bluuebunny/crossref_metadata_2025_split huggingface dataset:
FluoMALDI microscopy: matrix co-crystallization simultaneously enhances fluorescence and MALDI imaging
Authors: Yang Ethan , Shen Xinyi Elaine , West-Foyle Hoku , Brown Dalton R. , Johnson Cole C. , Kim Jeong Hee , Roker LaToya Ann , Tressler Caitlin M. , Barman Ishan , Kuo Scot C. , Glunde Kristine 
Published: May 2023

ABSTRACTWe report that co-crystallization of fluorophores with matrix-assisted laser desorption/ionization (MALDI) imaging matrices significantly enhances fluorophore brightness up to 79-fold, enabling the amplification of innate tissue autofluorescence. This discovery facilitates FluoMALDI, the imaging of the same biological sample by both fluorescence microscopy and MALDI imaging. Our approach combines the high spatial resolution and specific labeling capabilities of fluorescence microscopy with the inherently multiplexed, versatile imaging capabilities of MALDI imaging. This new paradigm eliminates the notion that MALDI matrices obscure and obstruct optical microscopy approaches, allowing to image the exact same cells in tissues, free of any physical changes between fluorescence and MALDI imaging, which minimizes data registration processes. Matrix-fluorophore co-crystallization also facilitates applications with insufficient fluorescence brightness. We showcase the capabilities of FluoMALDI imaging with endogenous and exogenous fluorophores and autofluorescence-based FluoMALDI of brain and kidney tissue sections. FluoMALDI will advance structural-functional microscopic imaging in cell biology, biomedicine, and pathology.
CD5L is a canonical component of circulatory IgM
Authors: Oskam Nienke , den Boer Maurits A. , Lukassen Marie V. , Heer Pleuni Ooijevaar-de , Veth Tim S. , Mierlo Gerard van , Lai Szu-Hsueh , Derksen Ninotska I.L. , Yin Victor C. , Streutker Marij , Franc Vojtech , Siborova Marta , Damen Mirjam , Kos Dorien , Barendregt Arjan , Bondt Albert , Goudoever Johannes B. van , Haas Carla J.C. , Aerts Piet C. , Muts Remy M. , Rooijakkers Suzan H.M. , Vidarsson Gestur , Rispens Theo , Heck Albert J.R. 
Published: May 2023

AbstractImmunoglobulin M (IgM) is an evolutionary conserved key component of humoral immunity, and the first antibody isotype to emerge during an immune response. IgM is a large (1 MDa), multimeric protein, for which both hexameric and pentameric structures have been described, the latter additionally containing a joining (J) chain. Using a combination of single-particle mass spectrometry and mass photometry, proteomics and immunochemical assays, we here demonstrate that circulatory (serum) IgM exclusively exists as a complex of J-chain-containing pentamers covalently bound to the small CD5 antigen-like (CD5L, 36 kDa) protein. In sharp contrast, secretory IgM in saliva and milk is principally devoid of CD5L. Unlike IgM itself, CD5L is not produced by B cells, implying that it associates with IgM in the extracellular space. We demonstrate that CD5L integration has functional implications, i.e., it diminishes IgM binding to two of its receptors, the FcαµR and the polymeric Immunoglobulin receptor (pIgR). On the other hand, binding to FcµR as well as complement activation via C1q seem unaffected by CD5L integration. Taken together, we redefine the composition of circulatory IgM as a J-chain containing pentamer, always in complex with CD5L.
Ontogeny and social context regulate the circadian activity patterns of Lake Malawi cichlids
Authors: Lloyd Evan , Rastogi Aakriti , Holtz Niah , Aaronson Ben , Albertson R. Craig , Keene Alex C. 
Published: May 2023

