bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium tuberculosis Gene Expression Associated With Fluoroquinolone Resistance and Efflux Pump Inhibition
Authors: van der Heijden Yuri F , Maruri Fernanda , Blackman Amondrea , Morrison Robert , Guo Yan , Sterling Timothy R 
Published: April 2023

Abstract

Background
We evaluated the relationship between response to efflux pump inhibition in fluoroquinolone-resistant Mycobacterium tuberculosis (Mtb) isolates and differences in gene expression and expression quantitative trait loci (eQTL).

Methods
We determined ofloxacin minimum inhibitory concentration (MIC) for ofloxacin-resistant and -susceptible Mtb isolates without and with the efflux pump inhibitor verapamil. We performed RNA sequencing (RNA-seq), whole genome sequencing (WGS), and eQTL analysis, focusing on efflux pump, transport, and secretion-associated genes.

Results
Of 42 ofloxacin-resistant Mtb isolates, 27 had adequate WGS coverage and acceptable RNA-seq quality. Of these 27, 7 had &gt;2-fold reduction in ofloxacin MIC with verapamil; 6 had 2-fold reduction, and 14 had &lt;2-fold reduction. Five genes (including Rv0191) had significantly increased expression in the MIC fold change &gt;2 compared to &lt;2 groups. Among regulated genes, 31 eQTLs (without ofloxacin) and 35 eQTLs (with ofloxacin) had significant allele frequency differences between MIC fold change &gt;2 and &lt;2 groups. Of these, Rv1410c, Rv2459, and Rv3756c (without ofloxacin) and Rv0191 and Rv3756c (with ofloxacin) have previously been associated with antituberculosis drug resistance.

Conclusions
In this first reported eQTL analysis in Mtb, Rv0191 had increased gene expression and significance in eQTL analysis, making it a candidate for functional evaluation of efflux-mediated fluoroquinolone resistance in Mtb.
Age Patterns of HSV-2 Incidence and Prevalence in Two Ugandan Communities: A Catalytic Incidence Model Applied to Population-Based Seroprevalence Data
Authors: Whittles Lilith K , Galiwango Ronald M , Mpagazi Josephine , Tobian Aaron A R , Ssekubugu Robert , Jackson Jade , Peer Austin D , Kennedy Caitlin , Nakalanzi Margaret , Ndyanabo Anthony , Kigozi Godfrey , Chang Larry W , Serwadda David , Manabe Yukari C , Gaydos Charlotte A , Laeyendecker Oliver , Quinn Thomas C , Reynolds Steven J , Kagaayi Joseph , Eaton Jeffrey W , Grabowski M Kate 
Published: April 2023

Abstract

Background
Herpes simplex virus type 2 (HSV-2) is an incurable sexually transmitted infection associated with increased risk of acquiring and transmitting human immunodeficiency virus (HIV). HSV-2 is highly prevalent in sub-Saharan Africa, but population-level estimates of incidence are sparse.

Methods
We measured HSV-2 prevalence from cross-sectional serological data among adults aged 18–49 years in 2 south-central Uganda communities (fishing, inland). We identified risk factors for seropositivity, then inferred age patterns of HSV-2 with a Bayesian catalytic model.

Results
HSV-2 prevalence was 53.6% (n = 975/1819; 95% confidence interval, 51.3%–55.9%). Prevalence increased with age, was higher in the fishing community, and among women, reaching 93.6% (95% credible interval, 90.2%–96.6%) by age 49 years. Factors associated with HSV-2 seropositivity included more lifetime sexual partners, HIV positive status, and lower education. HSV-2 incidence peakied at age 18 years for women and 19–20 years for men. HIV prevalence was up to 10-fold higher in HSV-2–positive individuals.

