bluuebunny/crossref_metadata_2025 huggingface dataset:
Angiogenin mediates paternal inflammation-induced metabolic disorders in offspring through sperm tsRNAs
Authors: Zhang Yanwen , Ren Li , Sun Xiaoxiao , Zhang Zhilong , Liu Jie , Xin Yining , Yu Jianmin , Jia Yimin , Sheng Jinghao , Hu Guo-fu , Zhao Ruqian , He Bin
Published: November 2021

Paternal environmental inputs can influence various phenotypes in offspring, presenting tremendous implications for basic biology and public health and policy. However, which signals function as a nexus to transmit paternal environmental inputs to offspring remains unclear. Here we show that offspring of fathers with inflammation exhibit metabolic disorders including glucose intolerance and obesity. Deletion of a mouse tRNA RNase, Angiogenin (Ang), abolished paternal inflammation-induced metabolic disorders in offspring. Additionally,Angdeletion prevented the inflammation-induced alteration of 5′-tRNA-derived small RNAs (5′-tsRNAs) expression profile in sperm, which might be essential in composing a sperm RNA ‘coding signature’ that is needed for paternal epigenetic memory. Microinjection of sperm 30–40 nt RNA fractions (predominantly 5′-tsRNAs) from inflammatoryAng+/+males but notAng–/–males resulted in metabolic disorders in the resultant offspring. Moreover, zygotic injection with synthetic 5′-tsRNAs which increased in inflammatory mouse sperm and decreased byAngdeletion partially resembled paternal inflammation-induced metabolic disorders in offspring. Together, our findings demonstrate that Ang-mediated biogenesis of 5′-tsRNAs in sperm contributes to paternal inflammation-induced metabolic disorders in offspring.
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
Authors: Koehler Leman Julia , Lyskov Sergey , Lewis Steven M. , Adolf-Bryfogle Jared , Alford Rebecca F. , Barlow Kyle , Ben-Aharon Ziv , Farrell Daniel , Fell Jason , Hansen William A. , Harmalkar Ameya , Jeliazkov Jeliazko , Kuenze Georg , Krys Justyna D. , Ljubetič Ajasja , Loshbaugh Amanda L. , Maguire Jack , Moretti Rocco , Mulligan Vikram Khipple , Nance Morgan L. , Nguyen Phuong T. , Ó Conchúir Shane , Roy Burman Shourya S. , Samanta Rituparna , Smith Shannon T. , Teets Frank , Tiemann Johanna K. S. , Watkins Andrew , Woods Hope , Yachnin Brahm J. , Bahl Christopher D. , Bailey-Kellogg Chris , Baker David , Das Rhiju , DiMaio Frank , Khare Sagar D. , Kortemme Tanja , Labonte Jason W. , Lindorff-Larsen Kresten , Meiler Jens , Schief William , Schueler-Furman Ora , Siegel Justin B. , Stein Amelie , Yarov-Yarovoy Vladimir , Kuhlman Brian , Leaver-Fay Andrew , Gront Dominik , Gray Jeffrey J. , Bonneau Richard
Published: November 2021

Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how scientific software applications can be created in a reproducible manner when simple design goals for reproducibility are met. We describe the implementation of a test server framework and 40 scientific benchmarks, covering numerous applications in Rosetta bio-macromolecular modeling. High performance computing cluster integration allows these benchmarks to run continuously and automatically. Detailed protocol captures are useful for developers and users of Rosetta and other macromolecular modeling tools. The framework and design concepts presented here are valuable for developers and users of any type of scientific software and for the scientific community to create reproducible methods. Specific examples highlight the utility of this framework, and the comprehensive documentation illustrates the ease of adding new tests in a matter of hours.
Location-specific co-benefits of carbon emissions reduction from coal-fired power plants in China
Authors: Wang Pu , Lin Cheng-Kuan , Wang Yi , Liu Dachuan , Song Dunjiang , Wu Tong
Published: November 2021

Climate policies that achieve air quality co-benefits can better align developing countries’ national interests with global climate mitigation. Since the effects of air pollutants are highly dependent on source locations, spatially nuanced policies are crucial to maximizing the achievement of co-benefits. Using the coal power industry as a case study, this study presents an interdisciplinary approach to assessing facility level co-benefits at every specific source location in China. We find that co-benefits range from US$51-$278 per ton CO2 reduction nationwide and are highly heterogeneous spatially, with “hotspot” regions that should be the priority of emissions reduction policies, and that provinces should use different techno-economic strategies to reduce emissions. The location-specific co-benefit value plus a carbon price serves as a unified environmental indicator that enables policy makers to more accurately understand the social costs of electricity generation from coal burning and provides a scientific framework for geographically nuanced policymaking.
High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control
Authors: Dreyfuss Jonathan M. , Yuchi Yixing , Dong Xuehong , Efthymiou Vissarion , Pan Hui , Simonson Donald C. , Vernon Ashley , Halperin Florencia , Aryal Pratik , Konkar Anish , Sebastian Yinong , Higgs Brandon W. , Grimsby Joseph , Rondinone Cristina M. , Kasif Simon , Kahn Barbara B. , Foster Kathleen , Seeley Randy , Goldfine Allison , Djordjilović Vera , Patti Mary Elizabeth
Published: November 2021

