebecca S. , Marcks Basia , Castañeda Isla S. , Starr Aidan , Hall Ian R. , Hemming Sidney R. , LeVay Leah J. ,   Expedition 361 Scientific Party
Published: June 2021

The meridional variability of the Subtropical Front (STF) in the Southern Hemisphere, linked to expansions or contractions of the Southern Ocean, may have played an important role in global ocean circulation by moderating the magnitude of water exchange at the Indian‐Atlantic Ocean Gateway, so called Agulhas Leakage. Here we present new biomarker records of upper water column temperature ( and ) and primary productivity (chlorins and alkenones) from marine sediments at IODP Site U1475 on the Agulhas Plateau, near the STF and within the Agulhas retroflection pathway. We use these multiproxy time‐series records from 1.4 to 0.3 Ma to examine implied changes in the upper oceanographic conditions at the mid‐Pleistocene transition (MPT, ca. 1.2–0.8 Ma). Our reconstructions, combined with prior evidence of migrations of the STF over the last 350 ka, suggest that in the Southwestern Indian Ocean the STF may have been further south from the Agulhas Plateau during the mid‐Pleistocene Interim State (MPIS, MIS 23–12) and reached its northernmost position during MIS 34–24 and MIS 10. Comparison to a Globorotalia menardii‐derived Agulhas Leakage reconstruction from the Cape Basin suggests that only the most extreme northward migrations of the STF are associated with reduced Agulhas Leakage. During the MPIS, STF migrations do not appear to control Agulhas Leakage variability, we suggest previously modeled shifting westerly winds may be responsible for the patterns observed. A detachment between STF migrations and Agulhas Leakage, in addition to invoking shifting westerly winds may also help explain changes in CO2 ventilation seen during the MPIS.
Loss Exponent Modeling for the Hilly Forested Region in the VHF Band III
Authors: Jawhly Thaisa , Chandra Tiwari Ramesh
Published: June 2021

Modeling forest propagation loss over a vast area is challenging, particularly for the hilly terrain regions where canopy obstacle depth varies with region. To consider such vegetation impact, we present a novel forest cover classification well defined with the line‐of‐sight (LoS). Furthermore, we incorporated the mobile antenna site elevation angle, which showed significant influence within the target frequencies selected at 182.25 and 203.25 MHz (VHF Band III). We proposed a loss exponent dependent on the elevation angle and the vegetation‐visibility classification, which is the basis of the model introduced in this paper. The resulting loss derived using this loss exponent showed a good agreement with the empirically derived loss variations. The proposed method offers easy forest classification approximations with precise determination of signal variation over a wide‐ranging forested area.
Strain Partitioning Within Bending Orogens, New Insights From the Variscan Belt (Chiroulet‐Lesponne Domes, Pyrenees)
Authors: Cochelin Bryan , Lemirre Baptiste , Denèle Yoann , de Saint Blanquat Michel
Published: June 2021

This study investigates how strain is partitioned within hot orogenic belts in a context of plate reorganization. We document crustal‐scale strike‐slip shear zones, plate‐scale oroclinal bending, and widespread exhumation of deep crustal domains in the core of nascent Pangea plate during late‐Variscan times (ca. 310–290 Ma). The role of strain partitioning in the finite strain patterns is first highlighted at regional scale by a new detailed structural, kinematic, and petrologic analysis of the Chiroulet and Lesponne gneiss domes in the Pyrenees. Vertical strain partitioning in response to N‐S shortening‐dominated dextral transpression is secondly documented at the scale of the Variscan domains of the Pyrenees, based on a synthesis of recent geochronological, thermobarometrical, and structural data. We show that the mid‐lower crust is affected by eastward lateral flow and the upper crust by penetrative thickening and localized thrusting. Local transverse extension in the mid‐lower crust illustrates gravity‐driven instability favored by the accumulation of anatectic melts in gneiss domes. Finally, we highlight the respective position of extended and shortened area within the Variscan belt during late‐Carboniferous/early‐Permian that suggests large‐scale lateral strain partitioning and reorganization of the weak continental crust in the core of the Pangea. This distribution appears significantly different from other orogens in a similar context of oroclinal bending, resulting in localization of the shortened zones in the core of the belt. This highlights the influence of the initial and boundary conditions, such as the obliquity of the belt to the applied stress field and the location of free‐boundaries, on finite strain patterns.
MyD88 determines the protective effects of fish oil and perilla oil against metabolic disorders and inflammation in adipose tissue from mice fed a high-fat diet
Authors: Wang Feng , Hu Mingyuan , Zhu Hangju , Yang Chao , Xia Hui , Yang Xian , Yang Ligang , Sun Guiju
Published: June 2021

