bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of viral interference in shaping RSV epidemics following the 2009 H1N1 influenza pandemic
Authors: Li Ke , Thindwa Deus , Weinberger Daniel M , Pitzer Virginia E 
Published: February 2024

ABSTRACTBackgroundDisruptions in respiratory syncytial virus (RSV) activity were observed in different countries following the 2009 influenza pandemic. Given the limited use of non-pharmaceutical interventions, these disruptions do provide an opportunity to probe viral interference due to the out-of-season epidemics. The objectives of the study are twofold: to characterize atypical RSV activity in the United States (US) and to explore the mechanisms underlying changes in RSV epidemics following the pandemic.MethodsLaboratory-confirmed RSV cases across 10 US regions from June 2007 to July 2019 were analyzed. A dynamic time warping method was used to characterize RSV activity in different seasons. A two-pathogen model was constructed to explore viral interference mechanisms. A sampling-importance resampling method was applied to estimate the effects of viral interference.ResultsWe found that RSV activity was reduced following the influenza pandemic in the 2009/10 season across all regions in the US. By contrast, we found an enhanced but delayed RSV epidemic across the US in the 2010/11 season. Using a mathematical model, we identified three potential viral interference mechanisms that could explain the change of RSV activity following the pandemic. The pandemic influenza may interfere with RSV to reduce susceptibility to RSV coinfection, or shorten the RSV infectious period, or decrease RSV infectivity in co-infections.ConclusionsThis study provides statistical evidence for atypical RSV seasons following the influenza pandemic in the US and sheds light on viral interference mechanisms affecting RSV epidemics, offering a model-fitting framework for analyzing surveillance data at the population level.
Investigating brain dynamics and their association with cognitive control in opioid use disorder using naturalistic and drug cue paradigms
Authors: Ye Jean , Mehta Saloni , Peterson Hannah , Ibrahim Ahmad , Saeed Gul , Linsky Sarah , Kreinin Iouri , Tsang Sui , Nwanaji-Enwerem Uzoji , Raso Anthony , Arora Jagriti , Tokoglu Fuyuze , Yip Sarah W. , Hahn C. Alice , Lacadie Cheryl , Greene Abigail S. , Constable R. Todd , Barry Declan T. , Redeker Nancy S. , Yaggi Henry , Scheinost Dustin 
Published: February 2024

AbstractObjectivesOpioid use disorder (OUD) impacts millions of people worldwide. The prevalence and debilitating effects of OUD present a pressing need to understand its neural mechanisms to provide more targeted interventions. Prior studies have linked altered functioning in large-scale brain networks with clinical symptoms and outcomes in OUD. However, these investigations often do not consider how brain responses change over time. Time-varying brain network engagement can convey clinically relevant information not captured by static brain measures.MethodsWe investigated brain dynamic alterations in individuals with OUD by applying a new multivariate computational framework to movie-watching (i.e., naturalistic; N=76) and task-based (N=70) fMRI. We further probed the associations between cognitive control and brain dynamics during a separate drug cue paradigm in individuals with OUD.ResultsCompared to healthy controls (N=97), individuals with OUD showed decreased variability in the engagement of recurring brain states during movie-watching. We also found that worse cognitive control was linked to decreased variability during the rest period when no opioid-related stimuli were present.ConclusionsThese findings suggest that individuals with OUD may experience greater difficulty in effectively engaging brain networks in response to evolving internal or external demands. Such inflexibility may contribute to aberrant response inhibition and biased attention toward opioid-related stimuli, two hallmark characteristics of OUD. By incorporating temporal information, the current study introduces novel information about how brain dynamics are altered in individuals with OUD and their behavioral implications.
School children’s oral health status, behaviours, and dental care utilization: the case of a northern Thailand elementary school
Authors: Pattanaporn Komkham , Kawong Warathaya , Wongwanichwattana Wassana , Chomphrom Kulnan , Chakkathamanukul Natchaphon , Kamsiriphiman Nalinporn , Prasomphon Panithi , Saksurasap Pitchaya , Nilniyom Pansuk , Brondani Mario 
Published: February 2024