To improve the power of mediation in high-throughput studies, here we introduce High-throughput mediation analysis (Hitman), which accounts for direction of mediation and applies empirical Bayesian linear modeling. We apply Hitman in a retrospective, exploratory analysis of the SLIMM-T2D clinical trial in which participants with type 2 diabetes were randomized to Roux-en-Y gastric bypass (RYGB) or nonsurgical diabetes/weight management, and fasting plasma proteome and metabolome were assayed up to 3 years. RYGB caused greater improvement in HbA1c, which was mediated by growth hormone receptor (GHR). GHR’s mediation is more significant than clinical mediators, including BMI. GHR decreases at 3 months postoperatively alongside increased insulin-like growth factor binding proteins IGFBP1/BP2; plasma GH increased at 1 year. Experimental validation indicates (1) hepatic GHR expression decreases in post-bariatric rats; (2) GHR knockdown in primary hepatocytes decreases gluconeogenic gene expression and glucose production. Thus, RYGB may induce resistance to diabetogenic effects of GH signaling.

Trial Registration: Clinicaltrials.gov NCT01073020.
Growth of lithium-indium dendrites in all-solid-state lithium-based batteries with sulfide electrolytes
Authors: Luo Shuting , Wang Zhenyu , Li Xuelei , Liu Xinyu , Wang Haidong , Ma Weigang , Zhang Lianqi , Zhu Lingyun , Zhang Xing
Published: November 2021

All-solid-state lithium-based batteries with inorganic solid electrolytes are considered a viable option for electrochemical energy storage applications. However, the application of lithium metal is hindered by issues associated with the growth of mossy and dendritic Li morphologies upon prolonged cell cycling and undesired reactions at the electrode/solid electrolyte interface. In this context, alloy materials such as lithium-indium (Li-In) alloys are widely used at the laboratory scale because of their (electro)chemical stability, although no in-depth investigations on their morphological stability have been reported yet. In this work, we report the growth of Li-In dendritic structures when the alloy material is used in combination with a Li6PS5Cl solid electrolyte and Li(Ni0.6Co0.2Mn0.2)O2 positive electrode active material and cycled at high currents (e.g., 3.8 mA cm−2) and high cathode loading (e.g., 4 mAh cm−2). Via ex situ measurements and simulations, we demonstrate that the irregular growth of Li-In dendrites leads to cell short circuits after room-temperature long-term cycling. Furthermore, the difference between Li and Li-In dendrites is investigated and discussed to demonstrate the distinct type of dendrite morphology.
Heterochromatin is a quantitative trait associated with spontaneous epiallele formation
Authors: Zhang Yinwen , Jang Hosung , Xiao Rui , Kakoulidou Ioanna , Piecyk Robert S. , Johannes Frank , Schmitz Robert J.
Published: November 2021

Epialleles are meiotically heritable variations in expression states that are independent from changes in DNA sequence. Although they are common in plant genomes, their molecular origins are unknown. Here we show, using mutant and experimental populations, that epialleles in Arabidopsis thaliana that result from ectopic hypermethylation are due to feedback regulation of pathways that primarily function to maintain DNA methylation at heterochromatin. Perturbations to maintenance of heterochromatin methylation leads to feedback regulation of DNA methylation in genes. Using single base resolution methylomes from epigenetic recombinant inbred lines (epiRIL), we show that epiallelic variation is abundant in euchromatin, yet, associates with QTL primarily in heterochromatin regions. Mapping three-dimensional chromatin contacts shows that genes that are hotspots for ectopic hypermethylation have increases in contact frequencies with regions possessing H3K9me2. Altogether, these data show that feedback regulation of pathways that have evolved to maintain heterochromatin silencing leads to the origins of spontaneous hypermethylated epialleles.
Mammographic texture features associated with contralateral breast cancer in the WECARE Study
Authors: Watt Gordon P. , Knight Julia A. , Lin Christine , Lynch Charles F. , Malone Kathleen E. , John Esther M. , Bernstein Leslie , Brooks Jennifer D. , Reiner Anne S. , Liang Xiaolin , Woods Meghan , Nguyen Tuong L. , Hopper John L. , Pike Malcolm C. , Bernstein Jonine L.
Published: November 2021

To evaluate whether mammographic texture features were associated with second primary contralateral breast cancer (CBC) risk, we created a “texture risk score” using pre-treatment mammograms in a case–control study of 212 women with CBC and 223 controls with unilateral breast cancer. The texture risk score was associated with CBC (odds per adjusted standard deviation = 1.25, 95% CI 1.01–1.56) after adjustment for mammographic percent density and confounders. These results support the potential of texture features for CBC risk assessment of breast cancer survivors.
Trajectories of performance change indicate multiple dissociable links between working memory and fluid intelligence
Authors: Cochrane Aaron , Green C. Shawn
Published: November 2021

Many areas of psychology assume that performance on tasks of interest is stable through time. Here, using time-sensitive modeling of working memory task performance, we show not only was this assumption incorrect, but that certain components of the performance trajectory (e.g., final task performance; rate of change) were independently predictive of fluid intelligence. This fact has clear implications for theoretical frameworks linking working memory and fluid intelligence, and beyond.
OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies
Authors: Moore Josh , Allan Chris , Besson Sébastien , Burel Jean-Marie , Diel Erin , Gault David , Kozlowski Kevin , Lindner Dominik , Linkert Melissa , Manz Trevor , Moore Will , Pape Constantin , Tischer Christian , Swedlow Jason R.
Published: November 2021