Background

The beneficial effects of ω−3 polyunsaturated fatty acids (PUFA) vary between different sources. However, there is a paucity of comparative studies regarding the effects and mechanisms of marine and plant ω−3 PUFA on obesity.

Objective

The aim of this study was to evaluate the effects of fish oil (FO) and perilla oil (PO) on glucolipid metabolism, inflammation, and adipokine in mice fed a high-fat (HF) diet in association with the contribution of toll-like receptor 4 (TLR4)/myeloid differentiation primary response 88 (MyD88) pathway.

Methods

C57BL/6J mice and MyD88−/− mice were randomly divided into 4 groups: normal chow diet, HF diet, HF diet accompanied by daily gavage with either FO or PO. After 4 weeks, blood biochemistries, adipocyte histology, mRNA, and protein expression of MyD88-dependent and -independent pathways of TLR4 signaling in epididymal adipose tissue were measured.

Results

In C57BL/6J mice, there were no statistical differences between FO and PO in decreasing body weight, glucose, insulin, triglyceride, total cholesterol, interleukin-6, and increasing adipocyte counts. FO and PO decreased mRNA and protein expression of TLR4, MyD88, tumor necrosis factor receptor-associated factor 6, inhibitor of nuclear factor kappa B kinase beta and nuclear factor-kappa B p65. In MyD88−/− mice, the beneficial effects of FO and PO on HF diet-induced metabolism abnormalities and inflammation were abolished. FO and PO had no impacts on mRNA and protein expression of receptor-interacting protein-1, interferon regulate factor 3, and nuclear factor-kappa B p65.

Conclusion

FO and PO exhibit similar protective effects on metabolic disorders and inflammation through inhibiting TLR4 signaling in a manner dependent on MyD88. These findings highlight plant ω−3 PUFA as an attractive alternative source of marine ω−3 PUFA and reveal a mechanistic insight for preventive benefits of ω−3 PUFA in obesity and related metabolic diseases.
Conditional depletion of macrophages ameliorates cholestatic liver injury and fibrosis via lncRNA-H19
Authors: Tian Xinbei , Wang Ying , Lu Ying , Wang Weipeng , Du Jun , Chen Shanshan , Zhou Huiping , Cai Wei , Xiao Yongtao
Published: June 2021

Although macrophages are recognized as important players in the pathogenesis of chronic liver diseases, their roles in cholestatic liver fibrosis remain incompletely understood. We previously reported that long noncoding RNA-H19 (lncRNA-H19) contributes to cholangiocyte proliferation and cholestatic liver fibrosis of biliary atresia (BA). We here show that monocyte/macrophage CD11B mRNA levels are increased significantly in livers of BA patients and positively correlated with the progression of liver inflammation and fibrosis. The macrophages increasingly infiltrate and accumulate in the fibrotic niche and peribiliary areas in livers of BA patients. Selective depletion of macrophages using the transgenic CD11b-diphtheria toxin receptor (CD11b-DTR) mice halts bile duct ligation (BDL)-induced progression of liver damage and fibrosis. Meanwhile, macrophage depletion significantly reduces the BDL-induced hepatic lncRNA-H19. Overexpression of H19 in livers using adeno-associated virus serotype 9 (AAV9) counteracts the effects of macrophage depletion on liver fibrosis and cholangiocyte proliferation. Additionally, both H19 knockout (H19−/−) and conditional deletion of H19 in macrophage (H19ΔCD11B) significantly depress the macrophage polarization and recruitment. lncRNA-H19 overexpressed in THP-1 macrophages enhance expression of Rho-GTPase CDC42 and RhoA. In conclusions, selectively depletion of macrophages suppresses cholestatic liver injuries and fibrosis via the lncRNA-H19 and represents a potential therapeutic strategy for rapid liver fibrosis in BA patients.
Fast food and sweet intake pattern is directly associated with the prevalence of asthma in a Qatari population
Authors: Shi Zumin , El-Obeid Tahra , Meftah Zainab , Alawi Amal , Said Suad , Ganji Vijay
Published: June 2021

