bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel SCCmec variants in clonal complex 398 and lineage-specific pseudo-SCCmec identified in ST88 MRSA from invasive bloodstream infections in China
Authors: Zhou Wangxiao , Jin Ye , Shen Ping , Chen Weiwei , Chen Yunbo , Xiao Yonghong 
Published: August 2023

Abstract

Background
Methicillin resistance in Staphylococcus aureus is primarily due to the mecA gene found in highly diverse staphylococcal cassette chromosome mec (SCCmec) elements, with an increasing number of variants being continually discovered.

Objectives
To characterize two novel SCCmec variants identified in clonal complex (CC) 398 strains and lineage-specific pseudo-SCCmec elements in the ST88 clone.

Methods
WGS and comparative genomic analysis were used to elucidate the SCCmec element diversity of representative isolates.

Results
The non-typeable 47 kb SCCmec found in the CC398 strain SKLX55795 represents a novel subtype of XIV, showing significant differences in structural organization and genetic content within the joining regions compared with the XIV element from the prototype strain SC792. This unique subtype comprised remnants from various mobile genetic elements that encode antimicrobial resistance genes, ultimately forming a large MDR region. Genome analysis of CC398 strain SKLX61416 revealed the presence of a novel 50 kb composite SCCmec with two distinct domains, carrying the ccr gene complexes 5/8 and containing genes for the detoxification of arsenic and sulphide. Further sequence analysis disclosed that 44.23% (23/52) of ST88 strains in our collection carried a lineage-specific pseudo-SCCmec, termed ΨSCCmecST88. This ΨSCCmecST88 harboured the mec gene complex C2, along with a series of genes associated with heavy metal resistance, but lacked an approximately 28 kb region encompassing the ccr gene complex.

Conclusions
Our findings provide evidence for the ongoing evolution of SCCmec elements within the CC398 and ST88 clones, underscoring the need for further surveillance to understand the biological significance of these elements.
Disinfection by-products in drinking water and risk of colorectal cancer: a population-based cohort study
Authors: Helte Emilie , Säve-Söderbergh Melle , Larsson Susanna C , Martling Anna , Åkesson Agneta 
Published: August 2023

Abstract

Background
Colorectal cancer is the third most common malignancy worldwide and is strongly linked to lifestyle and environmental risk factors. Although several drinking-water disinfection by-products are confirmed rodent carcinogens, the evidence in humans for carcinogenicity associated with these by-products, including colorectal cancer, is still inconclusive.

Methods
We assessed the association of long-term exposure to trihalomethanes (THMs), the most prevalent disinfection by-products in chlorinated drinking water, with incidence of colorectal cancer in 58 672 men and women in 2 population-based cohorts. Exposure was assessed by combining long-term information of residential history with drinking water–monitoring data. Participants were categorized according to no exposure, low exposure (&lt;15 µg/L), and high exposure (≥15 µg/L). Incident cases of colorectal cancer were ascertained by use of the Swedish National Cancer Register.

Results
During an average follow-up of 16.8 years (988 144 person-years), 1913 cases of colorectal cancer were ascertained (1176 cases in men and 746 in women, respectively). High THM concentrations in drinking water (≥15 µg/L) were associated with increased risk of colorectal cancer in men (hazard ratio = 1.26, 95% confidence interval = 1.05-1.51) compared with no exposure. When subsites were assessed, the association was statistically significant for proximal colon cancer (hazard ratio = 1.59, 95% confidence interval = 1.11 to 2.27) but not for distal colon cancer or rectal cancer. In women, we observed overall no association of THMs with colorectal cancer.