AbstractActivity patterns tend to be highly stereotyped and critical for executing many different behaviors including foraging, social interactions and predator avoidance. Differences in the circadian timing of locomotor activity and rest periods can facilitate habitat partitioning and the exploitation of novel niches. As a consequence, closely related species often display highly divergent activity patterns, raising the possibility that a shift from diurnal to nocturnal behavior, or vice versa, can occur rapidly. In Africa’s Lake Malawi alone, there are over 500 species of cichlids, which inhabit diverse environments and exhibit extensive phenotypic variation. We have previously identified a substantial range in activity patterns across adult Lake Malawi cichlid species, from strongly diurnal to strongly nocturnal. In many species, including fishes, ecological pressures differ dramatically across life-history stages, raising the possibility that activity patterns may change over ontogeny. To determine if rest-activity patterns change across life stages we compared the locomotor patterns of six Lake Malawi cichlid species. While total rest and activity did not change between early juvenile and adult stages, rest-activity patterns did, with juveniles displaying distinct activity rhythms that are more robust than adults. One distinct difference between juveniles and adults is the emergence of complex social behavior. To determine whether social context is required for activity rhythms, we next measured locomotor behavior in group housed adult fish. We found that when normal social interactions were allowed, locomotor activity patterns were restored, supporting the notion that social interactions promote circadian regulation of activity in adult fish. These findings reveal a previously unidentified link between developmental stage and social interactions in the circadian timing of cichlid activity.
Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba
Authors: Scott Trey J. , Larsen Tyler J. , Brock Debra A. , Uhm So Yeon Stacey , Queller David C. , Strassmann Joan E. 
Published: May 2023

ABSTRACTSome endosymbionts living within a host must modulate their hosts’ immune systems in order to infect and persist. We studied the effect of a bacterial endosymbiont on a facultatively multicellular social amoeba host. Aggregates of the amoebaDictyostelium discoideumcontain a subpopulation of sentinel cells that function akin to the immune systems of more conventional multicellular organisms. Sentinel cells sequester and discard toxins fromD. discoideumaggregates and may play a central role in defense against pathogens. We measured the number and functionality of sentinel cells in aggregates ofD. discoideuminfected by bacterial endosymbionts in the genusParaburkholderia.InfectedD. discoideumproduced fewer and less functional sentinel cells, suggesting thatParaburkholderiamay interfere with its host’s immune system. Despite impaired sentinel cells, however, infectedD. discoideumwere less sensitive to ethidium bromide toxicity, suggesting thatParaburkholderiamay also have a protective effect on its host. By contrast,D. discoideuminfected byParaburkholderiadid not show differences in their sensitivity to two non-symbiotic pathogens. Our results expand previous work on yet another aspect of the complicated relationship betweenD. discoideumandParaburkholderia, which has considerable potential as a model for the study of symbiosis.
Expression and purification of the mitochondrial transmembrane protein FAM210A inEscherichia coli
Authors: Hollinger Jared , Wu Jiangbin , Awayda Kamel M. , O’Connell Mitchell R. , Yao Peng 
Published: May 2023

AbstractThe protein Family with sequence similarity 210 member A (FAM210A) is a mitochondrial inner membrane protein that regulates the protein synthesis of mitochondrial DNA encoded genes. However, how it functions in this process is not well understood. Developing and optimizing a protein purification strategy will facilitate biochemical and structural studies of FAM210A. Here, we developed a method to purify human FAM210A with deleted mitochondrial targeting signal sequence using the MBP-His10fusion inEscherichia coli. The recombinant FAM210A protein was inserted into theE. colicell membrane and purified from isolated bacterial cell membranes, followed by a two-step process using Ni-NTA resin-based immobilized-metal affinity chromatography (IMAC) and ion exchange purification. A pulldown assay validated the functionality of purified FAM210A protein interacting with human mitochondrial elongation factor EF-Tu in HEK293T cell lysates. Taken together, this study developed a method for purification of the mitochondrial transmembrane protein FAM210A partially complexed withE.coliderived EF-Tu and provides an opportunity for future potential biochemical and structural studies of recombinant FAM210A protein.
Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
Authors: Shepherdson James L. , Friedman Ryan Z. , Zheng Yiqiao , Sun Chi , Oh Inez Y. , Granas David M. , Cohen Barak A. , Chen Shiming , White Michael A. 
Published: May 2023

