bluuebunny/crossref_metadata_2025 huggingface dataset:
Studying Gangs in Central and South America
Authors: Méndez María José , Van Damme Ellen
Published: January 2024

By accounting for the perspectives of gang members, qualitative studies in Central and South America have challenged the heavy reliance on secondary material that characterizes literature in the region, including moralized preconceptions of gangs. This chapter acknowledges this important contribution but argues that qualitative gang researchers must be more attuned to methodological reflections on their positionality, particularly how their gendered status informs every aspect of the research process and requires grappling consciously with gendered power relations. How researchers navigate gender dynamics influences the narratives shared by their interlocutors, as well as their research outcomes and the way they present their results. Drawing on insights gleaned from our respective studies on gangs in Central America, the chapter contends that failure to engage with questions of positionality will only reify the marginalization of women’s perspectives, the privileging of a male gaze, and the reinforcement of gender stereotypes on gangs.
Women in Gang Research
Authors: Urbanik Marta-Marika , Bucerius Sandra M.
Published: January 2024

This chapter is multipronged, broadly evaluating women in gang ethnography. First, the chapter provides an overview of the women who have produced notable works in this area and documents the contributions of female gang ethnographers across disciplines to the growing field of gang studies. It highlights how female scholars have extended the field, especially pertaining to unmasking the roles of girls and women in gangs, gender theory, feminist and queer methodology in gang research, as well as other methodological innovations. Second, the chapter critically evaluates the process of conducting gang ethnography as a woman, unmasking the unique and complex fieldwork realities women must often navigate. In this respect, this chapter explores the challenges and benefits of this type of research. It then outlines directions for future research with respect to encouraging and expanding both the topics of inquiry and the scholars who undertake this work.
The Legacy of Finn-Aage Esbensen
Authors: Carson Dena C. , Freng Adrienne , Melde Chris , Peterson Dana
Published: January 2024

Finn-Aage Esbensen’s contribution to research and practice in the areas of gangs, youth violence, juvenile delinquency, school-based prevention, and evaluation research is extensive. His published and highly cited work includes over 80 articles, 30 book chapters, 5 books, and a plethora of presentations and government reports. To support this work, Finn was successful in securing grant funding primarily from the National Institute of Justice totaling nearly $8 million. Additionally, he has been integral in bringing together individuals from various countries to examine gangs from an international perspective. This record ensued from his perpetual passion for answering novel questions, ensuring the practical utility of research findings, and training the next generation of scholars. As a result, his work has become nationally and internationally known and has led to Finn being identified as one of the premier gang and juvenile violence researchers.
The Legacy of John M. Hagedorn
Authors: Aspholm Roberto R.
Published: January 2024

John M. Hagedorn has left an indelible legacy in the field of gang research. His first book, People and Folks: Gangs, Crime and the Underclass in a Rustbelt City, published in 1988, is arguably the founding document in the domain of critical gang studies. In the decades that followed, his research exploded in manifold directions, illuminating empirically and theoretically neglected dimensions of street gangs as a social phenomenon and their connections to the broader contexts in which they are embedded. Each epoch of Hagedorn’s work has been characterized by a steadfast commitment to inductive discovery and a willingness to question not only received criminological wisdom, but his own earlier conclusions as well. Hagedorn’s oeuvre stands as a remarkable testament to his personal motto, “research, not stereotypes,” and to the capacity of committed researchers to render gang members as human beings no less complex than those who might study them.
Making Sense of the Models
Authors: Jannetta Jesse , Thompson Paige S. , Robin Lily
Published: January 2024

This chapter draws out points of comparison and contrast among the three most prominent models addressing youth gun violence connected to gangs and groups: focused deterrence, public health, and the Comprehensive Gang Model. There is considerable overlap in intervention components across them, including being driven by analysis that combines data and ground-level knowledge of local dynamics, meeting young people and others at high risk with trust-building engagement and positive supports, working proactively to interrupt conflicts and other violence transmission vectors, and building broad partnerships to mobilize the community and government support necessary to mitigate gun violence. Despite these continuities, there are important differences, particularly around their relationship to enforcement and suppression. The extant research base provides promising evidence about what these models can achieve in reducing gun violence, but concerns about shortcomings in that research base must be addressed if the research community is to consider any of them “proven.”
Gang Identity Across the Life Course
Authors: Lee Sou , Bubolz Bryan F.
Published: January 2024

While identity—the social meanings attached to a role—has been documented across various aspects of gang life, examinations of identity have rarely extended beyond “being” a gang member. Exacerbating this is the relative absence of symbolic interactionism in the study of gangs. Thus, a more useful approach is to view gang identity as a situational resource for performance. Conceptualized in this way, the chapter encourages scholars to reimagine how gang identity is managed and what factors facilitate and discourage the “doing” of gang identity. Advancing a “soft” or dynamic version of gang identity presents new avenues for future research and provides practical considerations for understanding gang membership among scholars and practitioners alike. As such, this chapter reviews the importance of gang identity across the life course and concludes with suggestions for future research and practice.
Rational Choice, Gang Membership, and Crime
Authors: Thomas Kyle J.
Published: January 2024

