bluuebunny/crossref_metadata_2025_split huggingface dataset:
A versatilein situcofactor enhancing system for meeting cellular demands for engineered metabolic pathways
Authors: Jaroensuk Juthamas , Sutthaphirom Chalermroj , Phonbuppha Jittima , Chinantuya Wachirawit , Kesornpun Chatchai , Akeratchatapan Nattanon , Kittipanukul Narongyot , Phatinuwat Kamonwan , Atichartpongkul Sopapan , Fuangthong Mayuree , Pongtharangkul Thunyarat , Hollmann Frank , Chaiyen Pimchai 
Published: January 2023

AbstractCofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase levels of a pool of sugar-phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN and ATP inEscherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells; demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase, GDH) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increasein vivocofactor generation upon cellular demand for synthetic biology.TeaserUse of sugar and sugar reductase to increase sugar phosphates for enhancingin situsynthesis of cofactors upon cellular demand for synthetic biology.
Establishment and Characterization of Three Novel CAF Cell Lines from HNSCC Patients
Authors: Dwivedi Nehanjali , Bahaar Hafsa , Shashank DN , Cherry Christine Elizabeth , Gangadharan Charitha , Suresh Amritha , Kuriakose Moni A , Pillai Vijay , Das Manjula , Smitha P.K 
Published: January 2023

AbstractDue to the high rates of tobacco chewers, smokers, and alcohol consumers in India, Head and Neck Squamous Cell Carcinoma (HNSCC) is one of the primary causes of mortality. Being profoundly varied in nature, treating patients diagnosed with HNSCC can be difficult. An in vitro cell line model is needed to better comprehend the heterogeneity especially via the interaction with components of the microenvironment like Cancer Associated Fibroblasts (CAFs). The effectiveness of creating cell lines from head and neck cancers is, however, poor. Furthermore, except for the two reported earlier by us, no other CAF cell lines are available to study the cross-talk of the tumor with its microenvironment. In this study, we report three novel CAF lines, spontaneously immortalized from HPV negative male patients with habits of tobacco and diagnosed with squamous cell carcinoma of the upper alveolus, larynx and buccal mucosa as opposed to HPV positive non-habitual female patients with cancer of the tongue as previously reported. The CAFs increased the tumorigenicity of epithelial cells in indirect co-culture experiments. Negative staining with EpCAM, CD31 and CD45, while positive staining with FSP-1 determined their fibroblast specific lineage. The developed CAF cultures are the first of their kind from the mentioned sites, and they will be an invaluable tool for learning how tumor-stroma and tumor interact with one another and discovering newer targets and pathways for treating HNSCC.
Pre-anthesis spike growth dynamics and its association to yield components among elite bread wheat cultivars (Triticum aestivumL. spp.) under Mediterranean climate
Authors: Roychowdhury Rajib , Zilberman Orian , Chandrasekhar Kottakota , Curzon Arie , Nashef Kamal , Abbo Shahal , Slafer Gustavo A. , Bonfil David J. , Ben-David Roi 
Published: January 2023