Conclusions
HSV-2 prevalence and incidence were extremely high, with most infections occurring in late adolescence. Interventions against HSV-2, such as future vaccines or therapeutics, must target young populations. Remarkably higher HIV prevalence among HSV-2–positive individuals underscores this population as a priority for HIV prevention.
Longitudinal trends in meconium drug detection in 46 US states between the years 2015 and 2020
Authors: Pandya Vrajesh , Wilker Chase , Johnson-Davis Kamisha L 
Published: April 2023

Abstract
Maternal drug use during pregnancy has significant health and socio-legal implications. The Substance Abuse and Mental Health Services Administration publishes self-reported rates of drug use during pregnancy; however, comprehensive long-term laboratory data on neonatal drug exposure are lacking. Over 175,000 meconium specimens originating from 46 US states were analyzed at ARUP Laboratories between the years 2015 and 2020. A retrospective investigation of drug positivity rates, multidrug detection and median drug concentrations was conducted for 28 compounds in six drug classes. The overall meconium drug positivity rate was lowest in 2015 (47.3%), which increased over 6 years, reaching a peak in 2020 (53.4%). 11-Nor-9-carboxy-tetrahydrocannabinol (THC-COOH) was the most frequently detected compound across all 6 years. The second most frequently detected analyte was morphine in 2015–2016 and amphetamines in 2017–2020. The THC-COOH positivity rate rose from 29.7% in 2015 to 38.2% in 2020. The positivity rates for stimulants also increased in the range of 0.4–2.9% in 2020 compared to 2015. Conversely, opioid positivity rates declined in the range of 1.6–2.3% in 2020 as compared to 2015. The most common two-drug combination was THC-COOH–opioids (2.4%) in 2015–2016, which was replaced by THC-COOH–amphetamines (2.6%) in 2017–2020. The most common three-drug combination was THC-COOH–opioids–amphetamines throughout all 6 years. Neonatal drug exposure positivity rates have increased over the past 6 years based on retrospective data analysis from the patient population submitted for testing at ARUP Laboratories.
In vitro biochemical characterization and identification of hemolytic bacteria associated with life history of Culicoides peregrinus (Diptera: Ceratopogonidae), a vector of bluetongue virus
Authors: Sarkar Ankita , Banerjee Paramita , Kar Surajit , Chatterjee Soumendranath , Mazumdar Abhijit 
Published: April 2023

Abstract
Gut bacterial communities in insects provide several beneficial roles like nutrition, digestion, fecundity, and survival of the host. The microbial communities of Culicoides spp. (Diptera: Ceratopogonidae) vary with parity, developmental stages, and environmental factors. Previous studies have revealed the presence of hemolytic bacteria in adult Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae), an important vector of bluetongue virus (BTV). Our objectives were (i) to identify bacterial communities with hemolytic activities associated with all life stages and (ii) to compare between reared and field-collected adults including age graded females. Bacterial identification followed Sanger sequencing of 16S rRNA. In vitro biochemical characterizations including antibiotic sensitivity tests were also done. The majority of bacterial species were beta hemolytic with one, Alcaligenes faecalis, showing alpha hemolysis. Most bacterial species were observed in field-collected adults except Proteus spp. Throughout the life history of the vector, Bacillus cereus (CU6A, CU1E) and Paenibacillus sp. (CU9G) were detected indicating their possible role in blood digestion within the gut of this vector species. In vivo hemolytic activities of these culturable bacterial communities within this vector may be addressed in future. These hemolytic bacterial communities may be targeted to develop novel and effective strategies for vector control.
Which Kind of Body in “Mental” Pathologies? Phenomenological Insights on the Nature of the Disrupted Self
Authors: Bizzari Valeria 
Published: April 2023

AbstractGuided by a phenomenological perspective, this paper aims to account for the existence of a corporeal consciousness—something that clinicians should take into account, not merely in the case of physical pathologies but especially in the case of mental disorders. Firstly, I will highlight three cases: schizophrenia, depression, and autism spectrum disorder. Then, I will show how these cases correspond to three different kinds of bodily existence: disembodiment (in the case of schizophrenia), chrematization (in melancholic depression), and dyssynchrony (in the autism spectrum disorder). Finally, I will argue for the importance of an “expressive common environment” between the patient and the clinician, who are two distinct, embodied conscious subjects resonating with one another. In this view, the primary goal of the therapeutic process seems to develop a shared understanding of the patient’s life-world, which finds its main expression through the disrupted body.
Cannabis use among cancer survivors before and during the COVID-19 pandemic, 2019-2021
Authors: Sarkar Sayantani , Braun Ilana M , Nayak Manan , Bryan Angela D , Poghosyan Hermine 
Published: April 2023