Rational choice perspectives derive from the standard economic idea that individuals choose to engage in actions when the marginal benefits exceed the marginal risks and costs. Although there is considerable support for rational choice predictions across a range of outcomes related to crime, scholars have rarely invoked choice ideas when explaining issues related to gang involvement. The chapter discusses the foundations of a rational choice model of gang involvement, gang offending and gang disengagement. This perspective differs from traditional sociological views which focus on “causal” factors that are external to the individual, and instead recognizes individuals as agents who play an active role in their own social lives. This approach further allows for macro-sociological characteristics to be linked to a micro-level theory of action that can improve our understanding of gang-related issues. Throughout, the chapter offers tractable models of rational choice explanations to account for selection into gangs, offending and gang disengagement.
Trigonometric parallax and proper motion of Sagittarius A* measured by VERA using the new broad-band back-end system OCTAVE-DAS
Authors: Oyama Tomoaki , Nagayama Takumi , Yamauchi Aya , Sakai Daisuke , Imai Hiroshi , Honma Mareki , Asakura Yu , Hada Kazuhiro , Hagiwara Yoshiaki , Hirota Tomoya , Jike Takaaki , Kono Yusuke , Suzuki Syunsaku , Kobayashi Hideyuki , Kawaguchi Noriyuki
Published: January 2024

We successfully measured the trigonometric parallax of Sagittarius A* (Sgr A*) to be 117 ± 17 micro-arcseconds ($\, \mu \mbox{as}$) using the VLBI Exploration of Radio Astrometry (VERA) with the newly developed broad-band signal-processing system named “OCTAVE-DAS.” The measured parallax corresponds to a Galactocentric distance at the Sun of $R_0 = 8.5^{+1.5}_{-1.1}\:$kpc. By combining the astrometric results with VERA and the Very Long Baseline Array (VLBA) over a monitoring period of 25 yr, the proper motion of Sgr A* is obtained to be (μα, μδ) = (−3.133 ± 0.003, −5.575 ± 0.005) mas yr−1 in equatorial coordinates, corresponding to (μl, μb) = (−6.391 ± 0.005, −0.230 ± 0.004) mas yr−1 in Galactic coordinates. This gives an angular orbital velocity of the Sun of Ω⊙ = 30.30 ± 0.02 km s−1 kpc−1. We find upper limits to the core wander, Δθ < 0.20 mas (1.6 au), peculiar motion, Δμ < 0.10 mas yr−1 (3.7 km s−1), and acceleration, a < 2.6 $\, \mu \mbox{as} \:$yr−2 (0.10 km s−1 yr−1) for Sgr A*. Thus, we obtained upper mass limits of $\approx 3 \times 10^{4}\, M_{\odot }$ and $\approx 3 \times 10^{3}\, M_{\odot }$ for the supposed intermediate-mass black holes at 0.1 and 0.01 pc from the Galactic center, respectively.
What Drives Ultra-Orthodox Jewish Men to Go to Work in Israel?
Authors: Perelman Yossi , Goldberg Chen , Yaish Meir
Published: January 2024

Only about half of the ultra-Orthodox men in Israel dedicate their lives mainly to religious studies, while the rest participate in the labor market. Utilizing siblings with different labor market outcomes sampling, we collected retrospective data on ultra-Orthodox men who earn a living (N = 107), matched to their brothers (N = 103) who study in yeshiva as a way of life. Our logit model indicates that aspirations for upward mobility are positively associated with the likelihood of an ultra-Orthodox man entering the labor market, whereas the preference for religious studies and economic support of wives are associated with a decrease in an ultra-Orthodox man’s chances to join the labor market. Just as important, our findings show that among the group of men who study in yeshiva as a way of life, there is a subgroup that leads a less conservative lifestyle than is customary in ultra-Orthodox society and has relatively high personal aspirations.
Fructose Potentiates Bone Loss and Marrow Adipose Tissue Accumulation by Inhibiting Adenosine 5ʹ-Monophosphate-Activated Protein Kinase in Mesenchymal Stem Cells
Authors: Yan Ziqi , Du Juan , Zhao Rui , Liu Xu , Xu Junji , Guo Lijia , Liu Yi
Published: January 2024

Increased fructose consumption has been elucidated to contribute to metabolic diseases. Bone is a dynamic organ that undergoes constant remodeling. However, the effects of fructose on bone health are still in dispute. Here, we identified fructose deteriorated bone mineral density while promoting the abundance of bone marrow adipose tissue. Fructose remarkably promoted the bone marrow mesenchymal stem cells’ (BMMSCs) adipogenic commitment at the expense of osteogenic commitment. Fructose boosted the glycolysis of BMMSCs and inhibited phosphorylation of adenosine 5ʹ-monophosphate-activated protein kinase (AMPK), which played a crucial role in bone-fat alteration. Our results suggested that fructose potentiated bone loss and marrow adipose tissue accumulation by suppressing AMPK activation in BMMSCs. Understanding fructose which affected bone metabolism was thus of primary importance in order to establish preventative measures or treatments for this condition.
Risk Factors for Hypoglycemia Among Neonates
Authors: Zhang Xiaoyan , Rehemutula Rehemayi , Jin Hongmei , Teng Yaoyao , Ma Jun , Mei Shanshan , Long Yan , Zhao Xueqin , Zeng Fangling , Huang Yaogang , Liu Fei , Gao Xiaoli , Zhu Chunyan
Published: January 2024

Objective:

Neonatal hypoglycemia (NH) is the most frequent complication in neonates born to pregnant people with gestational diabetes mellitus (GDM) and an important cause of brain damage and death of neonates. We explored the risk factors for NH in neonates of pregnant people with GDM.