The rapid pace of innovation in biological imaging and the diversity of its applications have prevented the establishment of a community-agreed standardized data format. We propose that complementing established open formats such as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of use cases in bioimaging. Critically, a common metadata format used in all these vessels can deliver truly findable, accessible, interoperable and reusable bioimaging data.
Response-locked classification image analysis of perceptual decision making in contrast detection
Authors: Maruyama Hironori , Ueno Natsuki , Motoyoshi Isamu
Published: November 2021

In many situations, humans make decisions based on serially sampled information through the observation of visual stimuli. To quantify the critical information used by the observer in such dynamic decision making, we here applied a classification image (CI) analysis locked to the observer's reaction time (RT) in a simple detection task for a luminance target that gradually appeared in dynamic noise. We found that the response-locked CI shows a spatiotemporally biphasic weighting profile that peaked about 300 ms before the response, but this profile substantially varied depending on RT; positive weights dominated at short RTs and negative weights at long RTs. We show that these diverse results are explained by a simple perceptual decision mechanism that accumulates the output of the perceptual process as modelled by a spatiotemporal contrast detector. We discuss possible applications and the limitations of the response-locked CI analysis.
Selective activation of central thalamic fiber pathway facilitates behavioral performance in healthy non-human primates
Authors: Janson A. P. , Baker J. L. , Sani I. , Purpura K. P. , Schiff N. D. , Butson C. R.
Published: November 2021

Central thalamic deep brain stimulation (CT-DBS) is an investigational therapy to treat enduring cognitive dysfunctions in structurally brain injured (SBI) patients. However, the mechanisms of CT-DBS that promote restoration of cognitive functions are unknown, and the heterogeneous etiology and recovery profiles of SBI patients contribute to variable outcomes when using conventional DBS strategies,which may result in off-target effects due to activation of multiple pathways. To disambiguate the effects of stimulation of two adjacent thalamic pathways, we modeled and experimentally compared conventional and novel ‘field-shaping’ methods of CT-DBS within the central thalamus of healthy non-human primates (NHP) as they performed visuomotor tasks. We show that selective activation of the medial dorsal thalamic tegmental tract (DTTm), but not of the adjacent centromedian-parafascicularis (CM-Pf) pathway, results in robust behavioral facilitation. Our predictive modeling approach in healthy NHPs directly informs ongoing and future clinical investigations of conventional and novel methods of CT-DBS for treating cognitive dysfunctions in SBI patients, for whom no therapy currently exists.
Multicast tree construction algorithm for dynamic traffic on software defined networks
Authors: Bijur Gururaj , Ramakrishna M. , Kotegar Karunakar A.
Published: November 2021

Dynamic traffic of multicast communication in the Software Defined Network environment focused less though it is more natural and practical. In multicast communication, the traffic is dynamic due to the dynamic group memberships (i.e., participants join and leave the group anytime), which are not explored much in the previous research works. The multicast in dynamic traffic requires a method to handle dynamic group membership and minimum tree alteration for every join and leave of participants from the multicast group. This paper proposes a multicast tree construction algorithm, which considers receiving devices and network capability as base parameters to construct the multicast path. The proposed routing method uses Dijkstra’s Shortest Path algorithm for initial tree formation, identifies a multicast path, and processes the Shortest Path Tree to reduce the overall hop count and path cost. The multicast tree generated by the proposed enables the dynamic join and leaves of participating devices with reduced tree alteration using more common paths to reach the devices. The implementation and results show that the proposed method works efficiently in resource utilization with a reduced hop count and quality for multicast communication in static and dynamic scenarios. Also, the results demonstrate that the proposed method generates a stable common path for multicast communication.
Methylated (−)-epigallocatechin 3-O-gallate potentiates the effect of split vaccine accompanied with upregulation of Toll-like receptor 5
Authors: Kumazoe Motofumi , Takamatsu Kanako , Horie Fuyumi , Yoshitomi Ren , Hamagami Hiroki , Tanaka Hiroshi , Fujimura Yoshinori , Tachibana Hirofumi
Published: November 2021

Split-virus vaccine serves as a major countermeasure against influenza virus, but its effectiveness and protective action are not complete. We previously demonstrated the effect of Benifuuki, a green tea cultivar in Japan, on enhancing the split-virus vaccine–elicited immune response. However, little is known about the detail mechanisms. Here, we show that EGCG3”Me intake significantly potentiated the vaccine-elicited hemagglutination inhibition titer increase. Flow cytometry analysis revealed the increased Toll-like receptor 5 (TLR5) expression after EGCG3”Me treatment in lamina propria dendritic cells (LPDCs) and macrophages, which play crucial roles in the humoral immune system. TLR5 expression correlated with the level of interleukin-6 (IL-6)/C–C chemokine type receptor 5, which are important mediators of the humoral immunity. Taken together, In vivo and ex vivo studies showed that EGCG3”Me potentiated the split-virus vaccine–elicited immune response accompanied with the upregulation of TLR5 in intestine and splenocyte macrophages.
Electrochemical oxidation of ferricyanide
Authors: Cheah Mun Hon , Chernev Petko
Published: November 2021

We report the electrochemical oxidation of ferricyanide, [FeIII(CN)6]3− and characterised the oxidation product by in-situ FTIR and XAS spectroelectrochemistry methods. Oxidation of [FeIII(CN)6]3− is proposed to proceed via a tentative Fe(IV) intermediate that undergoes reduction elimination to give cis-[FeIII(CN)4(CH3CN)2]1− as stable product in acetonitrile. Speciation of the oxidation product by DFT calculations is underpinned by good agreement to experimental data.
Individualized cyclic mechanical loading improves callus properties during the remodelling phase of fracture healing in mice as assessed from time-lapsed in vivo imaging
Authors: Wehrle Esther , Paul Graeme R. , Tourolle né Betts Duncan C. , Kuhn Gisela A. , Müller Ralph
Published: November 2021

