bluuebunny/crossref_metadata_2025_split huggingface dataset:
What Is It like to Have a Gender Identity?
Authors: Ashley Florence 
Published: July 2023

Abstract
By attending to how people speak about their gender, we can find diverse answers to the question of what it is like to have a gender identity. To some, it is little more than having a body whereas others may report it as more attitudinal or dispositional—seemingly contradictory views. In this paper, I seek to reconcile these disparate answers by developing a theory of how individual gender identity comes about. In the simplest possible terms, I propose that gender identity is how we make sense of our gender subjectivity, the totality of our gendered experiences of ourselves. Gender identity is constituted by gender subjectivity, but this constitutive relationship is underdetermined. While gender subjectivity may narrow the range of inhabitable gender identities, it is always compatible with more than one. To arrive at a gender identity, we arrange gender subjectivity like building materials. My theory helps us understand how different people offer seemingly incompatible accounts of their gender identity without questioning their authenticity or validity. They simply arrange similar building materials differently.
The formation of globular clusters with top-heavy initial mass functions
Authors: Fukushima Hajime , Yajima Hidenobu 
Published: July 2023

ABSTRACT
We study the formation of globular clusters (GCs) in massive compact clouds with the low metallicity of Z = 10−3 Z⊙ by performing three-dimensional radiative-hydrodynamic simulations. Considering the uncertainty of the initial mass function (IMF) of stars formed in low-metallicity and high-density clouds, we investigate the impacts of the IMF on the cloud condition for the GC formation with the range of the power-law index of IMF as γ = 1−2.35. We find that the threshold surface density (Σthr) for the GC formation increases from 800 M⊙ pc−2 at γ = 2.35 to 1600 M⊙ pc−2 at γ = 1.5 in the cases of clouds with Mcl = 106 M⊙ because the emissivity of ionizing photons per stellar mass increases as γ decreases. For γ &lt; 1.5, Σthr saturates with ∼2000 M⊙ pc−2 that is quite rare and observed only in local starburst galaxies due to e.g. merger processes. Thus, we suggest that formation sites of low-metallicity GCs could be limited only in the very high-surface density regions. We also find that Σthr can be modelled by a power-law function with the cloud mass (Mcl) and the emissivity of ionizing photons (s*) as $\propto M_{\rm cl}^{-1/5} s_{*}^{2/5}$. Based on the relation between the power-law slope of IMF and Σthr, future observations with e.g. the JWST can allow us to constrain the IMF of GCs.
Machine learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons
Authors: Meng Zhisen , Zhang Yong , Liang Enwei , Wang Zhao 
Published: July 2023

ABSTRACT
Machine learning feature importance calculations are used to determine the molecular substructures that are responsible for mid- and far-infrared (IR) emission features of neutral polycyclic aromatic hydrocarbons (PAHs). Using the extended-connectivity fingerprint as a descriptor of chemical structure, a random forest model is trained on the spectra of 14 124 PAHs to evaluate the importance of 10 632 molecular fragments for each band within the range of 2.761 to $1172.745\, \mu$m. The accuracy of the results is confirmed by comparing them with previously studied unidentified infrared emission (UIE) bands. The results are summarized in two tables available as Supplementary Data, which can be used as a reference for assessing possible UIE carriers. We demonstrate that the tables can be used to explore the relation between the PAH structure and the spectra by discussing about the IR features of nitrogen-containing PAHs and superhydrogenated PAHs.
Jasmonate-mediated gibberellin catabolism constrains growth during herbivore attack in rice
Authors: Jin Gaochen , Qi Jinfeng , Zu Hongyue , Liu Shuting , Gershenzon Jonathan , Lou Yonggen , Baldwin Ian T , Li Ran 
Published: July 2023