Objective

The relationship between dietary patterns and the prevalence of asthma is not well understood. We aimed to investigate the association between dietary patterns and asthma in adults in Qatar.

Methods

In this study, cross-sectional data from the Qatar Biobank were used (n = 986). Participants were Qatari or long-term Qatar residents aged ≥20 years old. A food frequency questionnaire was used to collect dietary intakes. Three dietary patterns were identified using factor analysis. Multivariable logistic regression was used to assess the association between dietary patterns scores and asthma.

Results

Among 986 eligible participants, 6.6% (n = 65) reported that they were diagnosed with asthma. Three dietary patterns were identified. These were (1) “Traditional” (high intake of rice, chicken/meat/fish, and breads); (2) “Prudent” (high intake of fruits, vegetables, and fish); and (3) “Fast Food/Sweets” (high intake of desserts, fast food, and soft drinks). The fast food/sweet dietary pattern was associated with increased likelihood of having asthma [comparing high vs. low tertile, OR for asthma = 1.25; 95% CI (1.02–1.54); p = 0.035]. Traditional and Prudent dietary patterns were not associated with the prevalence of asthma.

Conclusion

The fast food/sweet dietary pattern was directly associated with the prevalence of asthma among adults in Qatar. Reducing the fast foods and sugary-rich foods may be beneficial for respiratory health.
Contrasting responses of above- and belowground diversity to multiple components of land-use intensity
Authors: Le Provost Gaëtane , Thiele Jan , Westphal Catrin , Penone Caterina , Allan Eric , Neyret Margot , van der Plas Fons , Ayasse Manfred , Bardgett Richard D. , Birkhofer Klaus , Boch Steffen , Bonkowski Michael , Buscot Francois , Feldhaar Heike , Gaulton Rachel , Goldmann Kezia , Gossner Martin M. , Klaus Valentin H. , Kleinebecker Till , Krauss Jochen , Renner Swen , Scherreiks Pascal , Sikorski Johannes , Baulechner Dennis , Blüthgen Nico , Bolliger Ralph , Börschig Carmen , Busch Verena , Chisté Melanie , Fiore-Donno Anna Maria , Fischer Markus , Arndt Hartmut , Hoelzel Norbert , John Katharina , Jung Kirsten , Lange Markus , Marzini Carlo , Overmann Jörg , Paŝalić Esther , Perović David J. , Prati Daniel , Schäfer Deborah , Schöning Ingo , Schrumpf Marion , Sonnemann Ilja , Steffan-Dewenter Ingolf , Tschapka Marco , Türke Manfred , Vogt Juliane , Wehner Katja , Weiner Christiane , Weisser Wolfgang , Wells Konstans , Werner Michael , Wolters Volkmar , Wubet Tesfaye , Wurst Susanne , Zaitsev Andrey S. , Manning Peter
Published: June 2021

Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
Residue 6.43 defines receptor function in class F GPCRs
Authors: Turku Ainoleena , Schihada Hannes , Kozielewicz Pawel , Bowin Carl-Fredrik , Schulte Gunnar
Published: June 2021

