bluuebunny/crossref_metadata_2025_split huggingface dataset:
Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date
Authors: Wang Pengfei , Yang Ying , Li Daoyang , Yu Zhichao , zhang Bo , Zhou Xiangchun , Xiong Lizhong , Zhang Jianwei , Wang Lei , Xing Yongzhong 
Published: June 2024

ABSTRACT
The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of quantitative trait locus (QTL) mapping, but single nucleotide polymorphism (SNP)-based GWAS does not fully reach its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice. A total of 44 000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24 414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of &lt;55 kb for major effect genes and &lt;123 kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding.
Adaptations in Gastrointestinal Nutrient Absorption and its Determinants During Pregnancy in Monogastric Mammals: A Scoping Review
Authors: Overduin Teunis Sebastian , Page Amanda J , Young Richard L , Gatford Kathryn L 
Published: June 2024

Abstract

Context
Pregnancy increases nutrient demand, but how nutrient uptake and its determinants adapt to facilitate this is unclear.

Objective
This review aimed to identify and characterize evidence and evidence gaps regarding changes in gastrointestinal nutrient absorption and its determinants during pregnancy in monogastric mammals.

Data Sources
A scoping review of peer-reviewed sources was conducted across PubMed, Scopus, Web of Science, Embase, and ProQuest (theses and dissertations) databases.

Data Extraction
Data extracted included species, pregnancy stages and outcomes. Where sufficient data for a given outcome was available, relative values were summarized graphically or in tables, to allow comparison across pregnancy stages and/or small intestine regions. Searches identified 26 855 sources, of which only 159 were eligible. Mechanistic studies were largely restricted to rodents, and most compared non- and late-pregnant groups, with fewer studies including early- or mid-pregnant groups.

Data Analysis
During pregnancy, there is some evidence for greater capacity for glucose uptake but unchanged amino acid uptake, and good evidence for increased uptake of calcium, iron, and zinc, and slower gastrointestinal passage of nutrients. The available evidence indicates that acute glucose uptake, gastric emptying, and the activities of sucrase, maltase, and lactase do not change during pregnancy. Gaps in the knowledge include the effects of pregnancy on uptake of specific amino acids, lipids, and most minerals and vitamins.

Conclusion
The results indicate that the gastrointestinal tract adapts during pregnancy to facilitate increased nutrient absorption. Additional data is required in order to assess the underlying mechanisms for and impacts on the absorption of many nutrients, as well as to determine the timing of these adaptations.
Why is a small sample size not enough?
Authors: Cao Ying , Chen Ronald C , Katz Aaron J 
Published: June 2024

Abstract

Background
Clinical studies are often limited by resources available, which results in constraints on sample size. We use simulated data to illustrate study implications when the sample size is too small.

Methods and Results
Using 2 theoretical populations each with N = 1000, we randomly sample 10 from each population and conduct a statistical comparison, to help make a conclusion about whether the 2 populations are different. This exercise is repeated for a total of 4 studies: 2 concluded that the 2 populations are statistically significantly different, while 2 showed no statistically significant difference.

Conclusions
Our simulated examples demonstrate that sample sizes play important roles in clinical research. The results and conclusions, in terms of estimates of means, medians, Pearson correlations, chi-square test, and P values, are unreliable with small samples.
Multigenerational spaces: the usage and activities of different age groups within six community parks in Victoria, Australia
Authors: Levinger Pazit , Dreher Bronwyn L , Soh Sze-Ee , Dow Briony , Batchelor Frances , Hill Keith D 
Published: June 2024

Abstract

Background
This study investigated how different spaces within multigenerational local parks are being used by older people and other age groups.

Methods
Observation of park visitors occurred in six Victorian parks one month after park refurbishment. Parks were classified into six spaces based on equipment/amenities and associated expected activity. Observations were summarized descriptively, and negative binomial regression models were used to examine the association between visitor counts and classified targeted areas.