Abstract
Plant defense against herbivores is costly and often associated with growth repression. The phytohormone jasmonate (JA) plays a central role in prioritizing defense over growth during herbivore attack, but the underlying mechanisms remain unclear. When brown planthoppers (BPH, Nilaparvata lugens) attack rice (Oryza sativa), growth is dramatically suppressed. BPH infestation also increases inactive gibberellin (GA) levels and transcripts of GA 2-oxidase (GA2ox) genes, 2 (GA2ox3 and GA2ox7) of which encode enzymes that catalyze the conversion of bioactive GAs to inactive GAs in vitro and in vivo. Mutation of these GA2oxs diminishes BPH-elicited growth restriction without affecting BPH resistance. Phytohormone profiling and transcriptome analyses revealed that GA2ox-mediated GA catabolism was enhanced by JA signaling. The transcript levels of GA2ox3 and GA2ox7 were significantly attenuated under BPH attack in JA biosynthesis (allene oxide cyclase [aoc]) or signaling-deficient (myc2) mutants. In contrast, GA2ox3 and GA2ox7 expression was increased in MYC2 overexpression lines. MYC2 directly binds to the G-boxes in the promoters of both GA2ox genes to regulate their expression. We conclude that JA signaling simultaneously activates defense responses and GA catabolism to rapidly optimize resource allocation in attacked plants and provides a mechanism for phytohormone crosstalk.
Are unrefreshing naps associated with nocturnal sleep architecture specificities in idiopathic hypersomnia?
Authors: Mombelli Samantha , Deshaies-Rugama Anne-Sophie , Blais Hélène , Sekerovic Zoran , Thompson Cynthia , Desautels Alex , Montplaisir Jacques , Nigam Milan , Carrier Julie , Gosselin Nadia 
Published: July 2023

Abstract

Study Objectives
Unrefreshing naps are supportive clinical features of idiopathic hypersomnia (IH) and are reported by more than 50% of IH patients. They are, however, not mandatory for the diagnosis, and their pathophysiological nature is not understood. This study aimed at verifying whether IH patients with and without unrefreshing naps constitute two subtypes of IH based on their demographic/clinical characteristics, and sleep architecture.

Methods
One hundred twelve IH patients underwent a polysomnography (PSG) followed by a multiple sleep latency test (MSLT). They completed questionnaires on excessive daytime sleepiness, mood, and sleep quality. They were met by sleep medicine physicians who conducted a semi-structured clinical interview and questioned them on refreshing aspects of their naps. Patients who reported unrefreshing naps were compared to patients reporting refreshing naps on questionnaires, MSLT and PSG variables, with age as a covariable. As sensitivity analyses, we performed the same comparisons in participants presenting objective markers of IH and those diagnosed with IH based only on clinical judgment (subjective IH), separately.

Results
In the whole sample, 61% of patients reported unrefreshing naps. These participants had less awakenings, a lower percentage of N1 sleep, less sleep stage transitions, and a higher percentage of REM sleep on the nighttime PSG compared to the refreshing naps subgroup. When subjective and objective IH patients were tested separately, more group differences were observed on PSG for subjective IH patients.

Conclusions
Patients with unrefreshing naps have less fragmented sleep compared to those with refreshing naps. Future studies should investigate whether this group difference indicates a weaker arousal drive.
Influence of dietary oils rich in omega-6 or omega-3 fatty acids on rumen microbiome of dairy cows
Authors: Cancino-Padilla Nathaly , Gajardo Felipe , Neves André Luis Alves , Kholif Ahmed Eid , Mele Marcello , Huws Sharon A , Loor Juan J , Romero Jaime , Vargas-Bello-Pérez Einar 
Published: July 2023

Abstract
The objective of this study was to compare the effect of supplementing dairy cow diets with contrasting sources of omega-6 (soybean oil) and omega-3 (fish oil) PUFA on rumen microbiome. For 63 d, 15 mid-lactating cows were fed a control diet (n = 5 cows; no fat supplement) or control diet supplemented with 2.9% dry matter (DM) of either soybean oil (SO; n = 5 cows) or fish oil (FO; n = 5 cows). Ruminal contents were collected on days 0, 21, 42, and 63 for 16S rRNA gene sequencing. Beta diversity and Shannon, Simpson and Chao1 diversity indices were not affected by dietary treatments. In terms of core microbiome, Succiniclasticum, Prevotella, Rikenellaceae_RC9_gut_group, and NK4A214_group were the most prevalent taxa regardless of treatments. Bifidobacterium was absent in SO diet, Acetitomaculum was absent in FO, and Sharpea was only detected in SO. Overall, results showed that at 2.9% DM supplementation of either SO or FO over 63 days in dairy cow diets does not cause major impact on bacterial community composition and thus is recommended as feeding practice.
Zeb1 and Tle3 aretrans‐factors that differentially regulate the expression of myosin heavy chain‐embryonic and skeletal muscle differentiation
Authors: Kumar Pankaj , Zehra Aatifa , Saini Masum , Mathew Sam J. 
Published: July 2023