ABSTRACTBackgroundAlthough preventable, dental caries remain a serious global public health threat. There are a number of risk factors for the development of dental caries in the general population, and in elementary school children in Thailand in particular, especially if they are from suburban areas.ObjectiveTo identify the prevalence of dental caries in the form of decayed-missing-filled teeth for the permanent (DMFT) and primary (dmft) dentition, and their risk factors among children between 6 and 12 years of age attending a public school in Chiang Rai in northern Thailand.MethodsA cross-sectional study was conducted among 6–12-year-old children attending public education at Thesaban 1 School, Chiang Saen District, Chiang Rai Province in Thailand. All school children from grades 1 to 6 were examined by trained dental students from Mae Fah Luang University’s School of Dentistry in December 2023. Children were clinically examined for DMFT/dmft while demographic information about the children was collected from school records. Children also responded to a standardized 17-item survey about their oral health care behaviours. Descriptive and inferential statistics were used. All tests were set at 95% CI andp>0.05.ResultsA total of 232 children (100% of eligible participants) were examined and 96 (40%) responded to the survey. Most children were Buddhists (n=186, 80.1%), and had at least one permanent tooth with sealant (n=198, 85.3%); 82.5% of the 232 children exhibited dental caries/extraction/fillings in primary teeth. The average dmft was 4.1 (1.8–8.8) and the average DMFT was 1.6 (0.1–3.3). Fifty children (21.5%) had their grandparents as their main caregiver. Children who brushed their teeth without fluoridated toothpaste were 1.99 times more likely to have at least 1 permanent tooth with dental decay than children who used fluoridated toothpaste (p=0.065).ConclusionIn this study, a high percentage of dental caries was observed among children from suburban areas in the northernmost province of Thailand. Public health intervention and oral health promotion remain an immediate need among these children.
EmbB and EmbC Regulate the Sensitivity ofMycobacterium abscessusto Echinomycin
Authors: He Jing , Gao Yamin , Wang Jingyun , Hameed H.M. Adnan , Wang Shuai , Fang Cuiting , Tian Xirong , Zhang Jingran , Han Xingli , Ju Yanan , Tan Yaoju , Ma Junying , Ju Jianhua , Hu Jinxing , Liu Jianxiong , Zhang Tianyu 
Published: February 2024

Treatment ofMycobacterium abscessus(Mab) infection is a major challenge due to its intrinsic resistance to most available drugs. It is thus imperative to find new anti-Mab drugs. In this study, we investigated the activity and intrinsic resistance mechanism of echinomycin (ECH) against Mab. ECH is active against Mab (MIC: 2 µg/mL). TheembCgene knockout strain (MabΔembC) showed hyper-sensitive to ECH (MIC: 0.0078-0.0156 µg/mL). The MICs of ECH-resistant strains screened based on the MabΔembCstrain were 0.25-1 µg/mL. Mutations were found in the EmbB, including Asp306Ala, Asp306Asn, Arg350Gly, Val555Ile, and Gly581Ser, which led to increased resistance to ECH when overexpressed in MabΔembCindividually (0.25-0.5 µg/mL). The EmbB mutants edited by the CRISPR/Cpf1 system became more resistant to ECH (MIC: 0.25-0.5 µg/mL). The permeability of gene-edited and overexpressed Mab strains was reduced, as shown by the ethidium bromide accumulation assay, but it was still significantly higher than that of the parent Mab. To summarize, our study demonstrates that ECH has a strong anti-Mab activity and confirms that EmbB and EmbC are related to the sensitivity of Mab to ECH. EmbB mutation may partially compensate for the function of EmbC.Impact StatementMycobacterium abscessus(Mab) is a rapidly growing, intrinsic multidrug-resistant Mycobacterium. This study demonstrated that echinomycin (ECH) has potent antibacterial activity against Mab, and the mechanism of ECH resistance to Mab is related to EmbB and EmbC. EmbB and EmbC can alter the sensitivity of Mab to ECH by altering the permeability of its cell wall. In addition, there is a functional complementary evolution between EmbB and EmbC to regulate sensitivity to ECH. Overall, our study provides a novel anti-Mab drug candidate ECH and a scientific foundation for developing effective strategies to prevent and control Mab.
The sea urchin intestinal microbiome responds dynamically to food intake and contains nitrogen-fixing symbionts
Authors: Bengtsson Mia M. , Helgesen Marita , Wang Haitao , Fredriksen Stein , Norderhaug Kjell Magnus 
Published: February 2024

