bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore-based targeted sequencing test for direct tuberculosis identification, genotyping, and detection of drug resistance mutations: a side-by-side comparison of targeted next-generation sequencing technologies
Authors: Cabibbe Andrea Maurizio , Moghaddasi Kiarash , Batignani Virginia , Morgan Godstime Stephen Kojo , Di Marco Federico , Cirillo Daniela Maria 
Published: September 2024

ABSTRACT

We investigated the performance of the targeted next-generation sequencing (tNGS)-based Oxford Nanopore Diagnostics AmPORE TB assay, recently approved by the World Health Organization (WHO) as tuberculosis (TB) diagnostic test for the detection of drug resistance on respiratory specimens. A total of 104 DNA samples from Xpert MTB/RIF-positive TB sputum specimens were tested using the AmPORE TB kit, with the GenoScreen Deeplex Myc-TB as a comparative tNGS assay. For AmPORE TB, DNA samples were divided into five sequencing runs on the MinION device. Data analysis was performed using proprietary software. The WHO catalog of mutations was used for drug resistance interpretation. The assay achieved a high validity rate of 98% (102/104 DNA samples), homogeneous mean reads coverage across TB-positive specimens, and 100% positive and negative agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol, and capreomycin compared with Deeplex Myc-TB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs. The AmPORE TB turnaround time was approximately 5–6 hours from extracted DNA to tNGS reporting for batches of 22 DNA samples. The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed good performance for drug-resistant TB profiling compared with Deeplex Myc-TB.

IMPORTANCE

Targeted next-generation sequencing (tNGS) of
Mycobacterium tuberculosis
provides comprehensive resistance predictions matched to new multidrug-resistant/rifampicin-resistant tuberculosis regimens and received World Health Organization approval for clinical use in respiratory samples in 2024. The advanced version of the Oxford Nanopore Diagnostics AmPORE TB tNGS kit was evaluated in this study for the first time and demonstrated good performance, flexibility, and faster turnaround time compared with the existing solutions.
Complete genome sequence of a
Histophilus somni
strain 91 isolated from a beef calf with pneumonia
Authors: Menghwar Harish , Ma Hao , Briggs Robert E. , Tatum Fred M. , Casas Eduardo , Dassanayake Rohana P. 
Published: September 2024

ABSTRACT

Histophilus somni
is an important causative agent of bovine respiratory disease complex. Here, we report the complete genome sequence of a
Histophilus somni
strain 91, which was isolated from a pneumonic lung tissue sample collected from a beef calf.
Cerebral venous pressures, sinus trans-stenosis gradients, and intracranial pressures are dramatically augmented by head position
Authors: Fargen Kyle M , Midtlien Jackson P , Margraf Connor R , Wiater Angelina H , Marcet Paul A , Siddiqui Adnan H , Hui Ferdinand 
Published: September 2024

BackgroundCerebral venous pressures, sinus trans-stenosis gradients, and intracranial pressures are thought to be influenced by head position.ObjectiveTo investigate the intracranial manifestations of these changes in patients with cerebral venous outflow disorders (CVD).MethodsA retrospective chart review was conducted on 22 consecutive adult patients who underwent diagnostic cerebral venography with rotational internal jugular vein (IJV) venography and superior sagittal sinus (SSS) pressure measurements in multiple head positions. Data on venous sinus pressures, IJV pressures, and lumbar puncture (LP) opening pressures (OP) were collected and analyzed.ResultsThe study found that 21 (96%) patients experienced increases in SSS pressures with head rotation, with a mean increase of 25.4%. Intracranial trans-stenosis gradients showed significant variability with head position. Additionally, LP OP measurements increased by an average of 44.3% with head rotation. Dynamic IJV stenosis was observed in all patients during rotational testing.ConclusionHead position significantly affects cerebral venous pressures, trans-stenosis gradients, and intracranial pressures in patients with CVD or intracranial hypertension. These findings highlight the need for dynamic venography in the diagnostic evaluation of these conditions to better understand their pathophysiology and improve treatment strategies.
Thermodynamic properties and geometries of bardeen black hole surrounded by string clouds
Authors: Rani Shamaila , Jawad Abdul , Raza Hussnain , Shaymatov Sanjar , Muzaffar Maham , Riaz Hifza 
Published: September 2024

