bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs
Authors: Özden Furkan , Minary Peter 
Published: September 2024

Abstract
CRISPR-based genome editing technologies have revolutionised the field of molecular biology, offering unprecedented opportunities for precise genetic manipulation. However, off-target effects remain a significant challenge, potentially leading to unintended consequences and limiting the applicability of CRISPR-based genome editing technologies in clinical settings. Current literature predominantly focuses on point predictions for off-target activity, which may not fully capture the range of possible outcomes and associated risks. Here, we present crispAI, a neural network architecture-based approach for predicting uncertainty estimates for off-target cleavage activity, providing a more comprehensive risk assessment and facilitating improved decision-making in single guide RNA (sgRNA) design. Our approach makes use of the count noise model Zero Inflated Negative Binomial (ZINB) to model the uncertainty in the off-target cleavage activity data. In addition, we present the first-of-its-kind genome-wide sgRNA efficiency score, crispAI-aggregate, enabling prioritization among sgRNAs with similar point aggregate predictions by providing richer information compared to existing aggregate scores. We show that uncertainty estimates of our approach are calibrated and its predictive performance is superior to the state-of-the-art in silico off-target cleavage activity prediction methods. The tool and the trained models are available at https://github.com/furkanozdenn/crispr-offtarget-uncertainty.
Striving for clarity in language about gene expression
Authors: Cunningham Ana S G , Gorospe Myriam 
Published: September 2024

Abstract
What do we mean when we say ‘gene expression’? In the decades following Crick's 1958 central dogma of molecular biology, whereby genetic information flows from DNA (genes) to RNA (transcripts) to protein (products), we have learned a great deal about DNA, RNA, proteins, and the ensuing phenotypic changes. With the advent of high-throughput technologies (1990s), molecular biologists and computer scientists forged critical collaborations to understand the vast amount of data being generated, rapidly escalating gene expression research to the ‘omics’ level: entire sets of genes (genomes), transcribed RNAs (transcriptomes), and synthesized proteins (proteomes). However, some concessions came to be made for molecular biologists and computer scientists to understand each other—one of the most prevalent being the increasingly widespread use of ‘gene’ to mean ‘RNAs originating from a DNA segment’. This loosening of terminology, we will argue, creates ambiguity and confusion. We propose guidelines to increase precision and clarity when communicating about gene expression, most notably to reserve ‘gene’ for the DNA template and ‘transcript’ for the RNA transcribed from that gene. Striving to use perspicuous terminology will promote rigorous gene expression science and accelerate discovery in this highly promising area of biology.
CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters
Authors: He Fuqiang , Liu Xinpeng , Tang Min , Wang Haiyi , Wu Yun , Liang Shufang 
Published: September 2024

Abstract
The efficient refactoring of natural product biosynthetic gene clusters (BGCs) for activating silent BGCs is a central challenge for the discovery of new bioactive natural products. Herein, we have developed a simple and robust CRISETR (CRISPR/Cas9 and RecET-mediated Refactoring) technique, combining clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 and RecET, for the multiplexed refactoring of natural product BGCs. By this approach, natural product BGCs can be refactored through the synergistic interaction between RecET-mediated efficient homologous recombination and the CRISPR/Cas9 system. We first performed a proof-of-concept validation of the ability of CRISETR, and CRISETR can achieve simultaneous replacement of four promoter sites and marker-free replacement of single promoter site in natural product BGCs. Subsequently, we applied CRISETR to the promoter engineering of the 74-kb daptomycin BGC containing a large number of direct repeat sequences for enhancing the heterologous production of daptomycin. We used combinatorial design to build multiple refactored daptomycin BGCs with diverse combinations of promoters different in transcriptional strengths, and the yield of daptomycin was improved 20.4-fold in heterologous host Streptomyces coelicolor A3(2). In general, CRISETR exhibits enhanced tolerance to repetitive sequences within gene clusters, enabling efficient refactoring of diverse and complex BGCs, which would greatly accelerate discovery of novel bioactive metabolites present in microorganism.
Advancing microRNA target site prediction with transformer and base-pairing patterns
Authors: Bi Yue , Li Fuyi , Wang Cong , Pan Tong , Davidovich Chen , Webb Geoffrey I , Song Jiangning 
Published: September 2024