ABSTRACTKelp deforestation by sea urchin grazing is a widespread phenomenon globally, with vast consequences for coastal ecosystems. The ability of sea urchins to survive on a kelp diet of poor nutritional quality is not well understood and bacterial communities in the sea urchin intestine may play an important role in digestion. A no-choice feeding experiment was conducted with the sea urchinStrongylocentrotus droebachiensis, offering three different seaweeds as diet, including the kelpSaccharina latissima. Starved sea urchins served as experimental control. Amplicons of the 16S rRNA gene were analyzed from fecal pellets. One dominant symbiont (Psychromonas marina) accounted for 44 % of all sequence reads and was especially abundant in the sea urchins fed seaweed diets. The starved and field captured sea urchins consistently displayed higher diversity than the seaweed-fed sea urchins and displayed a higher predicted abundance of genes involved in nitrogen fixation. Cloning and sequencing of the NifH gene revealed diverse nitrogen fixers. We demonstrate that the sea urchin intestinal microbiome is dynamic, responds to diet and has the capacity for nitrogen fixation. The microbiome thereby reflects the dietary flexibility of these sea urchins, and could be a key component in understanding catastrophic kelp forest grazing events.
High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants
Authors: Fan Tingting , Cheng Yanhao , Wu Yuechao , Liu Shishi , Tang Xu , He Yao , Liao Shanyue , Zheng Xuelian , Zhang Tao , Qi Yiping , Zhang Yong 
Published: February 2024

AbstractCytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools to install precise C-to-T and A-to-G base edits in living organisms. In recently years, a highly efficient ABE based on engineered TadA-8e, known as ABE8e, has been developed to confer highly efficient A-to-G editing in mammalian cells and plants. Interestingly, TadA-8e can be further evolved and engineered to confer cytosine base editing. In this study, we compare in rice and tomato cells a serial of engineered CBEs derived from TadA-8e and identify TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high editing purity, while maintaining the relatively narrow editing window of ABE8e. Excitingly, we show TadDE is a new class of dual base editor where a single deaminase domain promotes simultaneous C-to-T and A-to-G base editing in plant cells. Multiplexed base editing is demonstrated in transgenic rice plants with TadCBEa and TadDE. Furthermore, no off-target effects of TadCBEa and TadDE can be detected by whole genome and transcriptome sequencing of the transgenic lines, suggesting high editing specificity. Finally, we demonstrate two gain-of-function crop engineering applications in rice by using the efficient dual base editor, TadDE. In the first case, herbicide resistance alleles ofOsALSare introduced by TadDE. In the second case, synonymous mutations are generated inOsSPL14, making its transcript resistant toOsMIR156-mediated degradation. Together, this study reports TadA-8e derived CBEs and a dual base editor with high editing activity, purity, and specificity. They are valuable additions to the expanding plant base editing toolbox.
Predictive and error coding for vocal communication signals in the songbird auditory forebrain
Authors: Rudraraju Srihita , Turvey Michael E. , Theilman Bradley H. , Gentner Timothy Q. 
Published: February 2024

AbstractPredictive coding posits that sensory signals are compared to internal models, with resulting prediction-error carried in the spiking responses of single neurons. Despite its proposal as a general cortical mechanism, including for speech processing, whether or how predictive coding functions in single-neuron responses to vocal communication signals is unknown. As a proxy internal model, we developed a neural network that uses current sensory context to predict future spectrotemporal features of a vocal communication signal, birdsong. We then represent birdsong as either weighted sets of latent predictive features evolving in time, or as time-varying prediction-errors that reflect the difference between ongoing network-predicted and actual song. Using these spectrotemporal, predictive, and prediction-error song representations, we fit linear/non-linear receptive fields to single neuron responses recorded from caudomedial nidopallium (NCM), caudal mesopallium (CMM) and Field L, analogs of mammalian auditory cortices, in anesthetized European starlings,Sturnus vulgaris, listening to conspecific songs. In all three regions, the predictive features of song yield the single best model of song-evoked spiking responses, but unique information about all three representations (signal, prediction, and error) is carried in the spiking responses to song. The relative weighting of this information varies across regions, but in contrast to many computational predictive coding models neither predictive nor error responses are segregated in separate neurons. The continuous interplay between prediction and prediction-error is consistent with the relevance of predictive coding for cortical processing of temporally patterned vocal communication signals, but new models for how prediction and error are integrated in single neurons are required.
KoRV-related retroviruses in diverse Australian and African rodent species
Authors: Hayward Joshua A. , Tachedjian Gilda 
Published: February 2024