Conclusion
These results add further evidence that disinfection by-products in drinking water may be a possible risk factor for proximal colon cancer in men. This observation was made at THM concentrations lower than those in most previous studies.
The Making of a Gentleman and a Detective: Tales of Crime, Respectability, and Surveillance from a Colonial Metropolis
Authors: Ghosh Anindita 
Published: August 2023

Abstract
Priyanath Mukhopadhyay (also referred to as PM subsequently) enjoyed an extraordinary career in the colonial police force in Calcutta, where he served as a detective from 1878 to 1911. In his later life, he wrote as a bhadralok and a detective—both important parts of his fashioned self-identity—using narratives of crime to showcase his rare professional expertise and his responsibilities as a cultured upholder of the law. Through an examination of Priyanath’s serialized police tales, it is possible to see how crime writing forged the values of respectability and civic sensibilities, and shaped the moral fiber of an urban society that appeared to be falling apart at its seams. Examining criminal activities in colonial Calcutta as recoverable from PM’s writings affords glimpses of a city being reordered by its material wealth, social aspirations, and moral attitudes. PM’s tales attempt to face this challenge by forging a moral authority in the finely calibrated colonial order. His readers too were evidently invested in it as they endorsed this stand with their purse, leading to soaring circulation figures. The middle classes of Calcutta emerge in these tales as part and parcel of Priyanath’s policing, providing neighborhood and community surveillance networks and backing up the efforts of their detective hero. PM wrote very much as a social commentator as well as a police officer, reaffirming traditional social and domestic values, and frowning upon transgression of class and gender boundaries. What also comes alive is the city itself—the spaces laid bare or concealed by crime—the writing providing access to different topographies of urban knowledge and information networks.
Promoter deletion in the soybean Compact mutant leads to overexpression of a gene with homology to the C20-gibberellin 2-oxidase family
Authors: Liu Xing , Wickland Daniel P , Lin Zhicong , Liu Quilin , Dos Santos Lucas Borges , Hudson Karen A , Hudson Matthew E 
Published: August 2023

Abstract
Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.
Gene editing of non-coding regulatory DNA and its application in crop improvement
Authors: Chen Yu-Hao , Lu Jun , Yang Xia , Huang Li-Chun , Zhang Chang-Quan , Liu Qiao-Quan , Li Qian-Feng 
Published: August 2023

Abstract
The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.
Inferring the Direction of Introgression Using Genomic Sequence Data
Authors: Thawornwattana Yuttapong , Huang Jun , Flouri Tomáš , Mallet James , Yang Ziheng 
Published: August 2023

Abstract
Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here, we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences from Heliconius butterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength.
Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
Authors: Sánchez-Barreiro Fátima , De Cahsan Binia , Westbury Michael V , Sun Xin , Margaryan Ashot , Fontsere Claudia , Bruford Michael W , Russo Isa-Rita M , Kalthoff Daniela C , Sicheritz-Pontén Thomas , Petersen Bent , Dalén Love , Zhang Guojie , Marquès-Bonet Tomás , Gilbert M Thomas P , Moodley Yoshan 
Published: August 2023

Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
CDK7 and CDK9 inhibition interferes with transcription, translation, and stemness, and induces cytotoxicity in GBM irrespective of temozolomide sensitivity
Authors: Bhutada Isha , Khambati Fatema , Cheng Shi-Yuan , Tiek Deanna M , Duckett Derek , Lawrence Harshani , Vogelbaum Michael A , Mo Qianxing , Chellappan Srikumar P , Padmanabhan Jaya 
Published: August 2023

Abstract

Background
Glioblastoma (GBM) is refractory to current treatment modalities while side effects of treatments result in neurotoxicity and cognitive impairment. Here we test the hypothesis that inhibiting CDK7 or CDK9 would effectively combat GBM with reduced neurotoxicity.

Methods
We examined the effect of a CDK7 inhibitor, THZ1, and multiple CDK9 inhibitors (SNS032, AZD4573, NVP2, and JSH150) on GBM cell lines, patient-derived temozolomide (TMZ)-resistant and responsive primary tumor cells and glioma stem cells (GSCs). Biochemical changes were assessed by western blotting, immunofluorescence, multispectral imaging, and RT-PCR. In vivo, efficacy was assessed in orthotopic and subcutaneous xenograft models.