The class Frizzled of G protein-coupled receptors (GPCRs), consisting of ten Frizzled (FZD1-10) subtypes and Smoothened (SMO), remains one of the most enigmatic GPCR families. While SMO relies on cholesterol binding to the 7TM core of the receptor to activate downstream signaling, underlying details of receptor activation remain obscure for FZDs. Here, we aimed to investigate the activation mechanisms of class F receptors utilizing a computational biology approach and mutational analysis of receptor function in combination with ligand binding and downstream signaling assays in living cells. Our results indicate that FZDs differ substantially from SMO in receptor activation-associated conformational changes. SMO manifests a preference for a straight TM6 in both ligand binding and functional readouts. Similar to the majority of GPCRs, FZDs present with a kinked TM6 upon activation owing to the presence of residue P6.43. Functional comparison of FZD and FZD P6.43F mutants in different assay formats monitoring ligand binding, G protein activation, DVL2 recruitment and TOPflash activity, however, underlines further the functional diversity among FZDs and not only between FZDs and SMO.
Role of backbone strain in de novo design of complex α/β protein structures
Authors: Koga Nobuyasu , Koga Rie , Liu Gaohua , Castellanos Javier , Montelione Gaetano T. , Baker David
Published: June 2021

We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.
Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway
Authors: Ho Joanne M. L. , Miller Corwin A. , Smith Kathryn A. , Mattia Jacob R. , Bennett Matthew R.
Published: June 2021

Pyrrolysine (Pyl, O) exists in nature as the 22nd proteinogenic amino acid. Despite being a fundamental building block of proteins, studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, we improve Pyl biosynthesis via rational engineering and directed evolution of the entire biosynthetic pathway. To accommodate toxicity of Pyl biosynthetic genes in Escherichia coli, we also develop Alternating Phage Assisted Non-Continuous Evolution (Alt-PANCE) that alternates mutagenic and selective phage growths. The evolved pathway provides 32-fold improved yield of Pyl-containing reporter protein compared to the rationally engineered ancestor. Evolved PylB mutants are present at up to 4.5-fold elevated levels inside cells, and show up to 2.2-fold increased protease resistance. This study demonstrates that Alt-PANCE provides a general approach for evolving proteins exhibiting toxic side effects, and further provides an improved pathway capable of producing substantially greater quantities of Pyl-proteins in E. coli.
Subcortical circuits mediate communication between primary sensory cortical areas in mice
Authors: Lohse Michael , Dahmen Johannes C. , Bajo Victoria M. , King Andrew J.
Published: June 2021

Integration of information across the senses is critical for perception and is a common property of neurons in the cerebral cortex, where it is thought to arise primarily from corticocortical connections. Much less is known about the role of subcortical circuits in shaping the multisensory properties of cortical neurons. We show that stimulation of the whiskers causes widespread suppression of sound-evoked activity in mouse primary auditory cortex (A1). This suppression depends on the primary somatosensory cortex (S1), and is implemented through a descending circuit that links S1, via the auditory midbrain, with thalamic neurons that project to A1. Furthermore, a direct pathway from S1 has a facilitatory effect on auditory responses in higher-order thalamic nuclei that project to other brain areas. Crossmodal corticofugal projections to the auditory midbrain and thalamus therefore play a pivotal role in integrating multisensory signals and in enabling communication between different sensory cortical areas.
High thermoelectric figure of merit of porous Si nanowires from 300 to 700 K
Authors: Yang Lin , Huh Daihong , Ning Rui , Rapp Vi , Zeng Yuqiang , Liu Yunzhi , Ju Sucheol , Tao Yi , Jiang Yue , Beak Jihyun , Leem Juyoung , Kaur Sumanjeet , Lee Heon , Zheng Xiaolin , Prasher Ravi S.
Published: June 2021