Fracture healing is regulated by mechanical loading. Understanding the underlying mechanisms during the different healing phases is required for targeted mechanical intervention therapies. Here, the influence of individualized cyclic mechanical loading on the remodelling phase of fracture healing was assessed in a non-critical-sized mouse femur defect model. After bridging of the defect, a loading group (n = 10) received individualized cyclic mechanical loading (8–16 N, 10 Hz, 5 min, 3 × /week) based on computed strain distribution in the mineralized callus using animal-specific real-time micro-finite element analysis with 2D/3D visualizations and strain histograms. Controls (n = 10) received 0 N treatment at the same post-operative time-points. By registration of consecutive scans, structural and dynamic callus morphometric parameters were followed in three callus sub-volumes and the adjacent cortex showing that the remodelling phase of fracture healing is highly responsive to cyclic mechanical loading with changes in dynamic parameters leading to significantly larger formation of mineralized callus and higher degree of mineralization. Loading-mediated maintenance of callus remodelling was associated with distinct effects on Wnt-signalling-associated molecular targets Sclerostin and RANKL in callus sub-regions and the adjacent cortex (n = 1/group). Given these distinct local protein expression patterns induced by cyclic mechanical loading during callus remodelling, the femur defect loading model with individualized load application seems suitable to further understand the local spatio-temporal mechano-molecular regulation of the different fracture healing phases.
Vulnerability of cities to toxic airborne releases is written in their topology
Authors: Fellini Sofia , Salizzoni Pietro , Ridolfi Luca
Published: November 2021

The incidental or malicious release of toxic gases in the atmosphere is one of the most critical scenarios for cities. The impact of these releases varies with the ventilation potential of the urban environment. To disentangle this crucial aspect, vulnerability to airborne releases is here traced back to essential properties of the urban fabric. To this aim, pollutant dispersion is disassembled in its fundamental bricks and the main drivers of the process are captured. The analysis is based on four cities with emblematic architectures: Paris, Firenze, Lyon and New York. Results show that vulnerability is driven by the topology of the city and by its interaction with the approaching wind. In this sense, fragility to toxic releases is written in the layout of the urban fabric and results from its historical evolution. This study paves the way to the assessment of air pollution-related issues from a morphological point of view.
Impact of vaginal douching products on vaginal Lactobacillus, Escherichia coli and epithelial immune responses
Authors: Hesham Helai , Mitchell Alissa J. , Bergerat Agnes , Hung Kristin , Mitchell Caroline M.
Published: November 2021

We compared the effect of commercial vaginal douching products on Lactobacillus crispatus, L. jensenii, L. gasseri, L. iners, E. coli, and immortalized vaginal epithelial cells (VK2). All studied douching products (vinegar, iodine and baking soda based) induced epithelial cell death, and all inhibited growth of E. coli. Co-culture of vaginal epithelial cells with any of the lactobacilli immediately following exposure to douching products resulted in a trend to less human cell death. However, co-culture of epithelial cells with L. iners was associated with higher production of IL6 and IL8, and lower IL1RA regardless of presence or type of douching solution. Co-culture with L. crispatus or L. jensenii decreased IL6 production in the absence of douches, but increased IL6 production after exposure to vinegar. Douching products may be associated with epithelial disruption and inflammation, and may reduce the anti-inflammatory effects of beneficial lactobacilli.
Expression and purification of a native Thy1-single-chain variable fragment for use in molecular imaging
Authors: Jugniot Natacha , Bam Rakesh , Paulmurugan Ramasamy
Published: November 2021

Molecular imaging using singlechain variable fragments (scFv) of antibodies targeting cancer specific antigens have been considered a non-immunogenic approach for early diagnosis in the clinic. Usually, production of proteins is performed within Escherichia coli. Recombinant proteins are either expressed in E. coli cytoplasm as insoluble inclusion bodies, that often need cumbersome denaturation and refolding processes, or secreted toward the periplasm as soluble proteins that highly reduce the overall yield. However, production of active scFvs in their native form, without any heterologous fusion, is required for clinical applications. In this study, we expressed an anti-thymocyte differentiation antigen-scFv (Thy1-scFv) as a fusion protein with a N-terminal sequence including 3 × hexa-histidines, as purification tags, together with a Trx-tag and a S-tag for enhanced-solubility. Our strategy allowed to recover ~ 35% of Thy1-scFv in the soluble cytoplasmic fraction. An enterokinase cleavage site in between Thy1-scFv and the upstream tags was used to regenerate the protein with 97.7 ± 2.3% purity without any tags. Thy1-scFv showed functionality towards its target on flow cytometry assays. Finally, in vivo molecular imaging using Thy1-scFv conjugated to an ultrasound contrast agent (MBThy1-scFv) demonstrated signal enhancement on a transgenic pancreatic ductal adenocarcinoma (PDAC) mouse model (3.1 ± 1.2 a.u.) compared to non-targeted control (0.4 ± 0.4 a.u.) suggesting potential for PDAC early diagnosis. Overall, our strategy facilitates the expression and purification of Thy1-scFv while introducing its ability for diagnostic molecular imaging of pancreatic cancer. The presented methodology could be expanded to other important eukaryotic proteins for various applications, including but not limited to molecular imaging.
Regulation of PP2A, PP4, and PP6 holoenzyme assembly by carboxyl-terminal methylation
Authors: Lyons Scott P. , Greiner Elora C. , Cressey Lauren E. , Adamo Mark E. , Kettenbach Arminja N.
Published: November 2021