Results
A total of 12 501 people visited the parks with 4.1% older visitors. The number of older visitors in each park area was consistently less than other age groups, with counts of older visitors being 50% less in mixed spaces (95% confidence interval [CI] 0.38, 0.65), 40% less in adult exercise equipment areas (95% CI 0.46, 0.77) and 59% less in walking paths (95% CI 0.31, 0.55). The number of older visitors engaging in physical activity were significantly greater in walking paths (incidence rate ratios 1.75; 95% CI 1.16, 2.64) compared with children’s play spaces.

Conclusion
The number of visitors across different age groups varied significantly between the park targeted areas. Most spaces were mainly used by the intended target age group/user, with no particular area used by all age groups in similar proportions.
Using Divide-and-Conquer to Improve Tax Collection
Authors: Kapon Samuel , Del Carpio Lucia , Chassang Sylvain 
Published: June 2024

Abstract
Tax collection with limited enforcement capacity may be consistent with both high- and low-delinquency regimes: high delinquency reduces the effectiveness of threats, thereby reinforcing high delinquency. We explore the practical challenges of unraveling the high-delinquency equilibrium using a mechanism design insight known as divide-and-conquer. Our preferred mechanism takes the form of prioritized iterative enforcement (PIE). Taxpayers are ranked using the ratio of expected collection to capacity use. Collection threats are issued in small batches to ensure high credibility and induce high compliance. Following repayments, liberated capacity is used to issue the next round of threats. In collaboration with a district of Lima, we experimentally assess PIE in a sample of 13,432 property taxpayers. The data validate and refine our theoretical framework. A semi-structural model suggests that keeping collection actions fixed, PIE would increase tax revenue by roughly 10%.
Effects of N-Methyl-d-Aspartate Receptor Antagonists on Gamma-Band Activity During Auditory Stimulation Compared With Electro/Magneto-encephalographic Data in Schizophrenia and Early-Stage Psychosis: A Systematic Review and Perspective
Authors: Bianciardi Bianca , Mastek Helena , Franka Michelle , Uhlhaas Peter J 
Published: June 2024

Abstract

Background and Hypothesis
N-Methyl-d-aspartate receptor (NMDA-R) hypofunctioning has been hypothesized to be involved in circuit dysfunctions in schizophrenia (ScZ). Yet, it remains to be determined whether the physiological changes observed following NMDA-R antagonist administration are consistent with auditory gamma-band activity in ScZ which is dependent on NMDA-R activity.

Study Design
This systematic review investigated the effects of NMDA-R antagonists on auditory gamma-band activity in preclinical (n = 15) and human (n = 3) studies and compared these data to electro/magneto-encephalographic measurements in ScZ patients (n = 37) and 9 studies in early-stage psychosis. The following gamma-band parameters were examined: (1) evoked spectral power, (2) intertrial phase coherence (ITPC), (3) induced spectral power, and (4) baseline power.

Study Results
Animal and human pharmacological data reported a reduction, especially for evoked gamma-band power and ITPC, as well as an increase and biphasic effects of gamma-band activity following NMDA-R antagonist administration. In addition, NMDA-R antagonists increased baseline gamma-band activity in preclinical studies. Reductions in ITPC and evoked gamma-band power were broadly compatible with findings observed in ScZ and early-stage psychosis patients where the majority of studies observed decreased gamma-band spectral power and ITPC. In regard to baseline gamma-band power, there were inconsistent findings. Finally, a publication bias was observed in studies investigating auditory gamma-band activity in ScZ patients.

Conclusions
Our systematic review indicates that NMDA-R antagonists may partially recreate reductions in gamma-band spectral power and ITPC during auditory stimulation in ScZ. These findings are discussed in the context of current theories involving alteration in E/I balance and the role of NMDA hypofunction in the pathophysiology of ScZ.
Intact Serial Dependence in Schizophrenia: Evidence from an Orientation Adjustment Task
Authors: Pascucci David , Roinishvili Maya , Chkonia Eka , Brand Andreas , Whitney David , Herzog Michael H , Manassi Mauro 
Published: June 2024

Abstract

Background and Hypothesis
For a long time, it was proposed that schizophrenia (SCZ) patients rely more on sensory input and less on prior information, potentially leading to reduced serial dependence—ie, a reduced influence of prior stimuli in perceptual tasks. However, existing evidence is constrained to a few paradigms, and whether reduced serial dependence reflects a general characteristic of the disease remains unclear.

