bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic signatures associated with the evolutionary loss of egg yolk in parasitoid wasps
Authors: Zhao Xianxin , Liu Yuanyuan , Yang Yi , He Chun , Chan Kevin C. , Lin Haiwei , Fang Qi , Ye Gongyin , Ye Xinhai 
Published: January 2024

AbstractTrait regression and loss have occurred repeatedly in numerous lineages throughout evolutionary history in response to changing environments. In parasitoid wasps, a mega-diverse group of hymenopteran insects, loss or reduction of yolk in the egg has been reported in many species. This phenotypic change likely evolved as a response to the shift from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein genevitellogenin(Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested thatVgloss occurred during genome rearrangement events. Analysis ofVgreceptor gene (VgR) loss, selection, and structural variation in lineages lackingVgdemonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver ofVgloss or the subsequentVgRevolution. A number of parallel and convergent genomic changes were observed betweenVg-loss lineages, including gene family evolution and selection of genes related to transport, development, and metabolism. These changes may have facilitated embryonic development without the yolk in these lineages. Together, these findings reveal the genomic basis underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.
Piggybacking functionalized DNA nanostructures into live cell nuclei
Authors: Roozbahani Golbarg M. , Colosi Patricia , Oravecz Attila , Sorokina Elena M. , Pfeifer Wolfgang , Shokri Siamak , Wei Yin , Didier Pascal , DeLuca Marcello , Arya Gaurav , Tora László , Lakadamyali Melike , Poirier Michael G. , Castro Carlos E. 
Published: January 2024

ABSTRACTDNA origami (DO) are promising tools forin vitroorin vivoapplications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.
Beyond Basic Characterization and Omics: Immunomodulatory Roles of Platelet-Derived Extracellular Vesicles Unveiled by Functional Testing
Authors: Palviainen Mari , Puutio Johanna , Østergaard Rikke Halse , Eble Johannes A. , Maaninka Katariina , Ndika Joseph , Kari Otto K. , Kamali-Moghaddam Masood , Kjaer-Sorensen Kasper , Oxvig Claus , Aransay Ana M , Falcon-Perez Juan , Federico Antonio , Greco Dario , Laitinen Saara , Hayashi Yuya , Siljander Pia RM 
Published: January 2024

AbstractRenowned for their role in hemostasis and thrombosis, platelets are also increasingly recognized for their contribution in innate immunity, immunothrombosis and inflammatory diseases. Platelets express a wide range of receptors, which allows them to reach a variety of activation endpoints and grants them immunomodulatory functions. Activated platelets release extracellular vesicles (PEVs), whose formation and molecular cargo has been shown to depend on receptor-mediated activation and environmental cues.This study compares the immunomodulatory profiles of PEVs generated via activation of platelets by different receptors, glycoprotein VI, C-type lectin-like receptor 2, and combining all thrombin-collagen receptors. Functional assaysin vivoin zebrafish andin vitroin human macrophages respectively highlighted distinct homing and secretory responses triggered by the PEVs. In contrast, omics analyses of protein and miRNA cargo combined with physicochemical particle characterization found only subtle differences between the PEV types, which were insufficient to explain their different functional immunomodulatory profiles. Constitutively released PEVs, formed in the absence of an exogenous activator, displayed a disparate activation profile from the receptor induced PEVs.Our findings underscore that PEVs are tunable through receptor-mediated activation. To truly comprehend their role(s) in mediating platelet functions among immune cells, conducting functional assays is imperative.Graphical Abstract
Cryo-EM images of phase separated lipid bilayer vesicles analyzed with a machine learning approach
Authors: Sharma Karan D. , Doktorova Milka , Waxham M. Neal , Heberle Frederick A. 
Published: January 2024

AbstractLateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground truth datasets mimicking a series of compositions along a tieline of Ld+Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase at 5 nm lateral resolution with > 90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain size distributions, number of domains, and phase area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.SignificanceLipid rafts are important for cell function, but in most cases cannot be detected with conventional optical microscopy because of their extremely small size. Cryogenic electron microscopy (cryo-EM), because of its much greater spatial resolution, is capable of imaging domains as small as 5-10 nm. In this report, we show how machine learning techniques can be used to automatically and accurately identify raft-like domains in simulated cryo-EM images, a powerful approach that could ultimately lead to a better understanding of raft properties.
Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase
Authors: Tong Huawei , Wang Haoqiang , Liu Nana , Li Guoling , Zhou Yingsi , Wu Danni , Li Yun , Jin Ming , Wang Xuchen , Li Hengbin , Wei Yinghui , Yuan Yuan , Shi Linyu , Yao Xuan , Yang Hui 
Published: January 2024