The family of Phosphoprotein Phosphatases (PPPs) is responsible for most cellular serine and threonine dephosphorylation. PPPs achieve substrate specificity and selectivity by forming multimeric holoenzymes. PPP holoenzyme assembly is tightly controlled, and changes in the cellular repertoire of PPPs are linked to human disease, including cancer and neurodegeneration. For PP2A, PP4, and PP6, holoenzyme formation is in part regulated by carboxyl (C)-terminal methyl-esterification (often referred to as “methylation”). Here, we use mass spectrometry-based proteomics, methylation-ablating mutations, and genome editing to elucidate the role of C-terminal methylation on PP2A, PP4, and PP6 holoenzyme assembly. We find that the catalytic subunits of PP2A, PP4, and PP6 are frequently methylated in cancer cells and that deletion of the C-terminal leucine faithfully recapitulates loss of methylation. We observe that loss of PP2A methylation consistently reduced B55, B56, and B72 regulatory subunit binding in cancer and non-transformed cell lines. However, Striatin subunit binding is only affected in non-transformed cells. For PP4, we find that PP4R1 and PP4R3β bind in a methylation-dependent manner. Intriguingly, loss of methylation does not affect PP6 holoenzymes. Our analyses demonstrate in an unbiased, comprehensive, and isoform-specific manner the crucial regulatory function of endogenous PPP methylation in transformed and non-transformed cell lines.
Theoretical explanation of rotational flow in the liquid-film motor
Authors: Najafi Ali , Shirsavar Reza
Published: November 2021

A liquid film that is under the action of two electric forces, an external electric field parallel to the film and a lateral voltage difference applied to both edges of the film, exhibits a universal rotational flow. In this article, we revisit this phenomena by considering an idealized so-called liquid-film motor and provide a theoretical description of the underlying physical mechanism that is responsible for the rotation. Based on this theory, the external electric field induces a non-uniform distribution of freely moving charges on the film. Then the internal field that is mainly resulted from the lateral voltage difference, will exert forces on induced charges and subsequently will result the rotational flow. We show, how the fields contribute in developing a universal flow pattern.
Earthquake source characterization by machine learning algorithms applied to acoustic signals
Authors: Gomez Bernabe , Kadri Usama
Published: November 2021

Underwater seismic events generate acoustic radiation (such as acoustic-gravity waves), that carries information about the source and can travel long distances before dissipating. Effective early warning, emergency response, and information dissemination for earthquakes and tsunamis require a rapid characterisation of the fault properties: geometry and dynamics. In this work, we analysed hydrophone recordings of 201 earthquakes, located in the Pacific and the Indian Ocean, by employing acoustic signal processing and classification methods. The analysis allows identifying the type of earthquake (i.e. slip type, magnitude) and provides near real-time estimation of the effective properties of the fault dynamics and geometry. The results were compared against values reported by the Harvard Global Centroid Moment Tensor catalog (gCMT), revealing statistical significance between the extracted acoustic properties used to feed machine learning algorithms and the predicted slip and magnitude values.
Ant nest architecture is shaped by local adaptation and plastic response to temperature
Authors: Sankovitz Madison , Purcell Jessica
Published: November 2021

Social insects are among the most abundant arthropods in terrestrial ecosystems, where they provide ecosystem services. The effect of subterranean activity of ants on soil is well-studied, yet little is known about nest architecture due to the difficulty of observing belowground patterns. Furthermore, many species’ ranges span environmental gradients, and their nest architecture is likely shaped by the climatic and landscape features of their specific habitats. We investigated the effects of two temperature treatments on the shape and size of nests built by Formica podzolica ants collected from high and low elevations in the Colorado Rocky Mountains in a full factorial experiment. Ants nested in experimental chambers with soil surface temperatures matching the local temperatures of sample sites. We observed a plastic response of nest architecture to conditions experienced during excavation; workers experiencing a high temperature excavated deeper nests than those experiencing a cooler temperature. Further, we found evidence of local adaptation to temperature, with a significant interaction effect of natal elevation and temperature treatment on nest size and complexity. Specifically, workers from high elevation sites built larger nests with more tunnels when placed in the cool surface temperature treatment, and workers from low elevation sites exhibited the opposite pattern. Our results suggest that subterranean ant nest architecture is shaped by a combination of plastic and locally adapted building behaviors; we suggest that the flexibility of this ‘extended phenotype’ likely contributes to the widespread success of ants.
Additive and interaction effects of working memory and motor sequence training on brain functional connectivity
Authors: Zuber Priska , Gaetano Laura , Griffa Alessandra , Huerbin Manuel , Pedullà Ludovico , Bonzano Laura , Altermatt Anna , Tsagkas Charidimos , Parmar Katrin , Hagmann Patric , Wuerfel Jens , Kappos Ludwig , Sprenger Till , Sporns Olaf , Magon Stefano
Published: November 2021