Abstract
MicroRNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson–Crick base pairings within the seed region, referred to as canonical sites. However, emerging evidence suggests that perfect seed matches are not a prerequisite for miRNA-mediated regulation, underscoring the importance of also recognizing imperfect, or non-canonical, sites. To address this challenge, we propose Mimosa, a new computational approach that employs the Transformer framework to enhance the prediction of miRNA targets. Mimosa distinguishes itself by integrating contextual, positional and base-pairing information to capture in-depth attributes, thereby improving its predictive capabilities. Its unique ability to identify non-canonical base-pairing patterns makes Mimosa a standout model, reducing the reliance on pre-selecting candidate targets. Mimosa achieves superior performance in gene-level predictions and also shows impressive performance in site-level predictions across various non-human species through extensive benchmarking tests. To facilitate research efforts in miRNA targeting, we have developed an easy-to-use web server for comprehensive end-to-end predictions, which is publicly available at http://monash.bioweb.cloud.edu.au/Mimosa.
Accelerated discovery and miniaturization of novel single-stranded cytidine deaminases
Authors: Deng Jiacheng , Li Xueyuan , Yu Hao , Yang Lin , Wang Ziru , Yi Wenfeng , Liu Ying , Xiao Wenyu , Xiang Hongyong , Xie Zicong , Lv Dongmei , Ouyang Hongsheng , Pang Daxin , Yuan Hongming 
Published: September 2024

Abstract
Cytidine base editors (CBEs) hold significant potential in genetic disease treatment and in breeding superior traits into animals. However, their large protein sizes limit their delivery by adeno-associated virus (AAV), given its packing capacity of &lt;4.7 kb. To overcome this, we employed a web-based fast generic discovery (WFG) strategy, identifying several small ssDNA deaminases (Sdds) and constructing multiple Sdd-CBE 1.0 versions. SflSdd-CBE 1.0 demonstrated high C-to-T editing efficiency, comparable to AncBE4max, while SviSdd-CBE 1.0 exhibited moderate C-to-T editing efficiency with a narrow editing window (C3 to C5). Utilizing AlphaFold2, we devised a one-step miniaturization strategy, reducing the size of Sdds while preserving their efficiency. Notably, we administered AAV8 expressing PCSK9 targeted sgRNA and SflSdd-CBEs (nSaCas9) 2.0 into mice, leading to gene-editing events (with editing efficiency up to 15%) and reduced serum cholesterol levels, underscoring the potential of Sdds in gene therapy. These findings offer new single-stranded editing tools for the treatment of rare genetic diseases.
Establishing Reference Intakes for Creatine in Infants Aged 0 to 12 Months
Authors: Ostojic Sergej M 
Published: September 2024

Abstract
Creatine is recognized as a conditionally essential nutrient in certain populations; however, there is a lack of established reference values across different life stages. Infants rely exclusively on dietary creatine from human milk for their first 6 months; evaluating creatine adequacy in this population can be estimated based on preliminary data regarding the intake needed to promote optimal growth. This special article explores creatine requirements for infants aged 0 to 12 months, presents a summary of creatine content in human milk, and proposes reference intakes for creatine in this population.
Rediscovering a Forgotten Link: TSPO and RIM-BP1 in Appetite Regulation
Authors: Wang Joshua , Moody Hayley , Beecher Kate , Chehrehasa Fatemeh 
Published: September 2024

Abstract
The translocator protein of 18 kDa (TSPO) and RIM binding protein 1 (RIM-BP1) are both heavily expressed in neurons at the olfactory bulb. These proteins have overlapping functional profiles and are both implicated in the development of obesity. Over 20 years ago, a yeast 2-hybrid experiment discovered that RIM-BP1 interacts with a peptide constructed from a fraction of the TSPO sequence. Considering these data, the authors predict that the interaction between RIM-BP1 and TSPO could alter the olfactory system’s mediation of appetite. Despite the therapeutic potential of this interaction, it has never been confirmed if the full TSPO protein and RIM-BP1 interact. The interaction is instead often cited as physiologically irrelevant. This commentary revisits the forgotten interaction between TSPO and RIM-BP1, reviewing all relevant literature discussing their relationship. Contrary to common discourse that the RIM-BP1 and TSPO are potential binding partners, while the interaction may regulate many neurological functions, existing evidence suggests that the interaction would have a specific role in odor-guided appetite. Further research into the nutritional neuroscientific consequences of TSPO/RIM-BP1 interactions should therefore be conducted.
Economic impact of large earthquakes: lessons from residential property values
Authors: Paudel Jayash 
Published: September 2024