AbstractDNA base editors could enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here, by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants, we developed a deaminase-free glycosylase-based thymine base editor (gTBE) with the ability of direct T editing. By several rounds of UNG mutagenesis via rational screening, we demonstrated that gTBE with engineered UNG variants could achieve T editing efficiency by up to 81.5%. Furthermore, the gTBE exhibited high T-to-S (i.e., T-to-C or T-to-G) conversion ratio with up to 0.97 in cultured human cells. Using similar strategy, we developed a deaminase-free cytosine base editor (gCBE) facilitating specifically direct C editing by engineered UNG with mutations different from gTBE. Thus, we provide two novel base editors, gTBE and gCBE, with corresponding engineered UNG variants, broadening the targeting scope of base editors.
Activation and depression of neural and hemodynamic responses induced by the intracortical microstimulation and visual stimulation in the mouse visual cortex
Authors: Suematsu Naofumi , Vazquez Alberto L , Kozai Takashi DY 
Published: January 2024

AbstractObjective. Intracortical microstimulation can be an effective method for restoring sensory perception in contemporary brain-machine interfaces. However, the mechanisms underlying better control of neuronal responses remain poorly understood, as well as the relationship between neuronal activity and other concomitant phenomena occurring around the stimulation site.Approach. Different microstimulation frequencies were investigatedin vivoon Thy1-GCaMP6s mice using widefield and two-photon imaging to evaluate the evoked excitatory neural responses across multiple spatial scales as well as the induced hemodynamic responses. Specifically, we quantified stimulation-induced neuronal activation and depression in the mouse visual cortex and measured hemodynamic oxyhemoglobin and deoxyhemoglobin signals using mesoscopic-scale widefield imaging.Main results. Our calcium imaging findings revealed a preference for lower-frequency stimulation in driving stronger neuronal activation. A depressive response following the neural activation preferred a slightly higher frequency stimulation compared to the activation. Hemodynamic signals exhibited a comparable spatial spread to neural calcium signals. Oxyhemoglobin concentration around the stimulation site remained elevated during the post-activation (depression) period. Somatic and neuropil calcium responses measured by two-photon microscopy showed similar dependence on stimulation parameters, although the magnitudes measured in soma was greater than in neuropil. Furthermore, higher-frequency stimulation induced a more pronounced activation in soma compared to neuropil, while depression was predominantly induced in soma irrespective of stimulation frequencies.Significance. These results suggest that the mechanism underlying depression differs from activation, requiring ample oxygen supply, and affecting neurons. Our findings provide a novel understanding of evoked excitatory neuronal activity induced by intracortical microstimulation and offer insights into neuro-devices that utilize both activation and depression phenomena to achieve desired neural responses.
Hints of a new leptophilic Higgs sector?
Authors: Afik Yoav , Dev P. S. Bhupal , Thapa Anil 
Published: January 2024

We show that a new leptophilic Higgs sector can resolve some intriguing anomalies in current experimental data across multiple energy ranges. Motivated by the recent CMS excess in the resonant eμ channel at 146 GeV, we consider a leptophilic two-Higgs-doublet model, and propose a novel resonant production mechanism for the neutral components of the second Higgs doublet at the LHC using the lepton content of the proton. Interestingly, the same Yukawa coupling Yeμ∼0.65–0.81 that explains the CMS excess also addresses the muon (g−2) anomaly. Moreover, the new Higgs doublet also resolves the recent CDF W-boson mass anomaly. The relevant model parameter space will be completely probed by future LHC data.

Published by the American Physical Society
2024
Amr Allam: outgrowing a family business
Authors: Apaydin Marina , Sand Martin Johannes Løkse , Hoogendoorn Rebecca A , Eshak Maha 
Published: January 2024

Learning outcomes
The expected learning outcomes are to understand key frameworks and tools for global leaders through the application of widely used theoretical frameworks on a written business case, understand the role of the leader in a team, apply theories of change to situations to anticipate courses of events and evaluate and apply relevant theory to assess a leader’s character and personality.