Results
CDK7 and CDK9 inhibitors suppressed the viability of TMZ-responsive and resistant GBM cells and GSCs at low nanomolar concentrations, with limited cytotoxic effects in vivo. The inhibitors abrogated RNA Pol II and p70S6K phosphorylation and nascent protein synthesis. Furthermore, the self-renewal of GSCs was significantly reduced with a corresponding reduction in Sox2 and Sox9 levels. Analysis of TCGA data showed increased expression of CDK7, CDK9, SOX2, SOX9, and RPS6KB1 in GBM; supporting this, multispectral imaging of a TMA revealed increased levels of CDK9, Sox2, Sox9, phospho-S6, and phospho-p70S6K in GBM compared to normal brains. RNA-Seq results suggested that inhibitors suppressed tumor-promoting genes while inducing tumor-suppressive genes. Furthermore, the studies conducted on subcutaneous and orthotopic GBM tumor xenograft models showed that administration of CDK9 inhibitors markedly suppressed tumor growth in vivo.

Conclusions
Our results suggest that CDK7 and CDK9 targeted therapies may be effective against TMZ-sensitive and resistant GBM.
Reply to Letter to the editor regarding “The effect of pistachio supplementation on metabolic syndrome and its components in adults: a systematic review and meta-analysis of randomized controlled trials”
Authors: Baghery Fatemeh , Mohammadifard Noushin , Khanamani Falahati-Pour Soudeh 
Published: August 2023

Abstract
Two researchers (F.B and S.K.F.-P.) reviewed the abstracts and titles of all of the acknowledged research to determine whether it was eligible for inclusion in the present meta-analysis according to the inclusion criteria. The authors included all of the relevant available data from 17 articles on interventional studies. Regarding the objection raised about the effect size calculation, the inclusion of the various effect sizes from 1 study is a routine approach used in numerous meta-analyses, and their inclusion in the study did not impair the accuracy of the findings. The included studies were homogeneous in terms of intervention, outcomes, and participants, and the high rate of heterogeneity between the included studies for the majority of the study outcomes may have derived from the different characteristics of the participant populations, especially differences in their health status. As no study included in the review reported the correlation coefficient between the placebo conditions and the experimental conditions, the authors reanalyzed the data by inputting a moderate correlation coefficient of 0.5. Our study showed that pistachio consumption has a positive effect in terms of reducing the components of metabolic syndrome. In conclusion, this study reanalyzed the data and justified the methods used for showing the positive effect of pistachio consumption on metabolic syndrome components, and the potential for further research to identify the underlying mechanisms and the effects on various populations. The study’s protocol was registered, and Comprehensive Meta-Analysis software was used in the statistical analyses. The authors recommend further research to investigate the potential effect of the consumption of pistachios.
Systematic Review Registration: PROSPERO registration no. CRD42021285424.
Police Effectiveness and Procedural Justice as Competing Public Values: Moving Beyond the Instrumental-Versus-Normative Model of Police Legitimacy
Authors: Na Chongmin , Lee Seulki , Kang Inkyu 
Published: August 2023

Abstract
This study argues that the dichotomy of instrumental-versus-normative motives in mainstream policing literature can mislead the ways in which police effectiveness and procedural justice shape people’s judgments about the police. Effective policing may be important even for individuals who do not directly benefit from it, while procedurally just policing can bring instrumental benefits, particularly for underprivileged social groups. We propose an alternative framework that characterizes police effectiveness and procedural justice as competing public values, of which the salience depends on political dynamics that vary across time and space. We explored the South Korean case where advocates for effective crime control and procedural justice are vying without one side decisively outweighing the other. Analysis of a representative cross-sectional survey shows that people’s perceptions of police effectiveness and procedural justice are both positively associated with trust in the police which, in turn, is positively associated with willingness for voluntary compliance and cooperation. Broader implications for theory and policy are discussed.
One-loop expressions for h → l l̅γ in Higgs extensions of the Standard Model
Authors: Hue L T , Tran Dzung Tri , Nguyen Thanh Huy , Phan Khiem Hong 
Published: August 2023