AbstractDozens of variants in the photoreceptor-specific transcription factor (TF) CRX are linked with human blinding diseases that vary in their severity and age of onset. It is unclear how different variants in this single TF alter its function in ways that lead to a range of phenotypes. We examined the effects of human disease-causing variants on CRXcis-regulatory function by deploying massively parallel reporter assays (MPRAs) in live mouse retinas carrying knock-ins of two variants, one in the DNA binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation caused by the variants corresponds with their phenotypic severity. The two variants affect similar sets of enhancers, while p.E168d2 has stronger effects on silencers.Cis-regulatory elements (CREs) near cone photoreceptor genes are enriched for silencers that are de-repressed in the presence of p.E168d2. Chromatin environments of CRX-bound loci were partially predictive of episomal MPRA activity, and silencers were notably enriched among distal elements whose accessibility increases later in retinal development. We identified a set of potentially pleiotropic regulatory elements that convert from silencers to enhancers in retinas that lack a functional CRX effector domain. Our findings show that phenotypically distinct variants in different domains of CRX have partially overlapping effects on itscis-regulatory function, leading to misregulation of similar sets of enhancers, while having a qualitatively different impact on silencers.
BOLA3 and NFU1 link mitoribosome iron-sulfur cluster assembly to multiple mitochondrial dysfunctions syndrome
Authors: Zhong Hui , Janer Alexandre , Khalimonchuk Oleh , Antonicka Hana , Shoubridge Eric A , Barrientos Antoni 
Published: May 2023

AbstractThe human mitochondrial ribosome contains three [2Fe-2S] clusters whose assembly pathway, role, and implications for mitochondrial and metabolic diseases are unknown. Here, structure-function correlation studies show that the clusters play a structural role during mitoribosome assembly. To uncover the assembly pathway, we have examined the effect of silencing the expression of Fe-S cluster biosynthetic and delivery factors on mitoribosome stability. We find that the mitoribosome receives its [2Fe-2S] clusters from the GLRX5-BOLA3 node. Additionally, the assembly of the small subunit depends on the mitoribosome biogenesis factor METTL17, recently reported containing a [4Fe-4S] cluster, which we propose is inserted via the ISCA1-NFU1 node. Consistently, fibroblasts from subjects suffering from “multiple mitochondrial dysfunction” syndrome due to mutations in BOLA3 or NFU1 display previously unrecognized attenuation of mitochondrial protein synthesis that contributes to their cellular and pathophysiological phenotypes. Finally, we report that, in addition to their structural role, one of the mitoribosomal [2Fe-2S] clusters and the [4Fe-4S] cluster in mitoribosome assembly factor METTL17 sense changes in the redox environment, thus providing a way to regulate organellar protein synthesis accordingly.
Toward single cell tattoos: Biotransfer printing of lithographic gold nanopatterns on live cells
Authors: Kwok Kam Sang , Zuo Yi , Choi Soo Jin , Pahapale Gayatri J. , Gu Luo , Gracias David H. 
Published: May 2023

AbstractLithographic nanopatterning techniques like photolithography, electron-beam lithography, and nanoimprint lithography (NIL) have revolutionized modern-day electronics and optics. Yet, their application for creating nano-bio interfaces is limited by the cytotoxic and two-dimensional nature of conventional fabrication methods. Here, we present a biocompatible and cost-effective transfer process that leverages (a) NIL to define sub-300 nm gold (Au) nanopattern arrays, (b) amine functionalization of Au to transfer the NIL-arrays from a rigid substrate to a soft transfer layer, (c) alginate hydrogel as a flexible, degradable transfer layer, and (d) gelatin conjugation of the Au NIL-arrays to achieve conformal contact with live cells. We demonstrate biotransfer printing of the Au NIL-arrays on rat brains and live cells with high pattern fidelity and cell viability and observed differences in cell migration on the Au NIL-dot and NIL-wire printed hydrogels. We anticipate that this nanolithography-compatible biotransfer printing method could advance bionics, biosensing, and biohybrid tissue interfaces.TOC Figure
Cross-cultural business-to-business communication – the experiences of Polish companies with the Chinese and Americans
Authors: Bartosik-Purgat Małgorzata , Rakowska Wiktoria 
Published: May 2023