Abstract
We estimated the prevalence of past 30-day cannabis use, evaluated reasons for use, and identified individual-level factors associated with cannabis use among cancer survivors before (2019) and during (2020 and 2021) the COVID-19 pandemic. Cancer survivors, aged 18 years and older, were identified from the 2019 (n = 8185), 2020 (n = 11 084), and 2021 (n = 12 248) Behavioral Risk Factor Surveillance System. Prevalence of past 30-day cannabis use among survivors held steady through the pandemic (8.7%, 7.4%, and 8.4% in 2019, 2020 and 2021, respectively). Of those who used cannabis, 48.7% used it for medical reasons in 2019, 54.5% in 2020, and 43.5% in 2021. Survivors were more likely to report past 30-day cannabis use if they were younger, male, current or former tobacco smokers, and binge alcohol consumers and if they experienced poor mental health in the past 30-days. Our study identified subpopulations of cancer survivors that need to be targeted for evidence-informed discussions about cannabis use.
Validation of the adapted female sexual function index among Chinese cisgender heterosexual women and sexual and gender minority women
Authors: Wu Chanchan , Chau Pui Hing , Choi Edmond Pui Hang 
Published: April 2023

AbstractBackgroundThe Female Sexual Function Index (FSFI) remains the most widely used scale for assessing female sexual function. However, while an adapted version of the FSFI has been proven to be suitable for Western sexual minority women, it has yet to be used in China.AimThis study aimed to validate the Mandarin Chinese version of the adapted FSFI among Chinese cisgender heterosexual women and sexual and gender minority women, and evaluate its psychometric properties.MethodsA cross-sectional online survey was conducted. The modified scoring method related to zero responses was examined, and structural validity, internal consistency, internal reliability, convergent validity, and known-group validity were evaluated.OutcomesThe primary measure was the adapted FSFI, and the Positive Sexuality Scale and the New Sexual Satisfaction Scale–Short Form were used to test convergent validity.ResultsA total of 431 Chinese adult women were recruited, including 193 cisgender heterosexual women and 238 sexual and gender minority women. Confirmatory factor analysis using the original scores supported the original 6-factor model. Using both Cronbach’s α and McDonald’s ω, the results showed that the values of the total scale and 6 subscales were in the 0.76 to 0.98 and 0.83 to 0.98 ranges, respectively, indicating satisfactory reliability. Moderate-to-strong correlations among the total FSFI scores and positive sexuality and sexual satisfaction were found (r = 0.32-0.71), supporting good convergent validity.Clinical ImplicationsThe adapted FSFI facilitates the use of more inclusive language in the clinical setting, allowing for a more comprehensive and unbiased assessment of sexual function in all women.Strengths and LimitationsThis study recruited both cisgender women of varied sexual orientations and gender minorities who were assigned female at birth, demonstrating that the adapted FSFI could be suitably applied to sexual minority populations. However, from a fully inclusive perspective of sex and gender, there is no research on how to accurately evaluate transgender women with female external genitalia or appropriately assess those with a female reproductive system but who do not self-identify as female. Therefore, more in-depth research is needed to further revise the FSFI for better use in the wider female population.ConclusionThis Chinese version of the adapted FSFI has good psychometric properties and is a reliable and valid instrument to assess female sexual function. Furthermore, the modified scoring method could be an effective alternative among samples of sexually inactive women.
Lessons from a century of apical dominance research
Authors: Beveridge Christine A , Rameau Catherine , Wijerathna-Yapa Akila 
Published: April 2023

Abstract
The process of apical dominance by which the apical bud/shoot tip of the plant inhibits the outgrowth of axillary buds located below has been studied for more than a century. Different approaches were used over time, with first the physiology era, the genetic era, and then the multidisciplinary era. During the physiology era, auxin was thought of as the master regulator of apical dominance acting indirectly to inhibit bud outgrowth via unknown secondary messenger(s). Potential candidates were cytokinin (CK) and abscisic acid (ABA). The genetic era with the screening of shoot branching mutants in different species revealed the existence of a novel carotenoid-derived branching inhibitor and led to the significant discovery of strigolactones (SLs) as a novel class of plant hormones. The re-discovery of the major role of sugars in apical dominance emerged from modern physiology experiments and involves ongoing work with genetic material affected in sugar signalling. As crops and natural selection rely on the emergent properties of networks such as this branching network, future work should explore the whole network, the details of which are critical but not individually sufficient to solve the ‘wicked problems’ of sustainable food supply and climate change.
Reliability of a terbinafine agar containing method for the screening of dermatophyte resistance
Authors: Bidaud Anne-Laure , Normand Anne-Cécile , Jabet Arnaud , Brun Sophie , Delliere Sarah , Cremer Geneviève , Foulet Françoise , Ayachi Aymen , Imbert Sébastien , Hennequin Christophe , Dannaoui Éric , Moreno-Sabater Alicia 
Published: April 2023