Abstract
Understanding how economic agents respond to seismic shocks in a developing country setting is crucial to evaluating the economic costs of natural disasters. This article makes use of the quasi-random spatial and temporal nature of ground tremors to estimate the economic impact of the April 2015 earthquake on residential property values in Nepal. Regression estimates from the difference-in-differences research design show that residential property values declined by about 40.52 percentage points in areas with high seismic intensity. The event study model illustrates that these negative economic effects are more pronounced between 12 and 24 months after the incidence of the earthquake. Findings further underscore the underlying mechanism of physical damage and indicate that residential properties with weaker outer walls, foundations and roof materials became more susceptible to the earthquake.
Evaluation of Turnaround Times for Antigen Testing in Hospitalized Patients With Histoplasmosis and Blastomycosis
Authors: Dalton Liam M , Kauffman Carol A , Richards Blair , Miceli Marisa H 
Published: September 2024

AbstractReview of histoplasmosis and blastomycosis antigen testing for 39 patients hospitalized with these diseases found that there were significantly longer turnaround times between the time of specimen collection and receipt of positive test results among those patients who had worse outcomes.
Optimization of the Diagnosis of Central Nervous System Infections in Vietnamese Hospitals: Results From a Retrospective Multicenter Study
Authors: Dong Do Van , Boutin Sébastien , Sang Vu Viet , Manh Nguyen Dang , Hoan Nghiem Xuan , Quang Hoang Xuan , Lien Tran Thi , Trang Van Dinh , The Nguyen Trong , Linh Le Thi Kieu , Schmauder Kristina , Ueltzhöffer Viola , Hafza Nourhane , Hauswaldt Susanne , Rupp Jan , Kremsner Peter G , Song Le Huu , Nurjadi Dennis , Peter Silke , Velavan Thirumalaisamy P 
Published: September 2024

Abstract

Introduction
Central nervous system infections pose significant health challenges, particularly in low- and middle-income countries, because of high morbidity and mortality rates. Rapid and accurate diagnosis is essential for effective treatment to prevent adverse outcomes. Traditional culture-based diagnostics are often slow and lack specificity. This study evaluates the BioFire FilmArray Meningitis/Encephalitis (FAME) Panel against standard diagnostics in Vietnam to assess its clinical impact and suitability for local epidemiology.

Methods
We conducted a prospective study involving 330 patients with suspected central nervous system infections at 4 hospitals in northern Vietnam from July 2022 to April 2023. Cerebrospinal fluid samples were analyzed using routine culture methods and FAME. We compared pathogen detection rates and assessed the potential clinical impact of FAME results on patient management.

Results
Of the 330 cerebrospinal fluid specimens, 64 (19%) were positive by either conventional diagnostics (n = 48) and/or FAME (n = 33). The agreement between FAME and conventional diagnostics was 87%. Key pathogens Mycobacterium tuberculosis (n = 7), Klebsiella pneumoniae (n = 5), Streptococcus suis (n = 5), Epstein-Barr virus (n = 3), Acinetobacter baumannii (n = 1), and Trichosporon asahii (n = 1) were not detected by FAME. Classical meningitis parameter clinical symptoms, altered glucose, protein, and pleocytosis were good predictors of FAME positivity, indicating their utility in optimizing local diagnostic algorithms.

Conclusions
FAME complements traditional diagnostics by offering rapid and broad pathogen detection, crucial for timely and appropriate therapy. However, its effectiveness varies with local epidemiology, and it should not replace conventional methods entirely. Tailoring diagnostic panels to regional pathogen prevalence is recommended to enhance diagnostic accuracy and clinical outcomes in low- and middle-income countries.
Gene-based drug therapy for children and youth treated with psychoactive medications
Authors: Verstegen Ruud H J , Cohn Iris , Feldman Mark E , Gorman Daniel , Ito Shinya 
Published: September 2024