Although shared behavioral and neural mechanisms between working memory (WM) and motor sequence learning (MSL) have been suggested, the additive and interactive effects of training have not been studied. This study aimed at investigating changes in brain functional connectivity (FC) induced by sequential (WM + MSL and MSL + WM) and combined (WM × MSL) training programs. 54 healthy subjects (27 women; mean age: 30.2 ± 8.6 years) allocated to three training groups underwent twenty-four 40-min training sessions over 6 weeks and four cognitive assessments including functional MRI. A double-baseline approach was applied to account for practice effects. Test performances were compared using linear mixed-effects models and t-tests. Resting state fMRI data were analysed using FSL. Processing speed, verbal WM and manual dexterity increased following training in all groups. MSL + WM training led to additive effects in processing speed and verbal WM. Increased FC was found after training in a network including the right angular gyrus, left superior temporal sulcus, right superior parietal gyrus, bilateral middle temporal gyri and left precentral gyrus. No difference in FC was found between double baselines. Results indicate distinct patterns of resting state FC modulation related to sequential and combined WM and MSL training suggesting a relevance of the order of training performance. These observations could provide new insight for the planning of effective training/rehabilitation.
The impact of bacterial diversity on resistance to biocides in oilfields
Authors: Pereira Gabriela Feix , Pilz-Junior Harry Luiz , Corção Gertrudes
Published: November 2021

Extreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and acid-producing bacteria (APB) are usually found in these places and can harm important processes due to increases in corrosion rates, biofouling and reservoir biosouring. Biocides such as glutaraldehyde, dibromo-nitrilopropionamide (DBNPA), tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and alkyl dimethyl benzyl ammonium chloride (ADBAC) are commonly used in oil fields to mitigate uncontrolled microbial growth. The aim of this work was to evaluate the differences among microbiome compositions and their resistance to standard biocides in four different Brazilian produced water samples, two from a Southeast Brazil offshore oil field and two from different Northeast Brazil onshore oil fields. Microbiome evaluations were carried out through 16S rRNA amplicon sequencing. To evaluate the biocidal resistance, the Minimum Inhibitory Concentration (MIC) of the standard biocides were analyzed using enriched consortia of SRB and APB from the produced water samples. The data showed important differences in terms of taxonomy but similar functional characterization, indicating the high diversity of the microbiomes. The APB and SRB consortia demonstrated varying resistance levels against the biocides. These results will help to customize biocidal treatments in oil fields.
Association between metabolic syndrome and incidence of ocular motor nerve palsy
Authors: Choi Daye Diana , Han Kyungdo , Oh Sei Yeul , Park Kyung-Ah
Published: November 2021

To assess the association between metabolic syndrome (MetS) and the development of third, fourth, and sixth cranial nerve palsy (CNP). Health checkup data of 4,067,842 individuals aged between 20 and 90 years provided by the National Health Insurance Service (NHIS) of South Korea between January 1, 2009, and December 31, 2009, were analyzed. Participants were followed up to December 31, 2017. Hazard ratio (HR) and 95% confidence interval (CI) of CNP were estimated using Cox proportional hazards regression analysis after adjusting for potential confounders. Model 1 included only incident CNP as a time-varying covariate. Model 2 included model 1 and individual’s age and sex. Model 3 included model 2, smoking status, alcohol consumption, and physical activity of individuals. We identified 5,835 incident CNP cases during the follow-up period (8.22 ± 0.94 years). Individuals with MetS (n = 851,004) showed an increased risk of CNP compared to individuals without MetS (n = 3,216,838) after adjustment (model 3: HR = 1.35, 95% CI 1.273–1.434). CNP incidence was positively correlated with the number of MetS components (log-rank p < 0.0001). The HR of CNP for males with MetS compared to males without MetS was higher than that of females with MetS compared to females without MetS (HR: 1.407, 95% CI 1.31–1.51 in men and HR: 1.259, 95% CI 1.13–1.40 in women, p for interaction = 0.0017). Our population-based large-scale cohort study suggests that MetS and its components might be risk factors for CNP development.
Real-world data analysis of patients with cancer of unknown primary
Authors: Kang Sora , Jeong Jae Ho , Yoon Shinkyo , Yoo Changhoon , Kim Kyu-pyo , Cho Hyungwoo , Ryoo Baek-Yeol , Jung Jinhong , Kim Jeong Eun
Published: November 2021

Cancer of unknown primary (CUP) is a heterogeneous malignancy in which the primary site of the tumor cannot be identified through standard work-up. The survival outcome of CUP is generally poor, and there is no consensus for treatment. Here, we comprehensively analyzed the real-world data of 218 patients with CUP (median age, 62 years [range, 19–91]; male, 62.3%). Next-generation sequencing was conducted in 22 (10%) patients, one of whom showed level 1 genetic alteration. Most (60.3%) patients were treated with empirical cytotoxic chemotherapy, and two patients received targeted therapy based on the NGS results. The median OS was 8.3 months (95% confidence interval [CI] 6.2–11.4), and the median progression-free survival of patients treated with chemotherapy was 4.4 months (95% CI 3.4–5.3). In multivariate Cox regression analysis, Eastern Cooperative Oncology Group performance status (ECOG PS) of 0 or 1 and localized disease were significantly associated with favorable survival outcomes. Collectively, we found that CUP patients had a poor prognosis after standard treatment, and those with localized disease who received local treatment and those with better PS treated with multiple lines of chemotherapy had better survival outcomes. Targeted therapies based on NGS results are expected to improve survival outcomes.
The implications of hyperoxia, type 1 diabetes and sex on cardiovascular physiology in mice
Authors: Bojkovic Katarina , Rodgers Jennifer Leigh , Vichare Riddhi , Nandi Asmita , Mansour Hussein , Saleem Faizan , Abidin Zain Ul , Vanthenapalli Sahit , Cheng Feng , Panguluri Siva Kumar
Published: November 2021