Methods:

A prospective cohort study was conducted involving 322 pregnant people with GDM at the Guangzhou Women and Children's Medical Centre. Maternal sociodemographic, clinical, and biochemical data, as well as general characteristics of neonates, were collected to analyze their associations with NH in neonates of pregnant people with GDM.

Results:

The incidence of NH among neonates of pregnant people with GDM was 19.57% (63/322). After adjustment for confounders, the factors significantly associated with an increased risk of NH were cesarean delivery (relative risk [RR] = 3.44; 95% confidence interval [CI], 1.83-6.45), red blood cell (RBC) count (RR = 2.19; 95% CI, 1.22-3.96), and 1-hour postprandial glucose (RR = 2.35; 95% CI, 1.23-4.46) during pregnancy, whereas later gestational age (RR = 0.58; 95% CI, 0.42-0.80) and multiparity (RR = 0.32; 95% CI, 0.16-0.66) were associated with a reduced risk of NH.

Conclusion:

Cesarean delivery, maternal 1-hour glucose of the oral glucose tolerance test, and increased RBC count of pregnant people with GDM are independent risk factors for NH, while later gestational age and multiparity are protective factors.
Navigating Nutrition Inequities
Authors: Scott Monique , Qamar Zubaida
Published: January 2024

Introduction:

The proposal to administer cuts for the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) could create deficiencies in nutrition for already food insecure, low-income Black, Indigenous, and Persons of Color (BIPOC) pregnant, postpartum women, and children. WIC is a US Department of Agriculturefunded nutritional program for women, infants, and children. The current proposal is to cut the funding by $800 million for the 2024 fiscal year, affecting 75% of its low-income recipients and predominantly BIPOC.

Methods:

Relevant websites and journal articles were analyzed to determine how the proposed cuts would create barriers within the social determinants of health that contribute to disparities in health outcomes of WIC recipients.

Results:

Many studies have demonstrated that nutrition in the first 1000 days is critical for the healthy development of newborns. Prior research suggests that maternal health outcomes for BIPOC populations are contingent upon the increased allocation of nutritional support programs such as WIC and SNAP (Supplemental Nutrition Assistance Program). Nutrients provided by the cash benefit voucher have been proven to contribute to participants' health outcomes, and allotment increases can benefit maternal and infant health outcomes.

Conclusion and future directions:

Neonatal nurses can help advocate for more robust policies that support the health of their patients. Future directions call for systematic changes in policies and legislation that directly affect maternal health outcomes, supportive breastfeeding policies, and applied research on solutions to improve maternal health outcomes of BIPOC populations in addition to increased awareness, education, and implementation of VeggieRx programs, investment in affordable, sustainable grassroots urban agriculture solutions.
A Dynamic Programming Approach for the Alignment of Molecules
Authors: Williams Ryan A. , Liberles David A.
Published: January 2024

I.

There is a need for computational approaches to compare molecules based upon chemical similarity or for evaluating biochemical transformations. Here, a new approach to molecular alignment in the Simplified Molecular Input Line Entry System (SMILES) format is introduced. Leveraging dynamic programming and scoring alignments to minimize differences in a measure of electronegativity, the study addresses the challenge of comprehending structural transformations in reaction pathways, notably transitions from linear to cyclical structures. The method is built from the Needleman-Wunsch algorithm for sequence alignment, but with a modified scoring function for different input data. Validation against a benchmarked dataset from the Krebs cycle based upon known chemical mechanisms of molecular transformations confirmed the efficacy of the approach. The transformations of the Pentose Phosphate Pathway were quantified using this algorithm and was compared with Glycolysis. The study introduces an algorithm that quantifies molecular transformations in metabolic pathways, highlighting a midpoint dissimilarity peak in cyclical pathways and a progressive decrease in molecular similarity in linear pathways. The software is available at:https://github.com/rwills5042/SMILES_Alignment.
Maternal manipulation of offspring size can trigger the evolution of eusociality in promiscuous species
Authors: Rees-Baylis Ella , Pen Ido , Kreider Jan J.
Published: January 2024