Study Design
We investigated serial dependence in 26 SCZ patients and 27 healthy controls (CNT) to evaluate the influence of prior stimuli in a classic visual orientation adjustment task, a paradigm not previously tested in this context.

Study Results
As expected, the CNT group exhibited clear serial dependence, with systematic biases toward the orientation of stimuli shown in the preceding trials. Serial dependence in SCZ patients was largely comparable to that in the CNT group.

Conclusions
These findings challenge the prevailing notion of reduced serial dependence in SCZ, suggesting that observed differences between healthy CNT and patients may depend on aspects of perceptual or cognitive processing that are currently not understood.
Personalized Cognitive Health in Psychiatry: Current State and the Promise of Computational Methods
Authors: Chen Cathy S , Vinogradov Sophia 
Published: June 2024

Abstract

Background
Decades of research have firmly established that cognitive health and cognitive treatment services are a key need for people living with psychosis. However, many current clinical programs do not address this need, despite the essential role that an individual’s cognitive and social cognitive capacities play in determining their real-world functioning. Preliminary practice-based research in the Early Psychosis Intervention Network early psychosis intervention network shows that it is possible to develop and implement tools that delineate an individuals’ cognitive health profile and that help engage the client and the clinician in shared decision-making and treatment planning that includes cognitive treatments. These findings signify a promising shift toward personalized cognitive health.

Study Design
Extending upon this early progress, we review the concept of interindividual variability in cognitive domains/processes in psychosis as the basis for offering personalized treatment plans. We present evidence from studies that have used traditional neuropsychological measures as well as findings from emerging computational studies that leverage trial-by-trial behavior data to illuminate the different latent strategies that individuals employ.

Study Result
We posit that these computational techniques, when combined with traditional cognitive assessments, can enrich our understanding of individual differences in treatment needs, which in turn can guide evermore personalized interventions.

Conclusion
As we find clinically relevant ways to decompose maladaptive behaviors into separate latent cognitive elements captured by model parameters, the ultimate goal is to develop and implement approaches that empower clients and their clinical providers to leverage individual’s existing learning capacities to improve their cognitive health and well-being.
Artificial intelligence and nonoperating room anesthesia
Authors: Pardo Emmanuel , Le Cam Elena , Verdonk Franck 
Published: June 2024

Purpose of review
The integration of artificial intelligence (AI) in nonoperating room anesthesia (NORA) represents a timely and significant advancement. As the demand for NORA services expands, the application of AI is poised to improve patient selection, perioperative care, and anesthesia delivery. This review examines AI's growing impact on NORA and how it can optimize our clinical practice in the near future.

Recent findings
AI has already improved various aspects of anesthesia, including preoperative assessment, intraoperative management, and postoperative care. Studies highlight AI's role in patient risk stratification, real-time decision support, and predictive modeling for patient outcomes. Notably, AI applications can be used to target patients at risk of complications, alert clinicians to the upcoming occurrence of an intraoperative adverse event such as hypotension or hypoxemia, or predict their tolerance of anesthesia after the procedure. Despite these advances, challenges persist, including ethical considerations, algorithmic bias, data security, and the need for transparent decision-making processes within AI systems.