Thermoelectrics operating at high temperature can cost-effectively convert waste heat and compete with other zero-carbon technologies. Among different high-temperature thermoelectrics materials, silicon nanowires possess the combined attributes of cost effectiveness and mature manufacturing infrastructures. Despite significant breakthroughs in silicon nanowires based thermoelectrics for waste heat conversion, the figure of merit (ZT) or operating temperature has remained low. Here, we report the synthesis of large-area, wafer-scale arrays of porous silicon nanowires with ultra-thin Si crystallite size of ~4 nm. Concurrent measurements of thermal conductivity (κ), electrical conductivity (σ), and Seebeck coefficient (S) on the same nanowire show a ZT of 0.71 at 700 K, which is more than ~18 times higher than bulk Si. This ZT value is more than two times higher than any nanostructured Si-based thermoelectrics reported in the literature at 700 K. Experimental data and theoretical modeling demonstrate that this work has the potential to achieve a ZT of ~1 at 1000 K.
Synaptic plasticity-dependent competition rule influences memory formation
Authors: Jeong Yire , Cho Hye-Yeon , Kim Mujun , Oh Jung-Pyo , Kang Min Soo , Yoo Miran , Lee Han-Sol , Han Jin-Hee
Published: June 2021

Memory is supported by a specific collection of neurons distributed in broad brain areas, an engram. Despite recent advances in identifying an engram, how the engram is created during memory formation remains elusive. To explore the relation between a specific pattern of input activity and memory allocation, here we target a sparse subset of neurons in the auditory cortex and thalamus. The synaptic inputs from these neurons to the lateral amygdala (LA) are not potentiated by fear conditioning. Using an optogenetic priming stimulus, we manipulate these synapses to be potentiated by the learning. In this condition, fear memory is preferentially encoded in the manipulated cell ensembles. This change, however, is abolished with optical long-term depression (LTD) delivered shortly after training. Conversely, delivering optical long-term potentiation (LTP) alone shortly after fear conditioning is sufficient to induce the preferential memory encoding. These results suggest a synaptic plasticity-dependent competition rule underlying memory formation.
Epithelial cell plasticity drives endoderm formation during gastrulation
Authors: Scheibner Katharina , Schirge Silvia , Burtscher Ingo , Büttner Maren , Sterr Michael , Yang Dapeng , Böttcher Anika , Ansarullah  , Irmler Martin , Beckers Johannes , Cernilogar Filippo M. , Schotta Gunnar , Theis Fabian J. , Lickert Heiko
Published: June 2021

It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock‐in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. Strikingly, while the mesoderm is formed by classical EMT, the endoderm is formed independent of the key EMT transcription factor Snail1 by mechanisms of epithelial cell plasticity. Importantly, forkhead box transcription factor A2 (Foxa2) acts as an epithelial gatekeeper and EMT suppressor to shield the endoderm from undergoing a mesenchymal transition. Altogether, these results not only establish the morphogenetic details of germ layer formation, but also have broader implications for stem cell differentiation and cancer metastasis.
Probiotics: their action against pathogens can be turned around
Authors: Gan Lian , Xu Wei-Hua , Xiong Yuanyan , Lv Zhaolin , Zheng Jianwei , Zhang Yu , Lin Jianhao , Liu Jingshu , Chen Shijun , Chen Mengqiu , Guo Qingqi , Wu Junfeng , Chen Jingjie , Su Zhenhua , Sun Jijia , He Yuhui , Liu Chuanhe , Wang Weifang , Verstraete Willy , Sorgeloos Patrick , Defoirdt Tom , Qin Qiwei , Liu Yiying
Published: June 2021