Abstract
The increase in terbinafine resistance worldwide due to Trichophyton indotineae underlies the need for surveillance networks, deploying easy to perform methods to correctly identify resistant isolates and thereby reduce their spread. In the present study, we evaluated the performances of the terbinafine containing agar method (TCAM). Different technical parameters, such as culture medium (RPMI agar [RPMIA] or Sabouraud dextrose agar [SDA]) and inoculum size, were evaluated. Our study showed that terbinafine susceptibility determined using the TCAM was reliable and independent of the inoculum or medium used. We then performed a multicenter, blinded study. 5 isolates of T. indotineae and 15 of genotype I or II of T. interdigitale, including 5 terbinafine-resistant isolates (4 T. indotineae and 1 T. interdigitale), were sent to eight clinical microbiology laboratories. Each laboratory analyzed the 20 isolates’ terbinafine susceptibility by the TCAM using both culture media. TCAM allowed all participants to correctly determine the terbinafine susceptibility of analyzed isolates without prior training. All participants agreed that the dermatophyte tested, regardless of species or genotype, grew better on SDA than on RPMIA medium but accumulated fungal growth after 14 days eventually minimized the effect of this difference. In conclusion, TCAM is a reliable, easy to perform screening method for assessing terbinafine resistance. However, despite good performances, TCAM is a qualitative method and minimal inhibitory concentrations must be determined by the European Committee for Antimicrobial Susceptibility Testing standardized method to follow the evolution of terbinafine resistance levels.
The DIVING3D Survey – Deep IFS View of Nuclei of Galaxies – III. Analysis of the nuclear region of the early-type galaxies of the sample
Authors: Ricci T V , Steiner J E , Menezes R B , Slodkowski Clerici K , da Silva M D 
Published: April 2023

ABSTRACT
We analysed the nuclear region of all 56 early-type galaxies from the DIVING3D Project, which is a statistically complete sample of objects that contains all 170 galaxies in the Southern Hemisphere with B &lt; 12.0 mag and galactic latitude |b| &lt; 15°. Observations were performed with the Integral Field Unit of the Gemini Multi-Object Spectrograph. Emission lines were detected in the nucleus of 86 ± 5 per cent of the objects. Diagnostic diagrams were used to classify 52 ± 7 per cent of the objects as LINERs or Seyferts, while the other 34 ± 6 per cent galaxies without H β or [O iii] lines in their spectra were classified as weak emission line objects. Transition Objects are not seen in the sample, possibly because the seeing-limited data cubes of the objects allow one to isolate the nuclei of the galaxies from their circumnuclear regions, avoiding contamination from H ii regions. A broad line region is seen in 29 ± 6 per cent of the galaxies. Of the 48 galaxies with emission-line nuclei, 41 have signs of AGNs. Some objects also have indications of shocks in their nuclei. Lenticular galaxies are more likely to have emission lines than ellipticals. Also, more luminous objects have higher [N ii]/H α ratios, which may be associated with the mass-metalicity relation of galaxies. A direct comparison of our results with the Palomar Survey indicates that the detection rates of emission lines and also of type 1 AGNs are higher in the DIVING3D objects. This is a consequence of using a more modern instrument with a better spatial resolution than the Palomar Survey observations.
DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations
Authors: Song Qianqian , Li Mingyu , Li Qian , Lu Xun , Song Kun , Zhang Ziliang , Wei Jiale , Zhang Liang , Wei Jiacheng , Ye Youqiong , Zha Jinyin , Zhang Qiufen , Gao Qiang , Long Jiang , Liu Xinyi , Lu Xuefeng , Zhang Jian 
Published: April 2023