AbstractThe koala retrovirus (KoRV) is a key contributor to the ongoing decline of Australia’s koala population. KoRV has only been found in koalas and its enigmatic origins, as well as that of its close relative, the gibbon ape leukemia virus (GALV), have been a source of enduring debate. Bats and rodents are each proposed as major reservoirs of interspecies transmission with ongoing efforts to identify additional animal hosts of KoRV-related retroviruses. In this study we identified nine rodent species as novel hosts of KoRV-related retroviruses. Included among these hosts are two African rodents, revealing the first appearance of this clade beyond the Australian and Southeast Asian region. One of these African rodents,Mastomys natalensis, carries an endogenous KoRV-related retrovirus that is fully intact and potentially still infectious. Our findings suggest that rodents are the major carriers of KoRV-related retroviruses, with a potential point of origin in Southeast Asia.
Centromedian thalamic deep brain stimulation for idiopathic generalized epilepsy – case series and target analysis
Authors: Park Sihyeong , Agashe Shruti , Osman Gamaleldin , Simpson Hugh D. , Miller Kai J. , Van Gompel Jamie J. , Starnes Keith , Lundstrom Brian N. , Worrell Gregory A. , Gregg Nicholas M. 
Published: February 2024

AbstractIntroductionThere is a lack of treatment options for individuals with drug resistant idiopathic generalized epilepsy (IGE). Small, limited case series suggest that centromedian thalamus deep brain stimulation (CM-DBS) may be an effective treatment option. The optimal CM-DBS target for IGE is underexamined. Here, we present a retrospective analysis of CM-DBS targeting and efficacy for five patients with drug-resistant IGE.MethodsThis single-center case series study included all patients with drug resistant IGE treated with CM-DBS to date. Seizure outcomes were measured with patient-reported seizure frequency. Baseline frequency was taken from the visit immediately before implantation, and it was compared with the seizure frequency from the most recent visit. Stimulation parameters from last clinic visit were used to determine the volume of tissue activated (VTA) by DBS. Lead proximity to target, and VTA overlap with CM nucleus was performed using an open-source toolbox (Lead-DBS 3.0, SimBio/FieldTrip). Associations between the intersection of the VTA and CM nucleus, and seizure outcomes were measured using Spearman’s rank correlation.ResultsFive patients were identified and included in the study. Median age was 31 (22-45). Median baseline frequency of convulsive seizure was 1.5 per month (0-3.5). Median follow-up time was 13 months (3-23). Median convulsive seizure frequency reduction was 60% (−200-100%). One patient had only absence seizures, with >99% absence seizure frequency reduction. Four out of five subjects had electrode contacts positioned within the CM nucleus target, all of whom had >50% reduction in primary semiology seizure frequency (3 subjects with convulsive seizures, 1 patient with absence seizures). Spearman’s rho was 0.90 (P=0.025). Volumetric “sweet-spot” mapping revealed best outcomes were correlated with stimulation of the middle ventral CM nucleus.ConclusionOur findings suggest that CM-DBS can be an effective treatment for patients with IGE. The extent of overlap between the VTA by DBS and CM nucleus is correlated with the degree of seizure reduction, highlighting the importance of accurate targeting and volumetric targeting analysis.
Proteomics data in vitiligo: a scoping review
Authors: Berrevoet Danique , Van Nieuwerburgh Filip , Deforce Dieter , Speeckaert Reinhart 
Published: February 2024

AbstractAn unbiased screening of which proteins are deregulated in vitiligo using proteomics can offer an enormous value. It could not only reveal robust biomarkers for detecting disease activity but can also identify which patients are most likely to respond to treatments. We performed a scoping review searching for all articles using proteomics in vitiligo. Eight manuscripts could be identified. Unfortunately, very limited overlap was found in the differentially expressed proteins between studies (15 out of 272; 5,51%) with variable degrees of the type of proteins and a substantial variety in the prevalence of acute phase proteins (range: 6-65%). Proteomics research has therefore brought little corroborating evidence on which proteins are differentially regulated between vitiligo patients and healthy controls or between active and stable vitiligo patients. While a limited patient size is an obvious weakness for several studies, an incomplete description of patient characteristics is an unfortunate and avoidable shortcoming. Additionally, the variations in the used methodology and analyses may further contribute to the overall observed variability. Nonetheless, more recent studies investigating the response to treatment seem to be more robust, as more differentially expressed proteins that have previously been confirmed to be involved in vitiligo were found. The further inclusion of proteomics analyses in clinical trials is recommended to increase insights into the pathogenic mechanisms in vitiligo and identify reliable biomarkers or promising drug targets. A harmonization in the study design, reporting and proteomics methodology could vastly improve the value of vitiligo proteomics research.
Patterns of blunt and cigar use in the United States, 2015-2019
Authors: Jensen Jessica K , Ganz Ollie , Tomaino Marisa , Glasser Allison M , Sterling Kymberle , Delnevo Cristine D , Bover Manderski Michelle T 
Published: February 2024