Probiotics when applied in complex evolving (micro-)ecosystems, might be selectively beneficial or detrimental to pathogens when their prophylactic efficacies are prone to ambient interactions. Here, we document a counter-intuitive phenomenon that probiotic-treated zebrafish (Danio rerio) were respectively healthy at higher but succumbed at lower level of challenge with a pathogenic Vibrio isolate. This was confirmed by prominent dissimilarities in fish survival and histology. Based upon the profiling of the zebrafish microbiome, and the probiotic and the pathogen shared gene orthogroups (genetic niche overlaps in genomes), this consequently might have modified the probiotic metabolome as well as the virulence of the pathogen. Although it did not reshuffle the architecture of the commensal microbiome of the vertebrate host, it might have altered the probiotic-pathogen inter-genus and intra-species communications. Such in-depth analyses are needed to avoid counteractive phenomena of probiotics and to optimise their efficacies to magnify human and animal well-being. Moreover, such studies will be valuable to improve the relevant guidelines published by organisations such as FAO, OIE and WHO.
Preparation and characterization of ancient recipe of organic Lime Putty-Evaluation for its suitability in restoration of Padmanabhapuram Palace, India
Authors: Shivakumar M. , Selvaraj Thirumalini , Dhassaih Magesh Peter
Published: June 2021

The study aims at preparation and characterization of six organic lime putty (hydraulic Lime + fermented plant extract) using regionally available plants namelyTerminalia Chebula (kadukkai), Rosa Sinensis(hibiscus), Palm jaggery(refined sugar),Xanthorrhoeaceae(aloe vera), andIndigofera Tinctoria(neelamari) as per the methods given in the ancient palm leaf of Padmanabhapuram Palace, India. Advanced analytical techniques like Gas chromatography-mass spectroscopy (GC–MS), UV-Spectrophotometer and carbon dioxide quantification were used to study the fermented plant extracts and Fourier transform-infrared spectroscopy (FT-IR), X-ray Diffraction (XRD), Field emission-scanning electron microscopy (FESEM) to study hydrated phases and microstructure of organic lime putty. GC–MS recorded the phytochemical compounds like fatty acids, traces of proteins, polysaccharides and carbohydrates. Fermented kadukkai and neelamari extracts reported as fatty acid, palm jaggery as carbohydrate, hibiscus as polysaccharide and aloevera rich in all the biomolecules. The detection limit of Quantification:0.013 and limit of detection:0.067 for polysaccharides, 0.026 and 0.088 for unsaturated fatty acids was reported through a U.V spectrophotometer for all the herbs. Aloevera and neelamari fermented extracts recorded the CO2release around 96,000 and 90,000 ppm on 4th day of fermentation, whereas for other herbs it ranged below the recorded readings. Supply of CO2has initiated the internal carbonation of the lime putty and precipitation of calcite in three different forms aragonite, calcite and vaterite minerals. The addition of organics resulted in high-intensity portlandite peaks and calcium carbonate polymorphs as reported in XRD graphs in agreement with FT-IR analysis. FESEM morphology validated the early formation of carbonate polymorphs, and EDX. has shown that kadukkai lime putty, jaggery lime putty and reference lime putty. mixes have calcium around 35–45%. From the overall results, 3% addition of eco-friendly biopolymers has altered the properties like setting time, water repellency and higher carbonation rate, which is the main reason behind longevity of the structure.
Venom duct origins of prey capture and defensive conotoxins in piscivorous Conus striatus
Authors: Himaya S. W. A. , Jin Ai-Hua , Hamilton Brett , Rai Subash K. , Alewood Paul , Lewis Richard J.
Published: June 2021

The venom duct origins of predatory and defensive venoms has not been studied for hook-and-line fish hunting cone snails despite the pharmacological importance of their venoms. To better understand the biochemistry and evolution of injected predatory and defensive venoms, we compared distal, central and proximal venom duct sections across three specimens of C. striatus (Pionoconus) using proteomic and transcriptomic approaches. A total of 370 conotoxin precursors were identified from the whole venom duct transcriptome. Milked defensive venom was enriched with a potent cocktail of proximally expressed inhibitory α-, ω- and μ-conotoxins compared to milked predatory venom. In contrast, excitatory κA-conotoxins dominated both the predatory and defensive venoms despite their distal expression, suggesting this class of conotoxin can be selectively expressed from the same duct segment in response to either a predatory or defensive stimuli. Given the high abundance of κA-conotoxins in the Pionoconus clade, we hypothesise that the κA-conotoxins have evolved through adaptive evolution following their repurposing from ancestral inhibitory A superfamily conotoxins to facilitate the dietary shift to fish hunting and species radiation in this clade.
Can wood-decaying urban macrofungi be identified by using fuzzy interference system? An example in Central European Ganoderma species
Authors: Michalíková Alžbeta , Beck Terézia , Gáper Ján , Pristaš Peter , Gáperová Svetlana
Published: June 2021