Case overview/synopsis
Hassan Allam Holding (HAH) was a family-owned Egyptian engineering, construction and infrastructure company managed by co-Chief Executive Officers and brothers Amr and Hassan Allam. HAH experienced significant growth and success, but eventually, it reached a point where its family governance structure could no longer sustain further growth. Amr and Hassan realized this and started planning to transition toward a corporate governance structure. In 2016, they managed to get the International Finance Corporation on board as an equity partner, and this helped propel the governance transition, but they still needed to find a way to convince the family to step back. This case study can help students understand the issues that may occur during a change within an established organization of any size. The case study considers the implications the change may have on the leader, his personality and his character and how it shapes the leader in question as an outcome. This case study has been designed to be used in one or two sessions and can be offered in management or leadership courses at an undergraduate or graduate level.

Complexity academic level
This case study is intended for graduate and undergraduate students studying a leadership or management course. It can help students comprehend the challenges of a family-owned business and how change is associated with such businesses. The case also considers how leaders are shaped by effectively managing conflict. This case can be considered as Level 1 on a 1–3 scale, as the full description of the situation is given in the case and the task of the students is to analyze the leader and his decisions using various academic concepts and theories (Erskin et al., 2003).

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 3: Entrepreneurship
Beyond the stethoscope: a COVID-19 lens on the halal, business and ethical dimensions of hospitals in a Muslim majority country
Authors: Gayatri Gita , Kamarulzaman Yusniza , Balqiah Tengku Ezni , Chalid Dony Abdul , Safira Anya , Hati Sri Rahayu Hijrah 
Published: January 2024

Purpose
This study aims to examine the perceptions and evaluations of Muslim COVID-19 survivors and health workers regarding the halal, business and ethical attributes of hospitals during their interactions related to COVID-19 treatment.

Design/methodology/approach
Descriptive qualitative research with semi-structured online interviews was used to gather insights from COVID-19 survivors and health workers who treated COVID-19 patients. The findings were then compared with existing literature on hospital services and Sharia attributes.

Findings
The study found that patients and health-care workers in hospitals are concerned about whether the hospital follows Sharia law, the quality of health-care and hospital services and the ethical conduct of hospital staff. This is especially true during the COVID-19 pandemic, when patients are more anxious about religious conduct and the afterlife.

Research limitations/implications
Hospitals need to address halal attributes in all aspects of their services for Muslim patients and business attributes such as standard health-care quality, service quality and ethical attributes. Participants indicated that when these needs are met, they are more likely to revisit the hospital and recommend it to others.

Originality/value
This study contributes to understanding the expectations of Muslim patients regarding hospital services that meet Islamic ethical and business requirements. Using the COVID-19 pandemic as a case study broadens the understanding of how to better serve Muslim customers.
A comparison of analysts’ and investors’ information efficiency of corporate social responsibility activities
Authors: Kang Grace Il Joo , Heo Kyongsun , Jeon Sungmin 
Published: January 2024

Purpose
This paper aims to examine the extent to which sell-side analysts efficiently incorporate firms’ corporate social responsibility (CSR) activities into their earnings forecasts. In addition, this paper also investigate the CSR information efficiency of analysts vis-à-vis that of investors.

Design/methodology/approach
This paper measures CSR activities by using CSR strength and CSR concern scores from the Morgan Stanley Capital International Environmental, Social and Governance database. This paper uses analysts’ earnings forecast errors and dispersion as proxies for their information efficiency. To compare the CSR information efficiency of analysts to that of investors, this paper uses the Vt/Pt ratio, which is the equity value estimates inferred from analysts’ earnings forecasts (a proxy for analysts’ CSR information efficiency) to the stock price of the focal company (a proxy for investors’ CSR information efficiency).

Findings
The regression analysis indicates that analysts’ earnings forecasts are optimistically biased and more dispersed for firms with positive CSR activities. The paper also finds that analysts’ forecasts are more optimistically biased than investors in interpreting CSR activities.

Practical implications
The lack of standardized protocols in CSR reporting and activities has raised the risk of mispricing by analysts, threatening the stability of sustainable investments. This paper suggests that regulators and standard-setters should establish a uniform framework governing firms’ CSR activities, along with their reporting and measurement, to ensure more consistent and reliable evaluations of CSR practices.