AbstractBackgroundThe use of cigars for blunts (i.e., cannabis rolled in cigar paper) is well-documented; proportions of cigar and blunt use and associated characteristics are less studied.MethodsPooled data from the 2015-2019 National Survey on Drug Use and Health (NSDUH) were analyzed in 2023. Respondents aged 12+ who reported past 30-day cigar use were categorized into three mutually exclusive use categories: (1) exclusively cigars, (2) exclusively blunts, and (3) both cigars and blunts. We examined associations between cigar-blunt use category and sociodemographic characteristics.ResultsAmong people 12 and older who reported past 30-day cigar use, 48.6% (95% CI=47.6-49.6) reported exclusive cigar use; 44.3% (95% CI=43.3-45.3) reported exclusive blunt use; and 7.2% (95% CI=6.8-7.6) reported cigars and blunts. The prevalence differed by age, with exclusively blunts most prevalent among youth (72.5% [95% CI=70.7-74.3]) and young adults (62.4% [95% CI=61.4-63.5]), and exclusively cigars most prevalent among adults 26+ (61.2% [95% CI=59.8-62.5]). Exclusive blunt users smoked more days in the past month (17.5; 95% CI=16.8-18.2), compared to 13.8 days (95% CI=13.2-14.4) for cigar and blunt users, and 7.7 days (95% CI=7.5-8.0) for exclusive cigar users. There were significant differences in characteristics, with exclusive blunt use more prevalent among female (41.6%; 95% CI=40.3-42.9) and Hispanic (18.2%; 95% CI=17.3-19.2) participants.ConclusionsExclusive blunt use was the most prevalent pattern of past-30-day cigar use among youth and young adults. Those who use cigars as blunts smoke more cigars per month, suggesting this may be an important group for additional education and policy efforts.
Global Assessment of Palliative Care Need: Serious Health-Related Suffering Measurement Methodology
Authors: Kwete Xiaoxiao J , Bhadelia Afsan , Arreola-Ornelas Héctor , Mendez Oscar , Rosa William E. , Connor Stephen , Downing Julia , Jamison Dean , Watkins David , Calderon Renzo , Cleary Jim , Friedman Joe , De Lima Liliana , Ntizimira Christian , Pastrana Tania , Pérez-Cruz Pedro E. , Spence Dingle , Rajagopal M.R. , Enciso Valentina Vargas , Krakauer Eric L. , Radbruch Lukas , Knaul Felicia Marie 
Published: February 2024

AbstractInequities and gaps in palliative care access are a serious impediment to health systems especially low- and middle-income countries and the accurate measurement of need across health conditions is a critical step to understanding and addressing the issue. Serious Health-related Suffering (SHS) is a novel methodology to measure the palliative care need and was originally developed by The Lancet Commission on Global Access to Palliative Care and Pain Relief. In 2015, the first iteration – SHS 1.0 – was estimated at over 61 million people worldwide experiencing at least 6 billion days of SHS annually as a result of life-limiting and life-threatening conditions. In this paper, an updated methodology - SHS2.0 - is presented building on the work of the Lancet Commission and detailing calculations, data requirements, limitations, and assumptions. The updates to the original methodology focus on measuring the number of people who die with (decedents) or live with (non-decedents) SHS in a given year to assess the number of people in need of palliative care across health conditions and populations. Detail on the methodology for measuring the number of days of SHS that was pioneered by the Lancet Commission, is also shared, as this second measure is essential for determining the health system responses that are necessary to address palliative care need and must be a priority for future methodological work on SHS. The discussion encompasses opportunities for applying SHS to future policy making assessment of future research priorities particularly in light of the dearth of data from low- and middle-income countries, and sharing of directions for future work to develop SHS 3.0.