Eusocial organisms typically live in colonies with one reproductive queen supported by thousands of sterile workers. It is widely believed that monogamous mating is a precondition for the evolution of eusociality. Here, we present a theoretical model that simulates a realistic scenario for the evolution of eusociality. In the model, mothers can evolve control over resource allocation to offspring, affecting offspring body size. The offspring can evolve body-size-dependent dispersal, by which they disperse to breed or stay at the nest as helpers. We demonstrate that eusociality evolves, even if mothers are not strictly monogamous, if mothers can constrain their offspring’s reproduction by manipulation. We also observe the evolution of social polymorphism with small individuals that help and larger individuals that disperse to breed. Our model unifies the traditional kin selection and maternal manipulation explanations for the evolution of eusociality and demonstrates that – contrary to current consensus belief – eusociality can evolve despite highly promiscuous mating.
Different fluorescent labels report distinct components of spHCN channel voltage sensor movement
Authors: Wojciechowski Magdalena N , McKenzie Chaseley E , Hung Andrew , Kuanyshbek Alibek , Soh Ming S , Reid Christopher A , Forster Ian C
Published: January 2024

Voltage clamp fluorometry was used to probe the S4 helix movement in the voltage sensing domain of the sea urchin HCN channel expressed inXenopusoocytes. Markedly different fluorescence responses were obtained with either ALEXA-488 or MTS-TAMRA covalently linked to Cys332 at the N-terminal end of S4. With hyperpolarizing steps, ALEXA-488 fluorescence increased rapidly showing characteristics consistent with it reporting the initial inward movement of S4 in agreement with previous studies. In contrast, MTS-TAMRA fluorescence was slower and correlated with the early phase of channel opening. In addition, a slow fluorescence component was resolved with both labels that tracked the development of the mode shift or channel hysteresis. This was quantitated as an increased deactivation tail current delay with concomitantly longer activation periods and was found to depend strongly on the presence of K+ions in the pore. This indicated that the microenvironment of the fluorescent probes attached to Cys332 was strongly influenced by conformational changes in the pore domain. Collisional quenching experiments established that ALEXA-488 was more exposed to solvent than MTS-TAMRA. This was supported by structural predictions based on homology modelling of spHCN in the closed and open conformations with covalently linked fluorophores. This study demonstrates that components of S4 movement during channel activation can be kinetically resolved using different fluorescent probes to reveal three distinct biophysical properties: voltage-sensor movement, early channel opening and mode-shift. These data support the use of different labelling probes to interrogate distinct biophysical aspects of voltage-gated membrane proteins.

Voltage clamp fluorometry was used to probe the S4 helix movement in the voltage sensing domain of the spHCN channel expressed inXenopusoocytes, labeled with either ALEXA-488 or MTS-TAMRA. Each fluorophore reported different components of S4 movement.
Explaining plant trait variation in response to soil water availability using an optimal height-growth model
Authors: Towers Isaac R. , O’Reilly-Nugent Andrew , Sabot Manon E.B. , Vesk Peter A. , Falster Daniel S.
Published: January 2024

1

Climate change is expected to bring about changes in precipitation and temperature regimes that, together with rising atmospheric CO2concentrations, will likely reorganise the functional trait composition of ecosystems. Predicting plant trait responses to emerging environmental conditions including, in particular, water availability, is a tremendous challenge, but is one that eco-evolutionary optimality theory (EEO) can help us undertake. However, most EEO approaches are based on the hypothesis that traits are selected to maximise carbon assimilation which omits the important role that size growth plays in determining fitness outcomes. Using a height-growth based EEO framework, we predict magnitude and directional shifts in four key traits: leaf mass per area, sapwood area to leaf area ratio (Huber value), wood density and sapwood-specific conductivity in response to variation in soil moisture availability, atmospheric aridity, CO2and light availability. Consistent with empirical patterns, we predict that trait optima shift from resource-acquisitive strategies characterised by low tissue constructions costs and high rates of tissue turnover and sapwood conductivity to resource-conservative strategies - characterised by low rates of tissue turnover and greater xylem embolism resistance - as conditions become increasingly dry. The EEO model that we use here highlights the important role that both carbon assimilation and tissue construction costs jointly play in predicting the response of trait optima to the environment, laying the groundwork for future height-growth based EEO models aiming to predict shifts in the functional composition of ecosystems in response to global change.
Can’t carve air, can’t weave names: Plant species used in Colombian artisan crafts are not equally assessed for vulnerability at the international and national level
Authors: Hernandez Katherine Victoria , Andrade-Rivas Federico , Zapata Felipe , Batista Natasha , Cárdenas-Navarrete Anaid , Dávila Arenas Armando , Herrera-R Guido A. , Langhans Kelley E. , Levey Dallas , Neill Andrew , Nguyen Oliver , Ocampo-Peñuela Natalia , Sánchez Lopez Sergio , Echeverri Alejandra
Published: January 2024

Humanity has maintained cultural connections with our environments for time immemorial. Plants and artisan crafts are a prime example, as craft purpose, skill, design, and species used can vary greatly between communities and the loss of a critical plant species can result in a loss of access to cultural craft practices. To mitigate global biodiversity loss, conservationists are faced with the challenge of assessing species vulnerability to extinction and prioritizing species for conservation funding using information instruments, like the IUCN red list. This process does not necessarily consider a species’ cultural importance. In this paper we sought to address this gap for plant species used in artisan crafts in Colombia. We aim to answer the following: (1) how represented are endemic species in artisan crafts; (2) how threatened are artisan craft species according to (a) international and (b) national vulnerability status? We used the number of species-associated common names as a proxy for cultural awareness. We found that continentally regional species were far more represented in Colombian artisan crafts than national endemics. We also found a strong positive relationship between number of common names and national vulnerability assessment status, but no statistically significant relationship for international vulnerability status. Based on our results, well-known plants used in Colombian artisan crafts are more likely to be assessed nationally than internationally. While the IUCN is thorough in their recommendations, more can be done to prioritize the inclusion of conservation assessments for species based on their contributions to cultural diversity.