Abstract
Psychoactive medications are increasingly used to treat children and youth with mental health conditions, but individual variations in response highlight the need for precision medicine. Pharmacogenetic (PGx) testing is a key component of precision medicine. The number of commercial pharmacogenetic testing companies promoting PGx, with the promise of achieving individualized and effective treatment of mental health conditions, has grown exponentially in recent years. Scientific evidence supporting the use of PGx to manage mental health conditions is limited, especially for paediatric populations. This practice point outlines steps guiding the use and interpretation of PGx testing for psychoactive medications in clinical settings, along with key supportive resources. Practice guidelines have been developed for variants in pharmacogenes encoding cytochrome P450 drug-metabolizing enzymes (e.g., CYP2C19, CYP2D6, CYP2C9) as one determinant of drug concentrations in blood, which can support both drug choice and dosing strategy for certain anti-psychotics, anti-depressants, and anti-epileptics. Adverse drug reactions to some anti-epileptic drugs (e.g., carbamazepine and phenytoin) have been associated with certain human leukocyte antigen types and variants in DNA polymerase gamma (POLG; valproic acid). Evidence remains limited for genetic variants of drug target proteins, making it challenging to identify patients with altered treatment responses at a therapeutic blood concentration.
Improving cycling safety for children and youth
Authors: Rosenfield Daniel , Fuselli Pamela , Beno Suzanne 
Published: September 2024

Abstract
Cycling remains a popular activity for children and youth around the world, combining the fun of moving at speed with numerous health and societal benefits. However, cycling is also associated with risk for serious injury and death. Over the past decade, research has increasingly shown that improving safety for cyclists depends, in large part, on the environment they are cycling in as well as on individual safety measures such as helmet use. The pandemic provided greater opportunity for many children and youth to engage in cycling, and refocused public attention on safer cycling infrastructure such as protected bike lanes. This statement reviews the evidence supporting safer cycling infrastructure for children and youth along with the physical and mental health benefits of cycling. The advantages of active transportation for young people, and how the built environment influences their cycling safety and uptake, are discussed. An overview of measures individuals can take to improve cycling safety is followed by recommendations for clinicians, the cycling community, parents, and policy-makers.
At2-MMP Is Required for Attenuation of Cell Proliferation during Wound Healing in Incised Arabidopsis Inflorescence Stems
Authors: Machfuudzoh Afiifah , Pitaksaringkarn Weerasak , Koshiba Ryo , Higaki Takumi , Rakwal Randeep , Ohba Yusuke , Asahina Masashi , Satoh Shinobu , Iwai Hiroaki 
Published: September 2024

Abstract
Wound healing of partially incised Arabidopsis inflorescence stems constitutes cell proliferation that initiates mainly in pith tissues about 3 d after incision and the healing process that completes in about 7 d. Although the initiation mechanisms of cell proliferation have been well documented, the suppression mechanisms remain elusive. Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases well known as proteolytic enzymes in animal system functioning in extracellular matrix remodeling during physiological and pathological processes, including tissue differentiation, growth, defense, wound healing and control of cancer growth. In this study, we report that At2-MMP might contribute to the suppression mechanism for cell proliferation during the tissue-repair process of incised inflorescence stems. At2-MMP transcript was gradually upregulated from day 0 to 5 after incision and slightly decreased on day 7. Morphological analysis of incised stem of defected mutant at2-mmp revealed significantly enhanced cell proliferation around the incision site. Consistent with this, semi-quantitative analysis of dividing cells displayed a significant increment in the number of dividing cells in at2-mmp as compared to wild type. These results showed that the upregulation of At2-MMP at a later stage of the wound-healing process is likely to be involved in the completion of the process by attenuating cell proliferation.
Dominant-Negative KAI2d Paralogs Putatively Attenuate Strigolactone Responses in Root Parasitic Plants
Authors: White Alexandra R F , Kane Annalise , Ogawa Satoshi , Shirasu Ken , Nelson David C 
Published: September 2024