Summary
The findings underscore the substantial benefits of AI in NORA, which include improved safety, efficiency, and personalized care. AI's predictive capabilities in assessing hypoxemia risk and other perioperative events, have demonstrated potential to exceed human prognostic accuracy. The implications of these findings advocate for a careful yet progressive adoption of AI in clinical practice, encouraging the development of robust ethical guidelines, continual professional training, and comprehensive data management strategies. Furthermore, AI's role in anesthesia underscores the need for multidisciplinary research to address the limitations and fully leverage AI's capabilities for patient-centered anesthesia care.
Population pharmacokinetics of Ainuovirine and exposure–response analysis in human immunodeficiency virus-infected individuals
Authors: Han Xiaoxu , Sun Jin , Zhang Yihang , Jiang Taiyi , Zheng Qingshan , Peng Haiyan , Wang Yao , Xia Wei , Zhang Tong , Sun Lijun , Yun Xinming , Qin Hong , Wu Hao , Su Bin 
Published: June 2024

Abstract

Background:
Ainuovirine (ANV) is a new generation of non-nucleoside reverse transcriptase inhibitor for the treatment of human immunodeficiency virus (HIV) type 1 infection. This study aimed to evaluate the population pharmacokinetic (PopPK) profile and exposure–response relationship of ANV among people living with HIV.

Methods:
Plasma concentration-time data from phase 1 and phase 3 clinical trials of ANV were pooled for developing the PopPK model. Exposure estimates obtained from the final model were used in exposure–response analysis for virologic responses and safety responses.

Results:
ANV exhibited a nonlinear pharmacokinetic profile, which was best described by a two-compartment model with first-order elimination. There were no significant covariates correlated to the pharmacokinetic parameters of ANV. The PopPK parameter estimate (relative standard error [%]) for clearance adjusted for bioavailability (CL/F) was 6.46 (15.00) L/h, and the clearance of ANV increased after multiple doses. The exposure–response model revealed no significant correlation between the virologic response (HIV-RNA <50 copies/mL) at 48 weeks and the exposure, but the incidence of adverse events increased with the increasing exposure (P value of steady-state trough concentration and area under the steady-state curve were 0.0177 and 0.0141, respectively).

Conclusions:
Our PopPK model supported ANV 150 mg once daily as the recommended dose for people living with HIV, requiring no dose adjustment for the studied factors. Optimization of ANV dose may be warranted in clinical practice due to an increasing trend in adverse reactions with increasing exposure.

Trial registration:
Chinese Clinical Trial Registry https://www.chictr.org.cn (Nos. ChiCTR1800018022 and ChiCTR1800019041).
Prenatal efavirenz exposure is independently associated with maternal, but not fetal CYP2B6 genotype
Authors: Eniayewu Oluwasegun , Akinloye Abdulafeez , Shenkoya Babajide , Azuka Uche , Bolaji Oluseye , Adejuyigbe Ebunoluwa , Owen Andrew , Olagunju Adeniyi 
Published: June 2024

Objectives
Understanding the influence of fetal and maternal genetics on prenatal drug exposure could potentially improve benefit-risk evaluation. In this study, we investigated the impact of two functional polymorphisms in CYP2B6 on prenatal exposure to efavirenz.

Methods
Dried blood spot (DBS) samples were collected from HIV-positive pregnant women (n = 112) and their newborns (n = 107) at delivery. They were genotyped for single nucleotide polymorphisms in CYP2B6. Efavirenz was quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

Results
Significant correlations were observed in efavirenz concentration between maternal and newborn (r = 0.46, R
2 = 0.21, P < 0.001), and maternal and cord (r = 0.83, R
2 = 0.68, P < 0.001) samples. Median (interquartile range) newborn plasma-to-maternal plasma and cord-to-maternal plasma ratios were 0.85 (0.03–3.49) and 0.78 (0.23–1.96), respectively. Newborn efavirenz concentration in DBS varied significantly based on composite maternal CYP2B6 genotype: fast (CYP2B6 516GG and 983TT, n = 26), 747 ng/ml (602–1060); intermediate (CYP2B6 516GT or 983TC n = 50), 1177 ng/ml (898–1765); and slow (CYP2B6 516GT and 983TC or 516TT or 983CC, n = 14), 3094 ng/ml (2126–3812). Composite newborn CYP2B6 genotype was, however, not significantly associated with prenatal exposure. Efavirenz concentration in newborn stratified as fast (n = 25), intermediate (n = 36), and slow metabolizers (n = 19) from prenatal exposure was 999.7 (774–1285), 1240 (709–1984), and 1792 ng/ml (1201–3188), respectively.