AbstractWheat (Triticumspp.) grain yield (GY) is highly associated with grain number per unit area (GN m-2). Biomass accumulation and partitioning are essential to understand pre-anthesis spike growth dynamics which determines spike dry matter at anthesis (SDMa) - a GN determinant. Spike growth takes place during the stem elongation period (SE), from terminal spikelet to anthesis, following leaf and spikelet initiation (LS) from sowing to terminal spikelet. In this study, bread wheat cultivars were examined under Mediterranean semi-arid conditions to determine (i) the varietal differences in pre-anthesis phase duration, (ii) whether this variability influences biomass partitioning and spike-related traits, and (iii) to what extent, the genotypic variations in pre-anthesis phase duration and spike growth are associated with yield components. A panel of Israeli commercial bread wheat cultivars were grown in the field during 2016-17 (three environments) and 2017-18 (two environments) and characterized for pre-anthesis phases, floral conditions and spike fertilityviahistological measurements, spike traits and dry matter accumulation and partitioning at anthesis and maturity and for yield components. Significant variability in the timing of pre-anthesis phases was detected within the tested panel. LS duration, and occasionally SE, favourably related with a better dry matter of fertile florets spike-1(at anthesis) and SDM (at both anthesis and maturity). Two cultivar pairs ‘Zahir-Yuval’ and ‘Negev-Gedera’, which flowered concurrently, revealed significant differences in the durations of LS and SE phases across the environments. Longer LS (e.g., in cultivars Zahir and Negev) exhibited increased spikelets number spike-1, whereas longer SE (e.g., in Yuval and Gedera) enhanced spike fertility through improving the survival rate of floret primordia (FSR%) of central spikelets. However, there was a trade-off for FSR at the proximal and distal spike portions, resulting reduction of final GN (or GY) in cultivars with longer SE. It is concluded that, in this panel, the duration of both LS and SE contribute to spike fertility. However, under short wheat growing cycle, LS duration seemed a stronger driver than SE for GN and yield enhancement. These highlights the novel importance of pre-anthesis phases, especially the role of LS in wheat yield increment during the short growing cycle. The varietal combination with variable LS and SE duration could be implemented in the breeding pipeline and used as pre-breeding materials for GN improvement. Furthermore, the findings will improve pre-anthesis traits adoption in Mediterranean bread wheat future breeding programs.
ColMA/PEGDA Bioink for Digital Light Processing 3D Printing in Biomedical Engineering
Authors: Chen Jishizhan 
Published: January 2023

AbstractIntroductionDigital light processing (DLP) represents a rapid approach to constructing 3D structures with superior resolution. However, it imposes demanding requirements on the properties of bioink. Gelatine methacryloyl has long been the major option but results in limited mechanical properties. The development of collagen-based bioink provides a wider stiffness adjustment range, native bioactivities, and versatility in biomedical engineering applications.MethodCollagen solution was obtained via enzymolysis and ultrafiltration and then subjected to methacrylation. The photocrosslinkable bioink comprises collagen methacryloyl (ColMA), poly(ethylene glycol) diacrylate (PEGDA), acetic acid, yellow food dye, and photoinitiator LAP. The 3D structures were fabricated utilising a commercial DLP printer with 405 nm visible light.ResultsPurified type I collagen can be rapidly obtained via the developed process, and methacrylation is optimised for collagen with much less addition of methacrylic anhydride (MAA) and a high degree of substitution. The ColMA/PEGDA bioink is translucent and low viscosity and is suitable for DLP 3D printing. The printed scaffolds reached a compressive modulus over 100 kPa with 0.6 wt% collagen. Sharp-edged and fine structures (∼500 μm) were obtained by printing. The hydrogels show tunable mechanical properties by adjusting the concentration of the ColMA component. A series of models were fabricated to test the printability, including ear, cube with channels, and scaffolds, which display porous structures with pore sizes of 50 – 150 μm.ConclusionsAn optimised collagen-based bioink fabrication protocol was proposed for the DLP technique, covering steps from collagen extraction to ColMA/PEGDA bioink formulation and printing. Bioink with tunable mechanical properties is suitable for DLP printing. High-resolution structures can potentially be utilised for various biomedical engineering applications.
KARS mediates intra-translational deposition ofN6-acetyl-L-lysine in nascent proteins to contribute the acetylome in cells
Authors: Guo Dingyuan , Zhang Xiaoyan , He Jie , Yu Weixin , Zhou Runxin , Tong Fuqiang , Yin Sibi , Wang Yu , Yang Yuwen , Xu Xin , Wang Long , Fan Mingzhu , Feng Shan , Hong Changbao , Huang Chuixiu , Liu Ke , Ouyang Zhuqing , Wang Yugang 
Published: January 2023