Social implications
Analysts’ mispricing of CSR activities may distort sustainable investing, as it can overly focus on the positive impacts of stakeholder theory, overlooking agency theory’s warnings about managerial self-interest. Investors need to assess CSR efforts with a dual perspective, acknowledging their societal value but also examining their alignment with shareholder interests.

Originality/value
To the best of the authors’ knowledge, this research is the first to assess the efficiency of analysts versus investors in processing CSR information amidst growing sustainable investment interests. Furthermore, building on Dhaliwal et al. (2012), which found that voluntary CSR disclosures correlate with more accurate analyst forecasts, this research provides fresh perspectives on the evolving nature of how analysts assimilate CSR information over time.
Taking empirical evidence seriously v.2.01
Authors: Tilden Terje , Solem May‐Britt , Thuen Frode , Lorås Lennart , Stokkebekk Jan , Whittaker Kristoffer 
Published: January 2024

AbstractThis article discusses the status and challenges related to the basic perspective of knowledge and science in systemic practice. This article points out that some parts of the field (i.e. collaborative dialogical practice) have a preference for knowledge obtained through qualitative rather than quantitative studies. This is problematised, partly based on methodology and partly on the bias this entails in the provision of knowledge to students and systemic practitioners. The consequences of such a preference may be that systemic practitioners will lack significant knowledge, and that they are not encouraged to conduct or participate in quantitative studies. This issue highlights a stronger focus on the field's basic perspectives, as well as key political, ethical and professional policies. In response, the article presents the theories of interactive constructivism and critical realism and proposes that these become the guiding paradigm for systemic practice.
Examining the asymmetric effects of energy intensity in low‐ versus high‐income economies: New evidence using common correlated effects approach
Authors: Sim Khang Yi , Sek Siok Kun 
Published: January 2024

AbstractThis study aims to investigate the symmetric and asymmetric effects of total and renewable energy intensity on economic growth (GDP) in two panel groups classified by their income levels, namely, low‐ and lower‐middle‐income economies versus high‐income economies over 1990–2021. Heterogeneous estimators are adopted in the common correlated effects models, covering slope heterogeneity, cross‐sectional dependence and nonstationarity or cointegration (long‐run effect). New evidence is obtainable from this study because energy intensity is decomposed into its positive and negative series and incorporated into the model estimations so that the effect of its increases and decreases can be observed. Hence, our innovative models are improved and better mimic real economic situations. The results demonstrate that energy intensity and GDP are negatively correlated, and the causal effect is nonlinear or asymmetric. The effect also differs across the two panel groups. The decreases in total energy intensity (LTEI–) have a greater adverse impact on GDP than energy intensity increases (LTEI+) for low‐ and lower‐middle‐income economies. For high‐income economies, the detrimental influence of LTEI+ is more prominent than that of LTEI–. Moreover, the increases in renewable energy intensity (LREI+) also impede the GDP of high‐income economies, but with a relatively smaller impact compared to LTEI+ and LTEI–. On the contrary, the gain in GDP for both groups is driven by gross fixed capital formation although the conducive impact is rather small compared to the unfavourable effect of total energy intensity on the GDP. Besides, the labour force participation rate promotes a higher GDP in the high‐income group. Therefore, critical attention and proper energy policy formulation should be stipulated in achieving sustainable development and contributing to the Sustainable Development Goals.
Euthanasia, consensual homicide, and refusal of treatment
Authors: Rivera‐López Eduardo 
Published: January 2024

AbstractConsensual homicide remains a crime in jurisdictions where active voluntary euthanasia has been legalized. At the same time, both jurisdictions, in which euthanasia is legal and those in which it is not, recognize that all patients (whether severely ill or not) have the right to refuse or withdraw medical treatment (including life‐saving treatment). In this paper, I focus on the tensions between these three norms (the permission of active euthanasia, the permission to reject life‐saving treatment, and the prohibition of consensual homicide), assuming a justification of euthanasia based on the right to (personal) autonomy. I argue that the best way to provide a coherent account of these norms is to claim that patients have two distinct rights: the right to autonomy and the right to bodily integrity. This solution has some relevant implications for the discussion of the legalization of active euthanasia.