Conclusion
The clinical relevance of the observed influence of maternal genetics on prenatal efavirenz exposure requires further investigation.
Improving diversity in cardiac surgery clinical trials with ROMA:Women as an exemplar
Authors: Masterson Creber Ruth , Eslami Sarah , Gaudino Mario 
Published: June 2024

Purpose of review
To describe methods to improve representation of women in cardiac surgery clinical trials.

Recent findings
Cardiovascular disease risk among women is high. Historically, women have been excluded from cardiac surgery trials, in part due to restrictive inclusion criteria. Surgical outcomes, specifically after coronary artery bypass grafting, are consistently worse among female patients, and these outcomes have not improved over the last decade. Addressing treatment effects and clinical benefit among women requires accurate representation in cardiovascular surgery trials. ROMA:Women, is the first cardiac surgery trial to focus solely on women, with the goal of addressing underrepresentation. Through utilizing specific strategies, ROMA:Women is a promising first step in advancing health equity.

Summary
Strategies to ensure effective recruitment and representation among women in cardiac surgery clinical trials, such as tailored eligibility criteria and comprehensive strategies to improve communication and increase trust, are two of many potential approaches to address the structural barriers to female representation in cardiac surgery clinical trials. To date, ROMA:Women is an example of a trial that has shown extraordinary preliminary success enrolling women. Designing trials exclusively for women is one strategy to improve the diversity of clinical trial participation.
Docetaxel-induced pigmentary maculopathy
Authors: Skrehot Henry C. , Alsoudi Amer , Chang Emmanuel Y. , Holz Eric R. 
Published: June 2024

Purpose:
To report a case of bilateral docetaxel-induced pigmentary maculopathy in an adult.

Methods:
A 79-year-old male with prostate cancer was treated with docetaxel and subsequently developed progressively worsening blurred vision. Prior to initiation of docetaxel therapy, his best corrected visual acuity (BCVA) was 20/20 in the right and left eye. He presented to clinic 5 months after the initiation of docetaxel therapy with BCVA of 20/70 and 20/40 -2 in the right and left eye, respectively. Fundoscopic exam was notable for bilateral focal central areas of macular hyperpigmentation. Toxic maculopathy secondary to docetaxel was suspected and the recommendation to discontinue docetaxel was made to the oncologist.

Results:
Five months after discontinuation of docetaxel, the patient’s BCVA improved to 20/40 -2 in the right and left eye. Fundoscopic exam was stable in both eyes.

Conclusion:
Bilateral pigmentary maculopathy presenting as focal areas of macular hyperpigmentation developed after initiation of docetaxel in an adult with no previous ocular history. Prompt diagnosis and cessation of docetaxel resulted in stable disease.
Leber hereditary optic neuropathy: A case report of concurrent rare mitochondrial mutations and ABCA4 nuclear gene mutation
Authors: Ashrafkhorasani Maryam , Chou Brian , Sadun Alfredo A. 
Published: June 2024

Purpose:
This case report aims to describe the clinical presentation of a 21-year-old male patient with subacute bilateral painless vision loss, clinically consistent with Leber hereditary optic neuropathy (LHON), a mitochondrially inherited disorder and to investigate the genetic mutations associated with this condition.

Methods:
Genetic testing was performed on the patient to identify potential LHON-related mutations. Additionally, the patient's medical history and clinical examination findings were recorded.

Results:
The patient tested negative for the three most common LHON-related mutations but exhibited two homoplasmic mitochondrial mutations with unclear significance, m3461 C>T (MT-ND1) and m9358 C>T (MT_CO3). Furthermore, two pathogenic variants of ABCA4 (c.3322>T and c.4539+2028 C>T) were identified in the patient's genetic profile.
Discussion/conclusion: This case underscores the complex interplay between mitochondrial and nuclear mutations in the pathophysiology of LHON. Despite the absence of common LHON mutations, the presence of these mitochondrial and nuclear mutations likely contributed to the patient's LHON phenotype. This case also highlights the importance of considering environmental factors and genetic interactions in LHON development.