Abstract
Many root parasitic plants in the Orobanchaceae use host-derived strigolactones (SLs) as germination cues. This adaptation facilitates attachment to a host and is particularly important for the success of obligate parasitic weeds that cause substantial crop losses globally. Parasite seeds sense SLs through ‘divergent’ KARRIKIN INSENSITIVE2 (KAI2d)/HYPOSENSITIVE TO LIGHT α/β-hydrolases that have undergone substantial duplication and diversification in Orobanchaceae genomes. After germination, chemotropic growth of parasite roots toward a SL source also occurs in some species. We investigated which of the seven KAI2d genes found in a facultative hemiparasite, Phtheirospermum japonicum, may enable chemotropic responses to SLs. To do so, we developed a triple mutant Nbd14a,b kai2i line of Nicotiana benthamiana in which SL-induced degradation of SUPPRESSOR OF MORE AXILLARY GROWTH2 (MAX2) 1 (SMAX1), an immediate downstream target of KAI2 signaling, is disrupted. In combination with a transiently expressed, ratiometric reporter of SMAX1 protein abundance, this mutant forms a system for the functional analysis of parasite KAI2d proteins in a plant cellular context. Using this system, we unexpectedly found three PjKAI2d proteins that do not trigger SMAX1 degradation in the presence of SLs. Instead, these PjKAI2d proteins inhibit the perception of low SL concentrations by SL-responsive PjKAI2d in a dominant-negative manner that depends upon an active catalytic triad. Similar dominant-negative KAI2d paralogs were identified in an obligate hemiparasitic weed, Striga hermonthica. These proteins suggest a mechanism for attenuating SL signaling in parasites, which might be used to enhance the perception of shallow SL gradients during root growth toward a host or to restrict germination responses to specific SLs.
Unraveling the Magmatic-to-Carbothermal Processes in the Ba–Sr–REE Mineralization of the Sevattur Carbonatites, India
Authors: Dey Monojit , Chakrabarty Aniket , Mitchell Roger H , Bhattacharjee Sourav , Pal Supratim , Kynicky Jindrich , Drüppel Kirsten 
Published: September 2024

AbstractThe Neoproterozoic Sevattur carbonatite complex (India) consists of calcite carbonatite, silicate-poor- and silicate-rich (banded and blue) dolomite carbonatite. The trace element composition of the calcite and ferroan dolomite shows that most of them have magmatic characteristics. The predominance of dolomite carbonatite over calcite carbonatite and the absence of a genetically related silicate suite at Sevattur suggest a dolomitic parental magma derived by the direct melting of the mantle. Regardless of the prevalent magmatic character of the Sevattur carbonatites they host a plethora of Ba–Sr–REE minerals formed throughout the orthomagmatic-to-carbothermal stages under varying activities of ${\mathrm{F}}^{-}$,${\mathrm{CO}}_3^{2-}$, ${\mathrm{PO}}_4^{3-},\kern0.5em$and ${\mathrm{SO}}_4^{2-}$. The orthomagmatic stage begins with the crystallization of calcite carbonatite containing xenocrystic diopside, antecrystic Y-bearing calcite (Cal-I), and primary benstonite, apatite, and richterite in a Sr–Mg-rich calcite (Cal-II) matrix. Fractionation of apatite, carbocernaite, and cordylite-(Ce) together with the enrichment of Mg, Fe, Na, and F in late-magmatic stages, forms the dolomite carbonatite. The decomposition of benstonite to norsethite, Ba–Ca carbonate, and strontianite occurs within dolomite carbonatite at the same stage with minimal wall-rock assimilation. Interaction between the xenocrystal clinopyroxenite and the primary magma during late-magmatic stages has resulted in the formation of aegirine and phlogopite in calcite carbonatite. Similarly, the prolonged assimilation of clinopyroxenite by the evolving magma leads to the formation of magnesio-riebeckite and magnesio-arfvedsonite within the banded- and blue carbonatites. The increasing activities of ${\mathrm{PO}}_4^{3-},{\mathrm{SO}}_4^{2-}$, and H2O during the carbothermal stage, destabilizes precursor carbocernaite and cordylite-(Ce), resulting in an assemblage consisting of synchysite-(Ce), ancylite-(Ce), daqingshanite, hydroxylbastnäsite-(Ce), ferriallanite-(Ce), monazite-(Ce), and baryte in dolomite carbonatite. In the banded carbonatite, the carbothermal stage is characterized by ferri-winchite, tremolite-actinolite, and phlogopite crystallization. Further contamination and differentiation of the carbothermal fluid have resulted in the crystallization of quartz and albite in blue carbonatite. Phlogopitization within the blue carbonatite and clinopyroxenite results from late K enrichment in the carbothermal fluids.