Abstract
A systematic study of one-loop contributions to the decay channels $h\rightarrow l\bar{l}\gamma$ with l = νe, μ, τ, e, μ, performed in Higgs extended versions of the Standard Model (SM), is presented in the ’t Hooft–Veltman gauge. Analytic formulas for one-loop form factors are expressed in terms of the logarithm and di-logarithmic functions. As a result, these form factors can be reduced to those relating to the loop-induced decay processes h → γγ, Zγ, confirming not only previous results using different approaches but also close relations between the three kinds of loop-induced Higgs decay rates. For phenomenological study, we focus on the two observables, namely the enhancement factors defined as ratios of the decay rates calculated between the Higgs extended versions and the SM, and the forward-backward asymmetries of fermions, which can be used to search for Higgs extensions of the SM. We show that direct effects of mixing between neutral Higgs bosons and indirect contributions of charged Higgs boson exchanges can be probed at future colliders.
Effectiveness of self-management interventions for long-term conditions in people experiencing socio-economic deprivation in high-income countries: a systematic review and meta-analysis
Authors: Okpako Tosan , Woodward Abi , Walters Kate , Davies Nathan , Stevenson Fiona , Nimmons Danielle , Chew-Graham Carolyn A , Protheroe Joanne , Armstrong Megan 
Published: August 2023

Abstract

Background
Long-term conditions (LTCs) are prevalent in socio-economically deprived populations. Self-management interventions can improve health outcomes, but socio-economically deprived groups have lower participation in them, with potentially lower effectiveness. This review explored whether self-management interventions delivered to people experiencing socio-economic deprivation improve outcomes.

Methods
We searched databases up to November 2022 for randomized trials. We screened, extracted data and assessed the quality of these studies using Cochrane Risk of Bias 2 (RoB2). We narratively synthesized all studies and performed a meta-analysis on eligible articles. We assessed the certainty of evidence using GRADE for articles included in the meta-analysis.

Results
The 51 studies included in this review had mixed findings. For the diabetes meta-analysis, there was a statistically significant pooled reduction in haemoglobin A1c (−0.29%). We had moderate certainty in the evidence. Thirty-eight of the study interventions had specific tailoring for socio-economically deprived populations, including adaptions for low literacy and financial incentives. Each intervention had an average of four self-management components.

Conclusions
Self-management interventions for socio-economically deprived populations show promise, though more evidence is needed. Our review suggests that the number of self-management components may not be important. With the increasing emphasis on self-management, to avoid exacerbating health inequalities, interventions should include tailoring for socio-economically deprived individuals.
To govern or be governed: an integrated framework for AI governance in the public sector
Authors: Choi Hyeri , Park Min Jae 
Published: August 2023

AbstractThere has been a significantly increased amount of literature on various aspects of artificial intelligence (AI), but research on AI governance has been a considerably underdeveloped area. This study proposes a comprehensive framework for designing AI governance in the public sector to overcome the limitations of previous studies that primarily dealt with the fragmentary aspect of AI. Also, we applied the developed framework to the case of Korea by combining it with the rank-order survey questions that target experts. This case study presents how to use the framework and provides insight for other countries.
‘Of One Blood?’: Gendered Propaganda and Blood Donor Behaviour in Wartime Bristol and South West England, 1939–1945
Authors: Beales John 
Published: August 2023

Summary
This article explores civilian responses to the British army’s blood donor recruitment campaign in wartime Britain, revealing it to be an underexplored medium for the examination of the contribution of women to Britain’s war effort. However, despite extensive gender-targeted propaganda, it reveals evidence of a significant disparity between levels of volunteering to donate and actual donation throughout the war. Wartime donor behaviour was influenced by perceptions of personal or familial risk, with donor recruitment propaganda emphasising kinship ties to those in military service and promoting blood donation as a mutual insurance policy. Ultimately, this article argues that evidence of donor behaviour further undermines the mythologised narrative of Britain’s ‘People’s War’ and provides nuance to the understanding of blood donor motivation.