Oxygen supplementation, although a cornerstone of emergency and cardiovascular medicine, often results in hyperoxia, a condition characterized by excessive tissue oxygen which results in adverse cardiac remodeling and subsequent injurious effects to physiological function. Cardiac remodeling is further influenced by various risk factors, including pre-existing conditions and sex. Thus, the purpose of this experiment was to investigate cardiac remodeling in Type I Diabetic (Akita) mice subjected to hyperoxic treatment. Overall, we demonstrated that Akita mice experience distinct challenges from wild type (WT) mice. Specifically, Akita males at both normoxia and hyperoxia showed significant decreases in body and heart weights, prolonged PR, QRS, and QTc intervals, and reduced %EF and %FS at normoxia compared to WT controls. Moreover, Akita males largely resemble female mice (both WT and Akita) with regards to the parameters studied. Finally, statistical analysis revealed hyperoxia to have the greatest influence on cardiac pathophysiology, followed by sex, and finally genotype. Taken together, our data suggest that Type I diabetic patients may have distinct cardiac pathophysiology under hyperoxia compared to uncomplicated patients, with males being at high risk. These findings can be used to enhance provision of care in ICU patients with Type I diabetes as a comorbid condition.
Working hours are closely associated with depressive mood and suicidal ideation in Korean adults: a nationwide cross-sectional study
Authors: Han Sangsoo , Ko Yujin , Moon Ji Eun , Cho Young Soon
Published: November 2021

Long working hours have been presumed to negatively influence health. However, evidence is lacking regarding any associations of working hours with depressive mood or suicidal ideation. We investigated the relationships of working hours with depressive mood and suicidal ideation in a representative sample of the Korean general population. We analyzed data collected by the Korea National Health and Nutrition Examination Surveys VI and VII (2013–2018). Depressive mood and suicidal ideation were identified through self-reporting. We divided participants into four groups according to weekly working hours: 30–40, 41–50, 51–60, and > 60 h/week. Sampling weights were applied to obtain estimates for the general Korean population. We analyzed 14,625 participants, of whom 5383 (36.8%), 4656 (31.8%), 2553 (17.5%), and 2033 (13.9%) worked 30–40, 41–50, 51–60, and > 60 h/week, respectively. In these groups, 3.6%, 4.4%, 5.2%, and 6.3% of the participants reported depressive mood, while 1.8%, 1.9%, 2.2%, and 3.6% reported suicidal ideation. In multiple regression analyses, compared with the 30–40 h/week group, the adjusted odds ratios of the 41–50, 51–60, and > 60 h/week groups for depressive mood were 1.35 (1.08–1.69), 1.5 (1.14–1.97), and 1.6 (1.19–2.14). A similar trend was evident for suicidal ideation (odds ratios 1.16 [0.82–1.63], 1.48 [0.99–2.21], and 2.29 [1.53–3.42]). Long working hours are significantly associated with depressive mood and suicidal ideation.
Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification
Authors: Tsujino Shuhei , Dohra Hideo , Fujiwara Taketomo
Published: November 2021

Alcaligenes faecalis is a heterotrophic nitrifying bacterium that oxidizes ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as the sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using nitrifying and non-nitrifying cells of A. faecalis cultivated in media whose C/N ratios were 5 and 20, respectively, to evaluate the fluctuations of gene expression during induction of heterotrophic nitrification. Expression levels of genes involved in primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed a significant increase in the expression levels of four gene clusters: pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homolog (PODh), suf cluster involved in an iron-sulfur cluster biogenesis, and dnf cluster involved in a novel hydroxylamine oxidation pathway in the nitrifying cells. Our results provide valuable insight into the biochemical mechanism of heterotrophic nitrification.
The dynamics of decision-making and action during active sampling
Authors: Ozbagci Duygu , Moreno-Bote Ruben , Soto-Faraco Salvador
Published: November 2021

Embodied Cognition Theories (ECTs) of decision-making propose that the decision process pervades the execution of choice actions and manifests itself in these actions. Decision-making scenarios where actions not only express the choice but also help sample information can provide a valuable, ecologically relevant model for this framework. We present a study to address this paradigmatic situation in humans. Subjects categorized (2AFC task) a central object image, blurred to different extents, by moving a cursor toward the left or right of the display. Upward cursor movements reduced the image blur and could be used to sample information. Thus, actions for decision and actions for sampling were orthogonal to each other. We analyzed response trajectories to test whether information-sampling movements co-occurred with the ongoing decision process. Trajectories were bimodally distributed, with one kind being direct towards one response option (non-sampling), and the other kind containing an initial upward component before veering off towards an option (sampling). This implies that there was an initial decision at the early stage of a trial, whether to sample information or not. Importantly, in sampling trials trajectories were not purely upward, but rather had a significant horizontal deviation early on. This result suggests that movements to sample information exhibit an online interaction with the decision process, therefore supporting the prediction of the ECTs under ecologically relevant constrains.
Extraction, preparative monomer separation and antibacterial activity of total polyphenols from Perilla frutescens
Authors: Zhao Yana , Li Huizhen , Zhang Zhijun , Ren Zhiqing , Yang Fuhan
Published: November 2021