AbstractIn this work, we investigate the thermodynamic properties of Bardeen black hole which is coupled with cloud of strings and minimally coupled to nonlinear electrodynamics. The modified entropy in the form of Sharma–Mittal entropy is used to discuss these properties which include mass, temperature, pressure, Gibbs free energy and trace of Hessian matrix. We obtain stable behavior along with physical solution for some specific values of parameters a and q. Furthermore, our work provides a thermodynamic metric using the Hessian matrix of black hole mass, changing the conformal connection between Quevedo and Ruppeiner’s geometries. Investigating the first principle of thermodynamics for regular black holes, such as the Bardeen AdS black hole, exposes significant behavior changes during phase transitions in an extended phase space.
Equitable Efficiency and Decomposition of Preference Matrix in Multiobjective Optimization Problems
Authors: Ahmadi Fatemeh , Salajegheh Ali Reza , Foroutannia Davoud 
Published: September 2024

In equitable multiobjective optimization, all of the objectives are uniformly optimized, but in some cases, the decision maker believes that some of them should be uniformly optimized. In order to solve the proposed problem, we introduce the concept of equitable [Formula: see text]-efficiency, where [Formula: see text] is a partition of the index set of objective functions and the preference matrix [Formula: see text] is the direct sum of the matrices [Formula: see text], in which [Formula: see text] is a preference matrix for the objective functions in the class [Formula: see text] for [Formula: see text]. We examine some theoretical and practical aspects of equitably [Formula: see text]-efficient solutions and provide the some conditions that guarantee the relation of equitable [Formula: see text]-dominance is a [Formula: see text]-equitable rational preference. Furthermore, we introduce the new problem with the preference matrix [Formula: see text] and we decompose it into a collection of smaller subproblems. In continuation, the subproblems are solved by the concept of equitable efficiency. Finally, two models are demonstrated to coordinate equitably efficient solutions of the proposed subproblems.
Indole May Help the Horizontal Transmission of Antibiotic Resistance Genes in E. coli Under Subinhibitory Concentrations of Cefotaxime Stress
Authors: Dong Weiqi , Du Panpan , Huang Ruisen , Lv Shuoyan , Chen Hong , Guan Songlei 
Published: September 2024

Objectives: Subinhibitory concentration of antibiotics in the environment is an important risk factor for the horizontal transmission of antibiotic resistance genes (ARGs). The signaling mechanism of resistance gene transmission remains unknown. The aim of this study was to investigate whether indole could be used as a molecular signal to help the spread of ARGs under the stress of subinhibitory concentrations of antibiotics.Methods: The effect of indole on conjugation frequency was investigated through a conjugation test, and its effect on the Type IV secretion system and pili gene expression of E. coli was observed. Meanwhile, we were investigating the trend of changes in indole regulatory factors ibpA, tnaA, and concentration pumps. Subsequently, we predicted the receptors that specifically bind to indole. Finally, our study focused on elucidating the regulatory mechanism of indole synthesis.Results: Conjugate frequency was significantly increased under 1/5MIC concentration cefotaxime stress. The transferred ARGs were blaCTX-M and foxA. The mobile plasmid was IncY or IncI2. Meanwhile, the concentration of endogenous indole was also significantly increased. And, surprisingly, inhibition of endogenous indole production resulted in a significant decrease in conjugate frequency. However, the conjugate frequency increased once again when the strains reacquired the exogenous indole. Furthermore, the fluctuation trends of indole‐regulated factor (ibpA, tnaA) mRNA and concentration pumps (acrEF, mtr) mRNA consistently with that of indole. Then, we found that the receptors of indole may be four targets of TCSs: CreC, PhoB, AtoC, and UhpA. More than that, when strains retrieved the exogenous indole again, the mRNA levels of T4SS (virB2, virB6, and virD4) and pppA (coding Pili precursor) genes significantly increased. This indicates that there is a close relationship between indole and conjugated channels, which are necessary for horizontal transfer of genetic material. And then, the trends of indole and tnaA mRNA were consistent with that of ibpA (one of SOS response). So, this result confirmed that indole was regulated by SOS response under subinhibitory concentrations of antibiotics.Conclusions: It is always known that subinhibitory concentrations of antibiotics stimulate an SOS response in E. coli, which helps in the horizontal spread of ARGs by modulating indole.
MYC Drives mRNA Pseudouridylation to Mitigate Proliferation-Induced Cellular Stress during Cancer Development
Authors: Ding Jane , Bansal Mohit , Cao Yuxia , Ye Bingwei , Mao Rui , Gupta Anamika , Sudarshan Sunil , Ding Han-Fei 
Published: September 2024