AbstractN6-acetyl-L-lysine residue is abundant in dietary protein but less is known about its potential influences on the diet-consumers. We herein report that KARS mediates intra- translational deposition of diet-derivedN6-acetyl-L-lysine in nascent proteins to contribute the acetylome in cells. Acetylated dietary protein is a direct source ofN6-acetyl-L-lysine that can widely and substantially contribute the acetylome in multiple organs of mice. By analyzing the co-crystal structure of Lysyl-tRNA synthetase (KARS) in complex withN6- acetyl-L-lysyl-AMP and pyrophosphate, together within vitrobiochemical assays, we learned that KARS can utilizeN6-acetyl-L-lysine to produceN6-acetyl-L-lysyl-AMP and transfers theN6-acetyl-L-lysyl-moiety to lysine cognate tRNA to generateN6-acetyl-L- lysyl-tRNA, which introducesN6-acetyl-L-lysine into growing nascent polypeptide and intra-translationally results in protein acetylation. This undocumented protein modification mechanism is inherently different from post-translational modification (PTM) and termed as intra-translational modification (ITM). ITM can functionally mimic PTM mechanisms to deposit acetylation in histones to decondense chromatin. It can also modify PTM- inaccessible regions that are buried inside and functionally important to proteins. ITM is expected to extend the repertoire of acetylome and improve our understandings in protein modification modes in cells.
How coupled slow oscillations, spindles and ripples control neuronal processing and communication during human sleep
Authors: Staresina Bernhard P. , Niediek Johannes , Borger Valeri , Surges Rainer , Mormann Florian 
Published: January 2023

SummaryLearning and plasticity rely on fine-tuned regulation of neuronal circuits during offline periods. An unresolved puzzle is how the sleeping brain - in the absence of external stimulation or conscious effort – controls neuronal firing rates (FRs) and communication within and across circuits, supporting synaptic and systems consolidation. Using intracranial Electroencephalography (iEEG) combined with multiunit activity (MUA) recordings from the human hippocampus and surrounding medial temporal lobe (MTL) areas, we here show that governed by slow oscillation (SO) up-states, sleep spindles set a timeframe for ripples to occur. This sequential coupling leads to a stepwise increase in (i) neuronal FRs, (ii) short-latency cross-correlations among local neuronal assemblies and (iii) cross-regional MTL interactions. Triggered by SOs and spindles, ripples thus establish optimal conditions for spike-timing dependent plasticity and systems consolidation. These results unveil how the coordinated coupling of specific sleep rhythms orchestrates neuronal processing and communication during human sleep.
Artificial intelligence supports automated characterization of differentiated human pluripotent stem cells
Authors: Marzec-Schmidt Katarzyna , Ghosheh Nidal , Stahlschmidt Sören Richard , Küppers-Munther Barbara , Synnergren Jane , Ulfenborg Benjamin 
Published: January 2023

SummaryRevolutionary advances in AI and deep learning in recent years have resulted in an upsurge of papers exploring applications within the biomedical field. Within stem cell research, promising results have been reported from analyses of microscopy images to e.g., distinguish between pluripotent stem cells and differentiated cell types derived from stem cells. In this work, we investigated the possibility of using a deep learning model to predict the differentiation stage of pluripotent stem cells undergoing differentiation towards hepatocytes, based on morphological features of cell cultures. We were able to achieve close to perfect classification of images from early and late time points during differentiation, and this aligned very well with the experimental validation of cell identity and function. Our results suggest that deep learning models can distinguish between different cell morphologies, and provide alternative means of semi-automated functional characterization of stem cell cultures.
Flower patterns improve foraging efficiency in bumblebees by guiding approach flight and landing
Authors: Richter Robin , Dietz Alexander , Foster James , Spaethe Johannes , Stöckl Anna 
Published: January 2023

Abstract

Colourful patterns on flowers are thought to benefit both pollinators and the plants they visit, by increasing the plants' pollination success via an increased foraging efficiency of the pollinators. This increased efficiency is assumed to result from a guidance effect of the flower patterns, correspondingly termed ‘nectar guides’, which indicate the position of the nectary to visiting pollinators, thus reducing their flower handling time.