PurposeThe main purpose of the study is to identify the differences and similarities in the communication between B2B participants in cross-cultural environments.Design/methodology/approachThe research methods used in the study are two-fold: the literature analysis is complemented by primary qualitative research conducted in small- and medium-sized enterprises operating in Poland and doing business internationally. The research was focused on two culturally different markets: China and the United States. In the empirical research, the authors used one of the qualitative methods – Individual Depth Interview (IDI).FindingsGeneral findings showed that the strongest influence of culture was identified among older (+50 years old) business partners. The younger ones are eager to adapt and try to understand others' viewpoints. The research results may be used in creating business communication models in the countries researched for companies that plan to enter both American and Chinese markets.Practical implicationsThe results of the study may have useful applied managerial value and be used in cooperation between SMEs' B2B business partners, not only from Poland but also from the whole region of Central and Eastern Europe and the United States and China.Social implicationsThe findings may help to understand and communicate with culturally different social groups such as co-workers, students, teachers, etc.Originality/valueThe research presented in the paper covers the gap in the literature because it relates to some new factors (like cultural heritage, age and type of industry) which determine the effectiveness of personal business communication between partners in the international marketplace.
Measuring the economic performance of transition economies: DEA-bootstrapping approach
Authors: Jakšić Milena , Srejović Ana Krstić , Milanović Marina , Mimović Predrag 
Published: May 2023

PurposeThe paper analyzes the relative technical efficiency of the transition economies of the Western Balkans in the period 2007–2021, in comparison with the former countries with a socialist state system, today members of the European Union (EU), based on selected macroeconomic indicators and panel data.Design/methodology/approachData envelopment analysis (DEA), i.e. its extension, DEA Window analysis, is applied. Total technical efficiency, as a prerequisite of economic efficiency, is decomposed into pure technical efficiency (PTE) and scale efficiency (SE). Bootstrapping method and Mann–Whitney U test were used to check the robustness of the obtained results, i.e. efficiency values.FindingsThe results show that in 2020, all observed countries recorded a significant drop in economic efficiency as a result of a general, disproportionate drop in the value of selected macroeconomic variables, which occurred due to the global economic crisis and the slowdown in economic activity caused by the COVID-19 pandemic. This drop in efficiency was significantly greater in the former socialist states, now members of the European Union, which showed their greater sensitivity to global crises. None of the observed economies in the observed period was relatively efficient, that is, at the level of best practice, which occurred primarily as a consequence of the inefficiency of business conditions expressed in the economies of scale.Research limitations/implicationsThe main limitation of this study stems from the very nature of the concept of DEA efficiency, which is relative in nature. Also, the results and their interpretation are also significantly influenced by the choice of model variables, as shown by Lábaj et al. (2013), as well as a small number of decision-making units (DMUs). The mentioned limitations prevent unambiguous interpretation and generalization of the obtained results.Practical implicationsThe study may be of importance to economic policy makers in macroeconomic decision-making. The application of the DEA concept in measuring the technical efficiency of national economies is a useful tool in the analysis of macroeconomic performance and a benchmarking approach for positioning and achieving competitive advantage on the international market.Originality/valueSince research of this type is very limited, the results of this study make a theoretical and empirical contribution to the literature, creating a basis for future research and reexamination. The application of the DEA concept in measuring the technical efficiency of national economies is a useful tool in the analysis of macroeconomic performance and a benchmarking approach for positioning and achieving competitive advantage in the international market.
Safety in a public library: the perspective of visitors and staff
Authors: Ceccato Vania , Ercin Emrah , Hazanov Julia , Elfström Sara , Sampaio Adriana 
Published: May 2023

PurposeIn this study, the authors report visitors' and personnel's safety experiences and concerns in order to understand the safety conditions of a library.Design/methodology/approachThe analysis is based on answers from a small sample survey of library visitors, interviews with the personnel and incidents recorded in a library in Stockholm the capital of Sweden.FindingsDealing with visitors under influence of drugs/alcohol or feeling intimidated by groups of young individuals are examples of situations in which the staff feel most unsafe. Visitors declare witnessing problems of public disturbance and disorderly conduct, fights and other types of aggression. Although the vast majority of visitors declare feeling safe in the library, their perceptions vary according to the library's environment and their individual characteristics, including their previous victimization.Practical implicationsThe study is novel because it indicates the importance of the environment to ensure the safety conditions of the library for both visitors and staff. Finally, research on safety in libraries is often from North America and Western European contexts, while this study contributes to the international literature by illustrating libraries in a Nordic European context.Social implicationsThe study indicates that more social control, both formal and informal, is at the top of the list of recommendations for visitors. Among personnel, recommendations include the need for cooperation with other local actors to solve problems in surrounding areas as well as better education for librarians in dealing with the current safety challenges of libraries as multifunctional public facilities.Originality/valueCombine visitors' and personnel's safety experiences to better understand the safety conditions of a public library.
Enhanced abundance of generalist and litter saprotrophs explain increased tropical forest soil carbon with long‐term nitrogen deposition
Authors: Lu Zhe , Li Hui , Sayer Emma J. , Liu Zhanfeng , Li Luhua , Chen Yao , Qin Guoming , Li Jintian , Zhou Jinge , Huang Xingyun , Zhang Jingfan , Wu Jingtao , Thapa Poonam , Wang Faming 
Published: May 2023