Abstract
Pseudouridylation is a common RNA modification that is catalyzed by the family of pseudouridine synthases (PUS). Pseudouridylation can increase RNA stability and rigidity, thereby impacting RNA splicing, processing, and translation. Given that RNA metabolism is frequently altered in cancer, pseudouridylation may be a functionally important process in tumor biology. Here, we show that the MYC family of oncoproteins transcriptionally upregulates PUS7 expression during cancer development. PUS7 is essential for the growth and survival of MYC-driven cancer cells and xenografts by promoting adaptive stress responses and amino acid biosynthesis and import. ATF4, a master regulator of stress responses and cellular metabolism, was identified as a key downstream mediator of PUS7 functional activity. Induction of ATF4 by MYC oncoproteins and cellular stress required PUS7, and ATF4 overexpression overcame the growth inhibition caused by PUS7 deficiency. Mechanistically, PUS7 induced pseudouridylation of MCTS1 mRNA, which enhanced its translation. MCTS1, a noncanonical translation initiation factor, drove stress-induced ATF4 protein expression. A PUS7 consensus pseudouridylation site in the 3′ untranslated region of ATF4 mRNA was crucial for the induction of ATF4 by cellular stress. These findings unveil an MYC-activated mRNA pseudouridylation program that mitigates cellular stress induced by MYC stimulation of proliferation and biomass production, suggesting that targeting PUS7 could be a therapeutic strategy selectively against MYC-driven cancers.
Significance: Oncogene activation of mRNA pseudouridylation is a mechanism that facilitates metabolic reprogramming and adaptive responses to overcome cellular stress during cancer development.
Cancer Screening, Knowledge, and Fatalism among Chinese, Korean, and South Asian Residents of New York City
Authors: Curro Isabel I. , Teasdale Chloe A. , Wyatt Laura C. , Foster Victoria , Yusuf Yousra , Sifuentes Sonia , Chebli Perla , Kranick Julie A. , Kwon Simona C. , Trinh-Shevrin Chau , LeCroy Madison N. 
Published: September 2024

Abstract

Background:
Asian New York City residents have the lowest cancer screening uptake across race and ethnicity. Few studies have examined screening differences across Asian ethnic subgroups in New York City.

Methods:
Cross-sectional survey data were analyzed using multivariable logistic and multinomial regression analyses. Differences among Chinese, Korean, and South Asian adults in breast, cervical, and colorectal cancer screening uptake; breast and colorectal cancer screening knowledge; and cancer fatalism were examined. Associations between breast and colorectal cancer screening knowledge and their uptake were also assessed along with associations between cancer fatalism and breast, cervical, and colorectal cancer screening uptake.

Results:
Korean women reported 0.52 times [95% confidence interval (CI), 0.31–0.89] lower odds of Pap test uptake compared with Chinese women; South Asian adults had 0.43 times (95% CI, 0.24–0.79) lower odds of colorectal cancer screening uptake compared with Chinese adults. Korean adults reported 1.80 times (95% CI, 1.26–2.58) higher odds of knowing the correct age to begin having mammograms compared with Chinese adults; South Asian adults had 0.67 times (95% CI, 0.47–0.96) lower odds of knowing the correct age to begin colorectal cancer screening compared with Chinese adults. Korean adults had 0.37 times (95% CI, 0.27–0.53) lower odds of reporting cancer fatalism compared with Chinese adults.

Conclusions:
Low cancer screening uptake among Asian American adults, low screening knowledge, and high cancer fatalism were found. Cancer screening uptake, knowledge, and fatalism varied by ethnic subgroup.