Polyphenols exhibit potential functional activities, especially rosmarinic acid (RosA) and caffeic acid (CafA).
Chestnut polysaccharides restore impaired spermatogenesis by adjusting gut microbiota and the intestinal structure
Authors: Sun Zhong-Yi , Yu Shuai , Tian Yu , Han Bao-Quan , Zhao Yong , Li Ya-Qi , Wang Yan , Sun Yu-Jiang , Shen Wei
Published: November 2021

CPs treatment altered the gut microbiota composition and restored impaired spermatogenesis via the steroid hormone synthesis process.
Engineering of flat bands and Dirac bands in two-dimensional covalent organic frameworks (COFs): relationships among molecular orbital symmetry, lattice symmetry, and electronic-structure characteristics
Authors: Ni Xiaojuan , Li Hong , Liu Feng , Brédas Jean-Luc
Published: November 2021

An effective framework for the band engineering in 2D covalent organic frameworks is revealed by describing the fundamental relationships among the electronic structures, the lattice symmetries, and the frontier molecular orbitals of building units.
Culturing human iPSC-derived neural progenitor cells on nanowire arrays: mapping the impact of nanowire length and array pitch on proliferation, viability, and membrane deformation
Authors: Harberts Jann , Bours Katja , Siegmund Malte , Hedrich Carina , Glatza Michael , Schöler Hans R. , Haferkamp Undine , Pless Ole , Zierold Robert , Blick Robert H.
Published: November 2021

We tested the growth of human iPSC-derived NPCs on nanowire arrays across a wide range of array characteristics. The proliferation, viability, and interaction with the nanowire arrays were mapped depending on the array pitch and nanowire length.
Improving the stability of plasmonic magnesium nanoparticles in aqueous media
Authors: Asselin Jérémie , Hopper Elizabeth R. , Ringe Emilie
Published: November 2021

Plasmonic Mg nanoparticles can be stabilised up to a few hours in aqueous suspensions by protecting them inside core–shell architectures, which are prepared by condensation of either polydopamine or sol–gel silica.
Reversible assembly of silica nanoparticles at water–hydrocarbon interfaces controlled by SDS surfactant
Authors: Mohammed Sohaib , Kuzmenko Ivan , Gadikota Greeshma
Published: November 2021

Achieving reversible and tunable assembly of silica nanoparticles at liquid–liquid interfaces is vital for a wide range of scientific and technological applications including sustainable subsurface energy applications, catalysis, drug delivery and novel material synthesis.
Synergistic roles of vapor- and liquid-phase epitaxy in the seed-mediated synthesis of substrate-based noble metal nanostructures
Authors: Golze Spencer D. , Hughes Robert A. , Menumerov Eredzhep , Rouvimov Sergei , Neretina Svetlana
Published: November 2021

Seed-mediated liquid-state nanometal syntheses when carried out on substrate-immobilized seeds form connections at both the metal-seed and metal-substrate interfaces. From the standpoint of epitaxy, such growth modes behave unconventionally.
BF3·OEt2 catalyzed chemoselective CC bond cleavage of α,β-enones: an unexpected synthesis of 3-alkylated oxindoles and spiro-indolooxiranes
Authors: Muthusamy Sengodagounder , Prabu Ammasi
Published: November 2021

A BF3·OEt2 catalyzed highly chemoselective formal CC double bond cleavage reaction of α,β-enones with diazoamides for the synthesis of 3-alkylated oxindoles is developed.
Qualitative and quantitative adsorption mechanisms of zinc ions from aqueous solutions onto dead carp derived biochar
Authors: Qiao Hong-tao , Qiao Yong-sheng , Luo Xiao-hang , Zhao Bao-wei , Cai Qiu-ying
Published: November 2021

The adsorption mechanisms of Zn2+ on carp biochars mainly include precipitation with minerals, exchange with cations, and complexation with OFGs. The pyrolysis temperature of carp biochars has a significant effect on the mechanisms of Zn2+ adsorption.
Application of Pauson–Khand reaction in the total synthesis of terpenes
Authors: Heravi Majid M. , Mohammadi Leila
Published: November 2021

The Pauson–Khand reaction (PKR) is a formal [2 + 2 + 1] cycloaddition involving an alkyne, an alkene and carbon monoxide mediated by a hexacarbonyldicobaltalkyne complex to yield cyclopentenones in a single step.
Enhanced antibacterial activity of acid treated MgO nanoparticles on Escherichia coli
Authors: Li Xiaoyi , Hong Xiaoyu , Yang Yan , Zhao Jiao , Diko Catherine Sekyerebea , Zhu Yimin
Published: November 2021

Acid treatment of MgO NPs increased surface oxygen vacancies, leading to more adsorbed oxygen and enhanced antibacterial activity on E. coli.
The site pair matching of a tandem Au/CuO–CuO nanocatalyst for promoting the selective electrolysis of CO2 to C2 products
Authors: Zhou Jun-Hao , Yuan Chen-Yue , Zheng Ya-Li , Yin Hai-Jing , Yuan Kun , Sun Xiao-Chen , Zhang Ya-Wen
Published: November 2021

C2 product FE of 52.8% was achieved in eCO2RR at −1.0 V vs. RHE using a nanoporous hollow Au/CuO–CuO tandem catalyst due to the matching of optimal working potentials and charge-transfer resistances of the CO-production sites and CO-reduction sites.