Abstract
Driver mutations can contribute to the initial processes of cancer, and their identification is crucial for understanding tumorigenesis as well as for molecular drug discovery and development. Allostery regulates protein function away from the functional regions at an allosteric site. In addition to the known effects of mutations around functional sites, mutations at allosteric sites have been associated with protein structure, dynamics, and energy communication. As a result, identifying driver mutations at allosteric sites will be beneficial for deciphering the mechanisms of cancer and developing allosteric drugs. In this study, we provided a platform called DeepAlloDriver to predict driver mutations using a deep learning method that exhibited &gt;93% accuracy and precision. Using this server, we found that a missense mutation in RRAS2 (Gln72 to Leu) might serve as an allosteric driver of tumorigenesis, revealing the mechanism of the mutation in knock-in mice and cancer patients. Overall, DeepAlloDriver would facilitate the elucidation of the mechanisms underlying cancer progression and help prioritize cancer therapeutic targets. The web server is freely available at: https://mdl.shsmu.edu.cn/DeepAlloDriver.
Clinical Characteristics of the 2019 Eastern Equine Encephalitis Outbreak in Michigan
Authors: Ladzinski Adam T , Tai Aisha , Rumschlag Matthew T , Smith Christopher S , Mehta Aditya , Boapimp Pimpawan , Edewaard Eric J , Douce Richard W , Morgan Larry F , Wang Michael S , Fisher-Hubbard Amanda O , Cummings Matthew J , Jagger Brett W 
Published: April 2023

Abstract

Background
Eastern equine encephalitis virus is a mosquito-borne alphavirus responsible for unpredictable outbreaks of severe neurologic disease in animals and humans. While most human infections are asymptomatic or clinically nonspecific, a minority of patients develops encephalitic disease, a devastating illness with a mortality rate of ≥30%. No treatments are known to be effective. Eastern equine encephalitis virus infection is rare in the United States, with an annual average nationwide incidence of 7 cases between 2009 and 2018. However, in 2019, 38 cases were confirmed nationwide, including 10 in Michigan.

Methods
Data from 8 cases identified by a regional network of physicians in southwest Michigan were abstracted from clinical records. Clinical imaging and histopathology were aggregated and reviewed.

Results
Patients were predominantly older adults (median age, 64 years), and all were male. Results of initial arboviral cerebrospinal fluid serology were frequently negative, and diagnosis was not made until a median of 24.5 days (range, 13–38 days) after presentation, despite prompt lumbar punctures in all patients. Imaging findings were dynamic and heterogeneous, with abnormalities of the thalamus and/or basal ganglia, and prominent pons and midbrain abnormalities were displayed in 1 patient. Six patients died, 1 survived the acute illness with severe neurologic sequelae, and 1 recovered with mild sequelae. A limited postmortem examination revealed diffuse meningoencephalitis, neuronophagia, and focal vascular necrosis.

Conclusions
Eastern equine encephalitis is a frequently fatal condition whose diagnosis is often delayed, and for which no effective treatments are known. Improved diagnostics are needed to facilitate patient care and encourage the development of treatments.
Methodology in State Constitutional Rights Interpretation
Authors: Williams Robert F. , Friedman Lawrence 
Published: April 2023

Abstract
This chapter explores the mistaken premise underlying the perception of the power of decisions of the U.S. Supreme Court interpreting individual rights under the federal Constitution. It addresses the legitimacy of independent state constitutional decision-making before turning to issues of teaching and sequencing regarding state constitutional interpretive methodologies. The chapter examines the criteria approach to state constitutional interpretation and the search for factors justifying divergence from federal precedent. It canvasses the state experience with the criteria approach in Washington, New Jersey, Pennsylvania, Illinois, and Connecticut. The chapter employs two cases studies of state court use of the criteria approach in New Jersey and Washington, in the context of garbage search cases. The chapter critiques the criteria approach and addresses the continuing legitimacy and methodology debates and other procedural issues associated with the New Judicial Federalism. Finally, the chapter looks at substantive due process and economic regulation under state constitutions.
Amending and Revising State Constitutions
Authors: Williams Robert F. , Friedman Lawrence 
Published: April 2023

Abstract
Part V surveys the range of methods and processes for change in the texts of state constitutions—both individual amendments and more comprehensive revisions. Each of these processes differs from the others and also produces different kinds of constitutional history materials that remain available for the interpretation process. In addition, amending and revising state constitutions often leads to litigation over these processes. This leads to a substantial judicial involvement in the processes of state constitutional amendment and revision that generates a number of legal doctrines that must be taken into account; similar doctrines are virtually nonexistent in federal constitutional law. The use of state constitutional amendments as elements of governance has become more common in the states.