Impact:
Findings indicate the need for ethnicity-specific cultural and linguistic tailoring for future cancer screening interventions.
The University of North Carolina Cancer Survivorship Cohort: A Resource for Collaborative Survivorship Research
Authors: Anderson Chelsea , Bensen Jeannette T. , Allott Emma H. , Basta Patricia V. , Irwin Debra E. , Gerstel Adrian , Farnan Laura , Tan Hung-Jui , Kent Erin E. , Kuo Tzy-Mey , Baggett Christopher D. , Olshan Andrew F. , Earp H. Shelton , Nichols Hazel B. 
Published: September 2024

Abstract

Background:
Rapid growth in the number of US cancer survivors drives the need for ongoing research efforts to improve outcomes and experiences after cancer. In this study, we describe the University of North Carolina (UNC) Cancer Survivorship Cohort, a medical center–based cohort of adults with cancer that integrates medical record–abstracted cancer information, patient-reported outcomes, and biological specimens.

Methods:
Participants ages 18+ were recruited from UNC oncology clinics between April 2010 and August 2016. After enrollment, participants completed questionnaires on a range of topics including demographics, health history, healthcare access and utilization, quality of life, and symptoms. Blood samples and tumor tissue specimens were collected and processed by study staff, and cancer characteristics and other clinical data were abstracted from electronic medical records. Participants consented to recontact for future studies and linkage of their data with other data resources.

Results:
In total, 3,999 participants with a cancer diagnosis were enrolled in the cohort. The most common cancer types among those enrolled included breast (N = 866), uterine (N = 458), colorectal (N = 300), prostate (N = 296), and head and neck (N = 248) cancers. Blood specimens were collected for 3,027 participants (76%). Additional participants without cancer (N = 1,299) were also enrolled, and the majority (62%) provided biospecimen samples.

Conclusions:
We encourage a wide collaboration with investigators across institutions seeking to advance research in cancer survivorship. Procedures are in place to support proposals for use of existing or linked data and for proposals that require participant recontact or analysis of biospecimens.

Impact:
The UNC Cancer Survivorship Cohort is a unique resource for cancer survivorship research.
Advancing Sustainable Development Goals through Enhanced Literacy in Nuclear Science and Technology: Emphasizing Hands-On Experiences
Authors: Saengkaew Phannee , Chanyotha Supitcha , Pengvanich Phongphaeth , Srijaroen Benjawan , Phruksarojanakun Phiphat , Cherdchu Chainarong , Takaki Rieko , Iimoto Takeshi 
Published: September 2024

Abstract
In alignment with the United Nations’ sustainable development goals (SDG s), nuclear science and technology (NST) significantly contributes to nine out of seventeen SDG s. As an integral component of nuclear human resource development (HRD), it is imperative to introduce young students to NST through effective STEAM or STEM methodologies. However, Thailand’s progress in NST literacy and public awareness has been suboptimal, despite over five decades of nuclear HRD initiatives. While various nuclear-related organizations have undertaken numerous activities, their lack of coordination and comprehensiveness poses challenges for sustainable development. To address this, concerted efforts must involve collaboration with schoolteachers to integrate NST into the national science curriculum and syllabus. This entails a review and revision process aimed at incorporating more hands-on experiments to ignite students’ curiosity and enthusiasm for NST. Through strategic planning and implementation, Thai students will develop a deeper familiarity with NST, thereby enhancing their overall NST literacy and contributing to the nation’s sustainable development goals.
The Effects of the Developments in Artificial Intelligence and Open-Access Software on the Visions of Academicians
Authors: Deveciyan Meri Taksi , Bataklar Sinan 
Published: September 2024

Abstract
This research aims to examine the effects of developments in Artificial Intelligence (AI) and open-access software on the visions of academicians. The research was conducted using the phenomenology pattern, one of the qualitative research methods, and semi-structured in-depth interviews were preferred during the data collection process. Descriptive and coding-based qualitative content analysis methods were used in the research process. Emerging themes include the use of artificial intelligence in higher education; situation analysis of the use of AI in academics (SWOT); and strategic dimension of using AI in higher education. These themes explain in detail the potential effects of AI and open-access software on the strategy and competitiveness dimensions of academics’ visions. It is expected that the study will make significant contributions to understanding the changes that AI and open-access software will create in the academic world and how these technologies can be integrated into the way academics work.
The Bright Future of Liberal Democracy Explained through Revisited Modernization Theory
Authors: Danilenko Denis 
Published: September 2024