Ganoderma is a cosmopolitan genus of wood-decaying basidiomycetous macrofungi that can rot the roots and/or lower trunk. Among the standing trees, their presence often indicates that a hazard assessment may be necessary. These bracket fungi are commonly known for the crust-like upper surfaces of their basidiocarps and formation of white rot. Six species occur in central European urban habitats. Several of them, such as Ganoderma adspersum, G. applanatum, G. resinaceum and G. pfeifferi, are most hazardous fungi causing extensive horizontal stem decay in urban trees. Therefore, their early identification is crucial for correct management of trees. In this paper, a fast technique is tested for the determination of phytopathologically important urban macrofungi using fuzzy interference system of Sugeno type based on 13 selected traits of 72 basidiocarps of six Ganoderma species and compared to the ITS sequence based determination. Basidiocarps features were processed for the following situations: At first, the FIS of Sugeno 2 type (without basidiospore sizes) was used and 57 Ganoderma basidiocarps (79.17%) were correctly determined. Determination success increased to 96.61% after selecting basidiocarps with critical values (15 basidiocarps). These undeterminable basidiocarps must be analyzed by molecular methods. In a case, that basidiospore sizes of some basidiocarps were known, a combination of Sugeno 1 (31 basidiocarps with known basidiospore size) and Sugeno 2 (41 basidiocarps with unknown basidiospore size) was used. 84.72% of Ganoderma basidiocarps were correctly identified. Determination success increased to 96.83% after selecting basidiocarps with critical values (11 basidiocarps).
Analysing Twitter semantic networks: the case of 2018 Italian elections
Authors: Radicioni Tommaso , Saracco Fabio , Pavan Elena , Squartini Tiziano
Published: June 2021

Social media play a key role in shaping citizens’ political opinion. According to the Eurobarometer, the percentage of EU citizens employing online social networks on a daily basis has increased from 18% in 2010 to 48% in 2019. The entwinement between social media and the unfolding of political dynamics has motivated the interest of researchers for the analysis ofusers online behavior—with particular emphasis ongroup polarizationduring debates andecho-chambers formation. In this context,semantic aspectshave remained largely under-explored. In this paper, we aim at filling this gap by adopting a two-steps approach. First, we identify thediscursive communitiesanimating the political debate in the run up of the 2018 Italian Elections as groups of users with a significantly-similar retweeting behavior. Second, we study the mechanisms that shape their internal discussions by monitoring, on a daily basis, the structural evolution of the semantic networks they induce. Above and beyond specifying the semantic peculiarities of the Italian electoral competition, our approach innovates studies of online political discussions in two main ways. On the one hand, it grounds semantic analysis within users’ behaviors by implementing a method, rooted in statistical theory, that guarantees that our inference of socio-semantic structures is not biased by any unsupported assumption about missing information; on the other, it is completely automated as it does not rest upon any manual labelling (either based on the users’ features or on their sharing patterns). These elements make our method applicable to any Twitter discussion regardless of the language or the topic addressed.
In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin
Authors: Piplani Sakshi , Singh Puneet Kumar , Winkler David A. , Petrovsky Nikolai
Published: June 2021