AbstractMyosin heavy chain‐embryonic encoded by theMyh3gene is a skeletal muscle‐specific contractile protein expressed during mammalian development and regeneration, essential for proper myogenic differentiation and function. It is likely that multipletrans‐factors are involved in this precise temporal regulation ofMyh3expression. We identify a 4230 bp promoter‐enhancer region that drivesMyh3transcription in vitro during C2C12 myogenic differentiation and in vivo during muscle regeneration, including sequences both upstream and downstream of theMyh3TATA‐box that are necessary for completeMyh3promoter activity. Using C2C12 mouse myogenic cells, we find that Zinc‐finger E‐box binding homeobox 1 (Zeb1) and Transducin‐like Enhancer of Split 3 (Tle3) proteins are crucialtrans‐factors that interact and differentially regulateMyh3expression. Loss of Zeb1 function results in earlier expression of myogenic differentiation genes and accelerated differentiation, whereas Tle3 depletion leads to reduced expression of myogenic differentiation genes and impaired differentiation. Tle3 knockdown resulted in downregulation of Zeb1, which could be mediated by increased expression ofmiR‐200c, a microRNA that binds toZeb1transcript and degrades it. Tle3 functions upstream of Zeb1 in regulating myogenic differentiation since double knockdown ofZeb1andTle3resulted in effects seen uponTle3depletion. We identify a novel E‐box in theMyh3distal promoter‐enhancer region, where Zeb1 binds to repressMyh3expression. In addition to regulation of myogenic differentiation at the transcriptional level, we uncover post‐transcriptional regulation by Tle3 to regulateMyoGexpression, mediated by the mRNA stabilizing Human antigen R (HuR) protein. Thus, Tle3 and Zeb1 are essentialtrans‐factors that differentially regulateMyh3expression and C2C12 cell myogenic differentiation in vitro.
CD226 deficiency attenuates cardiac early pathological remodeling and dysfunction via decreasing inflammatory macrophage proportion and macrophage glycolysis in STZ‐induced diabetic mice
Authors: Hou Yongli , Wang Yazhen , Tang Kang , Yang Yan , Wang Yiwei , Liu Ruiyan , Wu Bin , Chen Xutao , Fu Zhaoyue , Zhao Feng , Chen Lihua 
Published: July 2023

AbstractDiabetic cardiomyopathy (DCM) is one of the main complications in type I diabetic patients. Activated macrophage is critical for directing the process of inflammation during the development of DCM. The present study focused on the roles of CD226 on macrophage function during the DCM progression. It has been found that the number of cardiac macrophages in the hearts of streptozocin (STZ)‐induced diabetes mice was significantly increased compared with that in non‐diabetes mice, and the expression level of CD226 on cardiac macrophages in STZ‐induced diabetes mice was higher than that in non‐diabetes mice. CD226 deficiency attenuated the diabetes‐induced cardiac dysfunction and decreased the proportion of CD86+F4/80+ macrophages in the diabetic hearts. Notably, adoptive transfer of Cd226−/−‐ bone marrow derived macrophages (BMDMs) alleviated diabetes‐induced cardiac dysfunction, which may be due to the attenuated migration capacity of Cd226−/−‐BMDM under high glucose stimulation. Furthermore, CD226 deficiency decreased the macrophage glycolysis accompanying by the downregulated hexokinase 2 (HK2) and lactate dehydrogenase A (LDH‐A) expression. Taken together, these findings revealed the pathogenic roles of CD226 played in the process of DCM and provided a basis for the treatment of DCM.
The Impact of an Emergency Department Bruising Pathway on Disparities in Child Abuse Evaluation
Authors: Crumm Caitlin E. , Brown Emily C.B. , Vora Surabhi B. , Lowry Sarah , Schlatter Adrienne , Rutman Lori E. 
Published: July 2023

Objectives
Previous research has shown racial, ethnic, and socioeconomic disparities in provider medical evaluations and reporting to child protective services (CPS) and law enforcement (LE) for cases of suspected child physical abuse. Our hospital standardized evaluation and reporting of high-risk bruising using a clinical pathway. We aimed to assess whether standardization impacted disparity.