Although it is well established that flower patterns play an important role in flower choice, the mechanisms by which they improve the foraging efficiency of flower‐visiting insects remain poorly understood.

In this study, we quantified the contributions of patterns to all phases of flower interaction in the buff‐tailed bumblebee Bombus terrestris. We analysed the bees' flight paths, as well as landing positions and walking tracks on artificial flowers with different pattern types.

We reveal that flower patterns reduced the overall flower handling time of the bees by up to 30%, by guiding their approach flight, landing positions and departure decisions. Surprisingly, we observed no improvement in nectary discovery time after the bees landed on the flower.

Since we tested experienced foragers, which represent the majority of insect pollinators active in nature, the newly described nectary‐independent guidance effects of flower patterns are of high ecological relevance.

Read the free Plain Language Summary for this article on the Journal blog.
Designing Deliberation for Decentralized Decisions
Authors: Patty John W. 
Published: January 2023

AbstractI describe and analyze a model of strategic communication and deliberation in decentralized decision‐making settings. I show that, in a cheap‐talk environment, inclusion and exclusion of agents can affect the credibility of messaging between agents and, accordingly, the quality of policy decisions and overall social welfare. Somewhat surprisingly, the inclusion of agents can aid information aggregation and social welfare even when the added agents do not themselves communicate truthfully. Analogously, the results suggest an informational, social welfare–based rationale for excluding agents not only from observing policy‐relevant deliberation but also from observing the product of the communication precisely because the excluded agents possess decision‐making authority.
Veto Institutions, Hostage‐Taking, and Tacit Cooperation
Authors: Fox Justin , Polborn Mattias 
Published: January 2023

AbstractWe analyze the effects of veto institutions in a dynamic model where control of the legislative and executive branches fluctuates between two parties. In our setting, there are universal projects (benefiting both parties) and partisan projects (benefiting one party at the expense of the other). When government is divided, the legislature can leverage the universal project to achieve a lopsided and dynamically inefficient distribution of partisan projects under the absolute veto. While the line‐item veto eliminates this type of hostage‐taking, it also prevents beneficial logrolls. A novel institution, the alternating line‐item veto, can both eliminate hostage‐taking and preserve beneficial interparty logrolls. No veto institution prevents dynamically inefficient, lopsided outcomes under unified government; this can only be done through norms, and we show that a no‐veto regime, or a regime with a line‐item veto, best facilitates such a cooperative norm.
Aquaporins in the male reproductive system: A chance for paternity or a road to nowhere?
Authors: Michałek Katarzyna , Oberska Patrycja 
Published: January 2023

AbstractAquaporins—small, “unusual” proteins, whose discovery revolutionized the view of membrane transport of water and other small molecules, are essential for all living organisms. Aquaporins located in the male reproductive system seem to play a key role in the proper course of many processes occurring within it, thus maintaining a high reproductive potential.
Exploring the Political Potential of the Local State: Building a Dialogue with Sheffield in the 1980s
Authors: Beveridge Ross , Cochrane Allan 
Published: January 2023

AbstractThis article explores the political potential of the local state through an engagement with the case of Sheffield City Council in the 1980s. The new municipalism movement has generated renewed interest in the “local” and “urban” as transformative projects. The local state holds a pivotal if problematic role in these debates, often seen as the decisive force facilitating or impeding transformation. In building a dialogue with 1980s Sheffield, we provide a less certain account of the local state's potential. Sheffield occupies an ambiguous position within and beyond traditional municipal labourism and therefore provides a potent example to explore tensions within municipalism between state and autonomist visions of politics. In Sheffield, radical intent turned into a more cautious governmental programme in the city, notwithstanding glimpses of political alternatives. The experience of those years provides insights on the contingencies of bringing movements and state politics together in what was then called “local socialism”.
Exotic species explain plant functional trait differences between seed mixes, restored and reference prairies
Authors: Kaul Andrew , Wilsey Brian J. 
Published: January 2023