Positionality statement

We are 14 scientists and practitioners who are deeply committed to the conservation of nature and culture in a changing world. We are trained in diverse fields including ecology, evolutionary biology, botany, music, anthropology, law, and public health. We all have postgraduate academic education (Masters or PhDs underway) but most of us are early career scholars. Six of us grew up in Colombia and we represent many places including Mexico, the United States, Ireland, Chile, Brazil, Germany, and Viet Nam. None of us self-identify as Indigenous.
The molecular core of transcriptome responses to abiotic stress in plants: a machine learning-driven meta-analysis
Authors: Sanchez-Munoz Raul , Depaepe Thomas , Samalova Marketa , Hejatko Jan , Zaplana Isiah , Van Der Straeten Dominique
Published: January 2024

Understanding how plants adapt their physiology to overcome severe stress conditions is vital in light of the current climate crisis. This remains a challenge given the complex nature of the underlying molecular mechanisms. To provide a full picture of stress mitigation mechanisms, an exhaustive analysis of publicly available stress-related transcriptomic data was conducted. We combined a meta-analysis with an unsupervised machine learning algorithm to identify a core of stress-related genes. To ensure robustness and biological significance of the output, often lacking in meta-analyses, a three-layered biovalidation was incorporated. Our results present a ‘stress gene core’, a set of key genes involved in plant tolerance to a multitude of adverse environmental conditions rather than specific ones. In addition, we provide a biologically validated database to assist in design of multi-stress resilience. Taken together, our results pave the way towards future-proof sustainable agriculture.

Teaser

Using a machine learning-driven meta-analysis, a plant ‘stress gene core’ was identified as a hub mediating multi-stress regulation
Plant response to intermittent heat stress involves modulation of mRNA translation efficiency
Authors: Dannfald Arnaud , Carpentier Marie-Christine , Merret Rémy , Favory Jean-Jacques , Deragon Jean-Marc
Published: January 2024

Acquired thermotolerance (also known as priming) is the ability of cells or organisms to better survive an acute heat stress if it is preceded by a milder one. In plants, acquired thermotolerance has been studied mainly at the transcriptional level, including recent descriptions of sophisticated regulatory circuits that are essential for this learning capacity. In this work, we tested the involvement of polysome-related processes (translation and cotranslational mRNA decay (CTRD)) in plant thermotolerance using two heat stress regimes with and without a priming event. We found that priming is essential to restore the general translational potential of plants shortly after acute heat stress. We observed that mRNAs not involved in heat stress suffer from a reduction in translation efficiency at high temperature, whereas heat stress-related mRNAs are translated more efficiently under the same condition. We also show that the induction of the unfolded protein response (UPR) pathway in acute heat stress is favoured by a previous priming event and that, in the absence of priming, ER-translated mRNAs become preferential targets of CTRD. Finally, we present evidence that CTRD can specifically regulate more than a thousand genes during heat stress and should be considered as an independent gene regulatory mechanism.
RNA Secondary Structure Prediction Using a Genetic Algorithm with a Selection Method Based on Free Energy Value and Topological Index
Authors: Benedetti Giorgio
Published: January 2024

This paper presents a genetic algorithm designed to predict RNA secondary structures, which utilizes selection criteria based on free energy (fitness) and topological similarity. This approach represents structural information using a simple number, facilitating comparisons between foldings. The simplified graph representation identifies similarities between structures that have the same type of branches. The results demonstrate that the algorithm identifies the final secondary structure with the same level of precision as the commonly used dynamic programming, but with the advantage of producing more optimal structures with different topologies. This approach maintains high population diversity and allows for the exploration of many suboptimal structures in parallel, avoiding the possibility of getting stuck in a local minimum. This permits the investigation of not only the structure with the minimum free energy, but also of other low-energy structures with different topologies that are closer to the natural fold.
Predicting assembly/disassembly orders of protein complexes using coarse-grained simulations
Authors: Lu Yunxiao , Liu Xin , Zhang Zhiyong
Published: January 2024

Assembly of a protein complex is very important to its biological function, which can be investigated by determining assembly/disassembly order of its protein subunits. Although static structures of many protein complexes are available in the protein data bank, their assembly/disassembly orders of subunits are largely unknown. In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex, computational methods can be used to predict the assembly/disassembly order. Since sampling is a nontrivial issue in simulating the assembly/disassembly process, coarse-grained simulations are more efficient than atomic simulations are. In this work, we developed computational protocols for predicting assembly/disassembly orders of protein complexes using coarse-grained simulations. The protocols were illustrated using two protein complexes, and the predicted assembly/disassembly orders are consistent with available experimental data.
Single-shot Echo Planar Time-resolved Imaging for multi-echo functional MRI and distortion-free diffusion imaging
Authors: Dong Zijing , Wald Lawrence L. , Polimeni Jonathan R. , Wang Fuyixue
Published: January 2024

Purpose

To develop EPTI, a multi-shot distortion-free multi-echo imaging technique, into a single-shot acquisition to achieve improved robustness to motion and physiological noise, increased temporal resolution, and high SNR efficiency for dynamic imaging applications.