The devastating impact of the COVID-19 pandemic caused by SARS–coronavirus 2 (SARS-CoV-2) has raised important questions about its origins and the mechanism of its transfer to humans. A further question was whether companion or commercial animals could act as SARS-CoV-2 vectors, with early data suggesting susceptibility is species specific. To better understand SARS-CoV-2 species susceptibility, we undertook an in silico structural homology modelling, protein–protein docking, and molecular dynamics simulation study of SARS-CoV-2 spike protein’s ability to bind angiotensin converting enzyme 2 (ACE2) from relevant species. Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested, forming the highest number of hydrogen bonds with hACE2. Interestingly, pangolin ACE2 showed the next highest binding affinity despite having a relatively low sequence homology, whereas the affinity of monkey ACE2 was much lower despite its high sequence similarity to hACE2. These differences highlight the power of a structural versus a sequence-based approach to cross-species analyses. ACE2 species in the upper half of the predicted affinity range (monkey, hamster, dog, ferret, cat) have been shown to be permissive to SARS-CoV-2 infection, supporting a correlation between binding affinity and infection susceptibility. These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission. This study highlights how in silico structural modelling methods can be used to rapidly generate information on novel viruses to help predict their behaviour and aid in countermeasure development.
An information theoretic approach to link prediction in multiplex networks
Authors: Jafari Seyed Hossein , Abdolhosseini-Qomi Amir Mahdi , Asadpour Masoud , Rahgozar Maseud , Yazdani Naser
Published: June 2021

The entities of real-world networks are connected via different types of connections (i.e., layers). The task of link prediction in multiplex networks is about finding missing connections based on both intra-layer and inter-layer correlations. Our observations confirm that in a wide range of real-world multiplex networks, from social to biological and technological, a positive correlation exists between connection probability in one layer and similarity in other layers. Accordingly, a similarity-based automatic general-purpose multiplex link prediction method—SimBins—is devised that quantifies the amount of connection uncertainty based on observed inter-layer correlations in a multiplex network. Moreover, SimBins enhances the prediction quality in the target layer by incorporating the effect of link overlap across layers. Applying SimBins to various datasets from diverse domains, our findings indicate that SimBins outperforms the compared methods (both baseline and state-of-the-art methods) in most instances when predicting links. Furthermore, it is discussed that SimBins imposes minor computational overhead to the base similarity measures making it a potentially fast method, suitable for large-scale multiplex networks.
Differences in in vitro microglial accumulation of the energy metabolism tracers [18F]FDG and [18F]BCPP-EF during LPS- and IL4 stimulation
Authors: Suzuki Chie , Han Sarina , Kesavamoorthy Gandhervin , Kosugi Mutsumi , Araki Kaori , Harada Norihiro , Kanazawa Masakatsu , Tsukada Hideo , Magata Yasuhiro , Ouchi Yasuomi
Published: June 2021

The positron emission tomography probes 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) and 2-tert-butyl-4-chloro-5-{6-[2-(2-[18F]fluoroethoxy)-ethoxy]-pyridin-3-ylmethoxy}-2H-pyridazin-3-one ([18F]BCPP-EF) are designed to evaluate glycolysis and oxidative phosphorylation, respectively, and are both used to estimate neuronal activity. However, previous studies have shown a discrepancy in these probes’ accumulation in the compromised region, possibly due to the presence of activated microglia acting like deleterious or neuroprotective phenotypes. Hence, we evaluated lipopolysaccharide (LPS)- and interleukin 4 (IL4)-stimulated microglial uptake of [14C]2DG and [18F]BCPP-EF to give a new insight into the hypothesis that different uptake of [18F]FDG and [18F]BCPP-EF can be ascribed to the different metabolic pathways activated during microglial activation. LPS or IL4 stimulation increased the proinflammatory or anti-inflammatory marker gene expression in microglial cells. In LPS-stimulated cells, [14C]2DG uptake and glycolysis related gene expression were elevated, and [18F]BCPP-EF uptake was reduced. In IL4-stimulated cells, [18F]BCPP-EF uptake was increased, and [14C]2DG uptake was decreased. The expression of genes involved in glycolysis and mitochondrial complex I subunits was not changed by IL4 stimulation. The uptake of [14C]2DG and [18F]BCPP-EF differs in LPS- and IL4-stimulated polarized microglial cells. The present results suggest that the in vivo accumulation of metabolic tracers [18F]FDG and [18F]BCPP-EF can be influenced by the different aspects of neuroinflammation.