Abstract

Nitrogen (N) deposition is a pervasive anthropogenic change that can alter the dynamics and storage of carbon (C) in tropical soils by altering the transformation of plant litter C to soil organic C (SOC). The response of fungi may be particularly important for explaining how N deposition affects SOC storage in tropical forests because they are the primary decomposers of plant litter. Fungi can be grouped into different ecological guilds, or functional groups, which often have contrasting responses to the same environmental change. However, little is known if shifts in fungal guilds and their functions explain increased tropical forest SOC storage under N deposition.

We addressed this knowledge gap by assessing the effects of long‐term (6 years) experimental N addition (+N) on fungal guilds, their functions and SOC fractions in a tropical forest.

Total SOC, dissolved organic C (DOC), particulate organic C and fungal necromass C were all higher in +N soils. The fungal community in +N soils was dominated by generalist saprotrophs, and leaf saprotroph abundance increased nearly 93‐fold compared to controls. These changes were accompanied by an increase in lignocellulolytic enzymes, indicating accelerated decomposition of recalcitrant litter C compounds. Chitosanase, which catalyses synthesis of glucosamine, was 1.37× higher in +N soils than controls; correspondingly, fungal necromass C contributed 1.42× more to SOC. Greater abundance of saprotrophic enzymes involved in organic acid synthesis in +N soils was associated with higher concentration of Ca2+ and DOC.

We propose that N deposition increases SOC storage by enhancing saprotroph abundance and activity, whereby increased organic acid production supports fungal growth both directly and indirectly via the release of nutrients and DOC, resulting in greater inputs of necromass to the soil. Our findings highlight the importance of considering shifts in guild‐level fungal abundance and function to investigate changes in SOC dynamics and storage.

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Outcomes of dose‐escalated IMRT and ADT in Octogenarians with prostate cancer
Authors: Le Tue , Armstrong Shreya , Shakespeare Thomas P 
Published: May 2023

AbstractIntroductionWe evaluated long‐term outcomes for octogenarians with localised prostate cancer treated using dose‐escalated image‐guided intensity‐modulated radiation therapy (IMRT) at our institution.MethodsThe charts of octogenarians treated for localised prostate cancer were retrospectively reviewed. Overall survival (OS), prostate cancer‐specific survival (PCaSS), toxicity rates and changes from baseline were collected.ResultsThe median follow‐up was 97 months. Of 107 eligible patients, 27.1% had intermediate‐risk and 72.9% had high‐risk localised prostate cancer. Median dose was 78Gy, and 97.2% received ADT. OS was 91.4% and 67.2% at 5 and 10 years. PCaSS was 98.0% and 88.7% at 5 and 10 years. In all, 39 (36.4%) of patients died, with the cause of death known in 30: in 26.7% of these patients, prostate cancer was the cause of death. Grade ≥ 2 late GI and GU toxicity was 0.9% and 24.3% respectively. In all, 11.2% and 22.4% of patients reported worsening of GI or GU function from baseline, and 13.1% and 21.5% reported improvement in GI and GU function compared to baseline.ConclusionSelected octogenarian patients with localised prostate cancer appear to benefit from radiation therapy and ADT. Despite excellent long‐term PCaSS, 26.7% of patients died of prostate cancer. Rates of GI and GU toxicity were acceptable, and deterioration of urinary and bowel function compared to baseline was just as common as improvement in function from baseline.