Methods

A new spatiotemporal encoding was developed to achieve single-shot EPTI by enhancing spatiotemporal correlation ink-tspace. The proposed single-shot encoding improves reconstruction conditioning and sampling efficiency, with additional optimization under various accelerations to achieve optimized performance. To achieve high SNR efficiency, continuous readout with minimized deadtime was employed that begins immediately after excitation and extends for an SNR-optimized length. Moreover,k-tpartial Fourier and simultaneous multi-slice acquisition were integrated to further accelerate the acquisition and achieve high spatial and temporal resolution.

Results

We demonstrated that ss-EPTI achieves higher tSNR efficiency than multi-shot EPTI, and provides distortion-free imaging with densely-sampled multi-echo images at resolutions ∼1.25–3 mm at 3T and 7T— with high SNR efficiency and withcomparabletemporal resolutions to ss-EPI. The ability of ss-EPTI to eliminate dynamic distortions common in EPI also further improves temporal stability. For fMRI, ss-EPTI also provides early-TE images (e.g., 2.9ms) to recover signal-intensity and functional-sensitivity dropout in challenging regions. The multi-echo images provide TE-dependent information about functional fluctuations, successfully distinguishing noise-components from BOLD signals and further improving tSNR. For diffusion MRI, ss-EPTI provides high-quality distortion-free diffusion images and multi-echo diffusion metrics.

Conclusion

ss-EPTI provides distortion-free imaging with high image quality, rich multi-echo information, and enhanced efficiency within comparable temporal resolution to ss-EPI, offering a robust and efficient acquisition for dynamic imaging.
An Evaluation of the Tumor Microenvironment through CALR, IL1R1, IFNB1, and IFNG to Assess Prognosis and Immunotherapy Response in Bladder Cancer Patients
Authors: Lilong Liu , Zhenghao Liu , Lei Fan , Zhipeng Yao , Junyi Hu , Yaxin Hou , Yang Li , Yuhong Ding , Yingchun Kuang , Ke Chen , Yi Hao , Zheng Liu
Published: January 2024

Immunogenic cell death (ICD) is a type of cell death sparking adaptive immune responses, can reshape the tumor microenvironment (TME). Exploring key ICD-related genes in bladder cancer (BLCA) could enhance personalized treatment. TCGA BLCA patients were divided into two ICD subtypes: ICD-high and ICD-low. High ICD expression linked to increased immune cell infiltration and longer survival, but with potentially suppressed immune function. The high ICD group responded better to PD1-targeted therapy. A risk-scoring model with four ICD-related genes (CALR, IL1R1, IFNB1, IFNG) was validated across TCGA, GEO datasets, and tissue samples, showing higher risk-score correlated with weaker anti-tumor immune function, more tumor-promoting elements, lower immunotherapy response rates, and shorter patient survival.This study connects ICD-related genes to BLCA prognosis and immune infiltration, offering a vital tool for personalized treatment guidance.
Developmental divergence in gene regulation among rapidly radiating cichlid species
Authors: Duenser Anna , Singh Pooja , Ahi Ehsan Pashay , Durdevic Marija , Schaeffer Sylvia , Gallaun Julian , Gessl Wolfgang , Seehausen Ole , Sturmbauer Christian
Published: January 2024

Developmental shifts in gene regulation underlying key innovations remain largely uncharacterized over short evolutionary timescales. Here, we investigate the gene regulatory landscape of trophic innovations in the fastest vertebrate adaptive radiation: cichlid fishes from Lake Victoria. By analyzing the whole-transcriptomes of the oral and pharyngeal jaws from two life stages in five species adapted to divergent trophic niches, we find that both gene and isoform expression are developmentally dynamic. Expression signatures are most similar across jaws at the early stage and then diverge into species-specific developmental programs in adults. However, even at the early stage, expression in the oral jaws of species adapted to herbivory is distinct from those of carnivores, a pattern not observed for the pharyngeal jaws. We further show that differentially expressed and spliced genes between herbivorous and carnivorous species regulate different genes and pathways, particularly in adults. Interestingly, we find that splicing-mediated exonization of a craniofacial development gene, kaznb, may have contributed to the evolution of herbivory in Lake Victoria cichlids. Overall, our results contribute to our understanding of how ontogenetic shifts in gene regulation can facilitate rapid adaptive evolution.
Evolution, diversity, function, and marker-based elimination of the disease susceptibility geneSnn1in wheat
Authors: Seneviratne Sudeshi , Shi Gongjun , Szabo-Hever Agnes , Zhang Zengcui , Peters Haugrud Amanda R. , Running Katherine L. D. , Singh Gurminder , Nandety Raja Sekhar , Fiedler Jason D. , McClean Phillip E. , Xu Steven S. , Friesen Timothy L. , Faris Justin D.
Published: January 2024