AbstractQuestionsAre community‐weighted plant functional traits related to the ‘fast–slow’ growth rate continuum different in seed mixes, restored and reference prairies? If so, then what are the traits that explain differences? Remnant prairies, which serve as reference sites for restorations, often have higher plant species diversity and a lower abundance of exotic (non‐native) species than their restoration counterparts. They may differ in their community‐weighted functional traits as well, although this is poorly studied.LocationTallgrass prairies and abandoned fields in Iowa, United States, North America.MethodsWe compared functional traits between remnant prairies, restoration seed mixes, and established restorations to determine if community‐weighted trait values (∑pi × traits) are comparable. Relative abundance was determined by previous sampling of 93 restorations, 48 seed mixes and five remnant sites. Functional traits, including leaf specific leaf area (SLA) and leaf dry matter content (LDMC), and plant height, were measured for 145 native and 39 non‐native plant species, 663 plants, and 1326 leaves.ResultsSeed mixes had greater community‐weighted LDMC and lower SLA than remnants, perhaps because of human selection for high grass abundance in mixes. Established restorations had lower community‐weighted LDMC and higher SLA than remnants and seed mixes, and restorations had a large exotic species component. The proportional abundance of exotics in restorations explained trait differences between remnants and restorations. After taking into account functional groupings, perennial exotic species, on average, had higher SLA and lower LDMC than perennial native species. Remnants and established restorations had similar plant heights, and height was not significantly different between native and exotic species.ConclusionsOur results indicate that seed mixes differ from remnants in a manner that was the opposite of the difference between seed mixes and established restorations. Although seed mixes favored species with slower growth rate trait compositions, the species that established in restored prairies tended to have traits associated with faster growth rates. We recommend developing prairie restoration seed mixes with a greater proportion of forbs, especially those with lower LDMC and higher SLA.
Extracting Low‐Dimensional Psychological Representations from Convolutional Neural Networks
Authors: Jha Aditi , Peterson Joshua C. , Griffiths Thomas L. 
Published: January 2023

AbstractConvolutional neural networks (CNNs) are increasingly widely used in psychology and neuroscience to predict how human minds and brains respond to visual images. Typically, CNNs represent these images using thousands of features that are learned through extensive training on image datasets. This raises a question: How many of these features are really needed to model human behavior? Here, we attempt to estimate the number of dimensions in CNN representations that are required to capture human psychological representations in two ways: (1) directly, using human similarity judgments and (2) indirectly, in the context of categorization. In both cases, we find that low‐dimensional projections of CNN representations are sufficient to predict human behavior. We show that these low‐dimensional representations can be easily interpreted, providing further insight into how people represent visual information. A series of control studies indicate that these findings are not due to the size of the dataset we used and may be due to a high level of redundancy in the features appearing in CNN representations.
What about the race between education and technology in the Global South? Comparing skill premiums in colonial Africa and Asia
Authors: Frankema Ewout , van Waijenburg Marlous 
Published: January 2023

AbstractHistorical research on the race between education and technology has focused on the West but barely touched upon ‘the rest’. A new occupational wage database for 50 African and Asian economies allows us to compare long‐run patterns in skill premiums across the colonial and post‐colonial eras (c. 1870–2010). Our data reveal three major patterns. First, skilled labour was considerably more expensive in colonial Africa and Asia than in pre‐industrial Europe. Second, skill premiums were distinctly higher in Africa than in Asia. Third, in both regions, skill premiums fell dramatically over the course of the twentieth century, ultimately converging to levels long observed in the West. Our paper takes a first step to explain both the origins of the Africa–Asia gap and the drivers of global skill premium convergence, paying special attention to the colonial context that shaped demand, supply, and labour market institutions.