Abstract
Many think that liberal democracy is currently under attack. This view leads to considering modernization theory as a fallacy because economic development indicators show that authoritarian economies continue to grow. This study challenges this idea and attempts to update modernization theory. We argue that not mere economic development is a requirement of liberal democracy, as initially advanced, but economic liberalization is. Economic development induces democratization only if it is accompanied by economic liberalization. This phenomenon occurs because economic development in free-market terms, accompanied by economic liberalization, not only produces socioeconomic consequences, as shown by classic modernization theory, but also institutional outcomes, such as legal restraints on political power. To update modernization theory, we propose revisiting other prerequisites. Social modernization supposes that education levels will increase, and secularization will change attitudes toward political power and sociocentered (non-liberal) values, which will serve as a prerequisite for democratization. The modernization of communication technologies makes people more independent of the government, which gives them more influence over the state. Thus, it plays a democratizing role. Finally, ecological modernization, particularly energy market modernization, will have a significant democratizing role because it will directly affect rentiers’ authoritarianism. These prerequisites not only demonstrate positive trends but also suggest that they continue to progress, which makes it possible to conclude that democracy has a bright future.
‘Parents Unknown’. Separation and Loss in a Context of Repeated Work-Led Mobility (Tuareg iklan 1970–2021)
Authors: Oxby Clare 
Published: September 2024

Abstract
This article explores the Sahelian practice of separating young children from their birth parents for work-related purposes. This occurred in the 1970s in certain elite Tuareg contexts, when alternative livelihood options were scarce; its impact was still being felt in 2010. The practice involves mostly those born into the lowest status group (iklan), especially women. This research seeks to explain what the practice of child separation from parents is, how it is expressed, and how it has changed. With this aim, it analyses the link between this practice, ideas and assumptions about the family and close relationships through women, and collective female dance and music rituals. The article is based on qualitative research conducted in Niger between 1973–2010, a 2002 anti-slavery report, and court proceedings concerning separated children between 2003–2021.
Exile, Humanitarian Governmentality, and Gender Relations Among the ‘Black Kel Tamasheq’ from Mali in Niger
Authors: Diallo Souleymane 
Published: September 2024

Abstract
This article discusses the ways in which forceful migration and humanitarian regulations in exile, have prompted redefinitions of gender roles and relations in Bellah families in the refugee camp of Abala, Niger. These include transformations in relations between the Bellah and their former masters, relations between Bellah men and women, and intergenerational relations between Bellah elders and children. The article proposes to view this development as a new sequence in the reformulations of the Bellah’s family structures, relations, and household economy that began under colonial rule. By probing these complex processes of changes in Bellah family relations, this article places, simultaneously, the empirical focus of a study of gender relations on men and women and elders and youth. It departs from and supplements accounts in gender studies that focus either only on women or men, or else on intergenerational tensions among elderly men and youth. The analysis draws its influence from studies that conceive of gender as the very process of structuring subjectivities and social positionalities through the performances of certain roles.
Humans at Last, Emotions at Least. Enslavement and Freedom Struggles of Four Iconic Haratin Women of Mauritania
Authors: Ould Brahim Elhadj 
Published: September 2024

Abstract
Using an ethnographic method, this article goes into the enslavement and liberation struggles of four iconic Haratin women in Mauritania, exploring the intricate dynamics of slavery, gender, sexuality, migration and emotional norms. By examining these women’s experiences, the research sheds light on enduring social, legal, and personal practices in modern Mauritania where slavery and post-slavery categorisation is difficult to distinguish. The article examines emotional norms linked to institutional slavery, contrasting these with the transformative experiences of freedom encountered by these women. Ultimately, the aim is to illuminate the interconnected narratives of enslavement, migration and emotional experiences, offering insights into the struggles and triumphs of Haratin women in their pursuit of liberation in Mauritania.