Septoria nodorum blotch (SNB), caused byParastagonospora nodorum,is a disease of durum and common wheat initiated by the recognition of pathogen-produced necrotrophic effectors (NEs) by specific wheat genes. The wheat geneSnn1encodes a wall-associated kinase that directly interacts with the NE SnTox1 leading to the development of SNB. Here, sequence analysis ofSnn1from 114 accessions including diploid, tetraploid and hexaploid wheat species revealed that some wheat lines possess two copies ofSnn1(designatedSnn1-B1andSnn1-B2) approximately 120 kb apart.Snn1-B2evolved relatively recently as a paralog ofSnn1-B1, and both genes have undergone diversifying selection. Three point mutations associated with the formation of the first SnTox1-sensitiveSnn1-B1allele from a primitive wild wheat were identified. Four subsequent and independent SNPs, three inSnn1-B1and one inSnn1-B2, converted the sensitive alleles to insensitive forms. Protein modeling indicated these four mutations could abolishSnn1-SnTox1 compatibility either through destabilization of the Snn1 protein or direct disruption of the protein-protein interaction. High-throughput markers were developed for the causal mutations and evaluated on panels of durum and common wheat. The markers were able to correctly identify 96.9 % of SnTox1-sensitive durum wheat accessions, and a marker for the null allele was 100% accurate at predicting SnTox1-insensitive lines in both durum and spring wheat. Results of this study increase our understanding of the evolution, diversity, and function ofSnn1-B1andSnn1-B2genes and will be useful for marker-assisted elimination of these genes for better host resistance.
Bridge RNAs direct modular and programmable recombination of target and donor DNA
Authors: Durrant Matthew G. , Perry Nicholas T. , Pai James J. , Jangid Aditya R. , Athukoralage Januka S. , Hiraizumi Masahiro , McSpedon John P. , Pawluk April , Nishimasu Hiroshi , Konermann Silvana , Hsu Patrick D.
Published: January 2024

Genomic rearrangements, encompassing mutational changes in the genome such as insertions, deletions, or inversions, are essential for genetic diversity. These rearrangements are typically orchestrated by enzymes involved in fundamental DNA repair processes such as homologous recombination or in the transposition of foreign genetic material by viruses and mobile genetic elements (MGEs). We report that IS110 insertion sequences, a family of minimal and autonomous MGEs, express a structured non-coding RNA that binds specifically to their encoded recombinase. This bridge RNA contains two internal loops encoding nucleotide stretches that base-pair with the target DNA and donor DNA, which is the IS110 element itself. We demonstrate that the target-binding and donor-binding loops can be independently reprogrammed to direct sequence-specific recombination between two DNA molecules. This modularity enables DNA insertion into genomic target sites as well as programmable DNA excision and inversion. The IS110 bridge system expands the diversity of nucleic acid-guided systems beyond CRISPR and RNA interference, offering a unified mechanism for the three fundamental DNA rearrangements required for genome design.
WRKY1 confers resistance to powdery mildew by accelerating SAR and preventing over-immunity in apple
Authors: Lan Liming , Cao Lifang , Zhang Lulu , Fu Weihong , Qu Shenchun , Wang Sanhong
Published: January 2024

Powdery mildew is one of the most serious diseases in apple production. SAR has a broad-spectrum immunity in plants against pathogen. Plants activate SAR against pathogen invasion and also prevent over-immunity. The relevant mechanism is still unknown in apple. In this study, we isolated and identified powdery mildew pathogen from the field and preserved them on the apple tissue culture seedlings. We performed DAP-seq of powdery mildew-inducible WRKY40. WRKY40 positively regulates NPR3like by directly binding to the W-box element of its promoter. NPR3like represses the expression of the PR1 gene in the presence of SA by competing with TGA2 for binding to NPR1. WRKY1 positively regulates WRKY40 by directly binding to the dual W-box element of its promoter, while WRKY1 positively regulates NPR3like by directly binding to the W-box element of its promoter. The expression trends of WRKY1, WRKY40, and NPR3like were basically the same as that of PR1 within 24 h after powdery mildew and SA treatments. Besides, WRKY1 increased SA content by positively regulating EPS1. After inoculation with powdery mildew, the up-regulation of PR1 in RNAi-silenced plants of WRKY1 was more slowly compared with the wild type, and the number of spores and mycelium increased significantly. In summary, we established a new model of NPR3like inhibition of NPR1 activity positively regulated by the WRKY1-WRKY40 module and found that the WRKY1-EPS1 module accelerated the up-regulation of PR1 by increasing the SA content. Finally, we elucidated WRKY1 confers resistance to powdery mildew by accelerating SAR and preventing over-immunity in apple.
A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.
Authors: Tesson Florian , Planel Remi , Egorov Artyom A , Georjon Heloise , Vaysset Hugo , Brancotte Bryan , Neron Bertrand , Mordret Ernest , Atkinson Gemma Catherine , Bernheim Aude , Cury Jean
Published: January 2024

In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021 (Tesson et al., 2022). DefenseFinder is a bioinformatic program designed for the systematic identification of known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 systems. Over the past three years, the number of antiphage systems incorporated into DefenseFinder has grown to 152. The increasing number of known systems makes it a challenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures offers novel possibilities of analysis and should be easily available. To overcome these challenges, we present a hub of resources on defense systems, including: 1) an updated version of DefenseFinder with a web-service search function, 2) a community-curated repository of knowledge on the systems, and 3) precomputed databases, which include annotations done on RefSeq genomes and structure predictions generated by AlphaFold. These pages can be freely accessed for users as a starting point on their journey to better understand a given system. We anticipate that these resources will foster the use of bioinformatics in the study of antiphage systems and will serve the community of researchers who study antiphage systems. This resource is available at: https://defensefinder.mdmlab.fr.
Context-dependent acetylation of the virulence regulator PhoP accounts for carbon-source specific intracellular growth program ofMycobacterium tuberculosis
Authors: Paul Partha , Mehta Khushboo , Ujjainiya Rajat , Bamniya Bhanwar , Thakur Bhuwaneshwar , Goar Harsh , Sarkar Dibyendu
Published: January 2024

Mycobacterium tuberculosisPhoP is essential for intracellular survival and virulence of the tubercle bacilli. Genetic evidences coupled with biochemical studies uncover that PhoP affects various aspects ofM. tuberculosispathophysiology including pH sensing during intracellular adaptation and carbon source utilization. Building on this observation, herein we report essentiality of thephoPlocus in carbon-source specific mycobacterial growth. Further, our results on mycobacterial growth in the presence of different carbon sources suggest accumulation of acetyl CoA, a metabolic intermediate which acetylates major transcription factors. To explore the mechanism, we examinedin vivoacetylation of PhoP, and our results suggest a link between acetylation of PhoP and mycobacterial carbon source utilization. Using a genetic screening, we identified PhoP-specific mycobacterial acetylases. Our two major findings that (a) acidic conditions of growth inhibit PhoP acetylation, which represses PhoP regulon by interfering with DNA binding activity of the regulator and (b) mycobacteria expressing acetylation-defective PhoP shows growth inhibition, together suggest a role of acetylation on mycobacterial growth via carbon-source utilization. These results have implications on intracellular survival and growth program of mycobacteria under varying environmental cues.
Chikungunya Virus Release is Reduced by TIM-1 Receptors Through Binding of Envelope Phosphatidylserine
Authors: Reyes Ballista Judith M. , Hoover Ashley J. , Noble Joseph T. , Acciani Marissa D. , Miazgowicz Kerri L. , Harrison Sarah A. , Tabscott Grace Andrea L. , Duncan Avery , Barnes Don N. , Jimenez Ariana R. , Brindley Melinda A.
Published: January 2024

T-cell immunoglobin and mucin domain protein-1 (TIM-1) mediates entry of Chikungunya virus (CHIKV) into some mammalian cells through the interaction with envelope phospholipids. While this interaction enhances entry, TIM has been shown to tether newly formed HIV and Ebola virus particles, limiting their efficient release. In this study, we investigate the ability of surface receptors such as TIM-1 to sequester newly budded virions on the surface of infected cells. We established a luminescence reporter system to produce Chikungunya viral particles that integrate nano-luciferase and easily quantify viral particles. We found that TIM-1 on the surface of host cells significantly reduced CHIKV release efficiency in comparison to other entry factors. Removal of cell surface TIM-1 through direct cellular knock-out or altering the cellular lipid distribution enhanced CHIKV release. Over the course of infection, CHIKV was able to counteract the tethering effect by gradually decreasing the surface levels of TIM-1 in a process that appears to be mediated by the nonstructural protein 2. This study highlights the importance of phosphatidylserine receptors in mediating not only the entry of CHIKV but also its release and could aid in developing cell lines capable of enhanced vaccine production.

Importance

Chikungunya virus (CHIKV) is an enveloped alphavirus transmitted by the bites of infectious mosquitoes. Infection with CHIKV results in the development of fever, joint pain, and arthralgia that can become chronic and last for months after infection. Prevention of this disease is still highly focused on vector control strategies. In December 2023, a new live attenuated vaccine against CHIKV was approved by the FDA. We aimed to study the cellular factors involved in CHIKV egress, to better understand CHIKV’s ability to efficiently infect and spread among a wide variety of cell lines. We found that TIM-1 receptors can significantly abrogate CHIKV’s ability to efficiently exit infected cells. This information can be beneficial for maximizing viral particle production in laboratory settings and during vaccine manufacturing.
An experimental census of retrons for DNA production and genome editing
Authors: Khan Asim G. , Rojas-Montero Matías , González-Delgado Alejandro , Lopez Santiago C. , Fang Rebecca F. , Shipman Seth L.
Published: January 2024

Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.