Methods
We performed a retrospective observational study including children evaluated in the emergency department who had a social work consult for concern for child abuse or neglect between June 2012 and December 2019. From this group, we identified children with high-risk bruising. We compared outcomes (receipt of skeletal survey, CPS report, or LE report) before and after implementation of a standard bruising evaluation pathway to determine how the intervention changed practice among various racial, ethnic, and socioeconomic groups.

Results
During the study period, 2129 children presented to the ED and received a social work consult for child abuse or neglect. Of these, 333 had high-risk bruising. Children without private insurance had a higher risk of having a CPS (adjusted relative risk, 1.32; 95% confidence interval, 1.09–1.60) or LE (adjusted relative risk, 1.48; 95% confidence interval, 1.11–1.97) report prepathway, but not after pathway implementation. No significant associations were seen for race or ethnicity.

Conclusions
A standardized clinical pathway for identification and evaluation of high-risk bruising may help to decrease socioeconomic disparities in reporting high-risk bruising. Larger studies are needed to fully evaluate disparities in assessment and reporting of child abuse.
Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency
Authors: Yue Ye , Read Timothy D. , Fedirko Veronika , Satten Glen A. , Hu Yi-Juan 
Published: July 2023

AbstractThe most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for the objective of testing differential abundance at the genus and community levels while overcoming these difficulties. We demonstrate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than twoad hocapproaches.
Comparative analysis of single-cell RNA sequencing methods with and without sample multiplexing
Authors: Xie Yi , Chen Huimei , Chellamuthu Vasuki Ranjani , Lajam Ahmad bin Mohamed , Albani Salvatore , Low Andrea Hsiu Ling , Petretto Enrico , Behmoaras Jacques 
Published: July 2023

AbstractSingle-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating biological heterogeneity at the single-cell level in human systems and model organisms. Recent advances in scRNA-seq have enabled the pooling of cells from multiple samples into single libraries, thereby increasing sample throughput while reducing technical batch effects, library preparation time, and the overall cost. However, a comparative analysis of scRNA-seq methods with and without sample multiplexing is lacking. In this study, we benchmarked methods from two representative platforms: Parse Biosciences (Parse; with sample multiplexing) and 10X Genomics (10x; without sample multiplexing). By using peripheral blood mononuclear cells (PBMCs) obtained from two healthy individuals, we demonstrate that demultiplexed scRNA-seq data obtained from Parse showed similar cell type frequencies compared to 10X data where samples are not multiplexed. Despite a relatively lower library and cell capture efficiencies, Parse can detect rare cell types (e.g. plasmablasts and dendritic cells) which is likely due to its relatively higher sensitivity in gene detection. Moreover, comparative analysis of transcript quantification between the two platforms revealed platform-specific distributions of gene length and GC content. These results offer guidance for researchers in designing high-throughput scRNA-seq studies.
A distributed theta network of error generation and processing in aging
Authors: Kolev Vasil , Falkenstein Michael , Yordanova Juliana 
Published: July 2023

AbstractBased on previous concepts that a distributed theta network with a central “hub” in the medial frontal cortex is critically involved in movement regulation, monitoring, and control, the present study explored the involvement of this network in error processing with advancing age in humans. For that aim, the oscillatory neurodynamics of motor theta oscillations was analyzed at multiple cortical regions during correct and error responses in a sample of older adults.Response-related potentials (RRPs) of correct and incorrect reactions were recorded in a four-choice reaction task. RRPs were decomposed in the time-frequency domain to extract oscillatory theta activity. Motor theta oscillations at extended motor regions were analyzed with respect to power, temporal synchronization, and functional connectivity.Major results demonstrated that errors had pronounced effects on motor theta oscillations at cortical regions beyond the medial frontal cortex by being associated with (1) theta power increase in the hemisphere contra-lateral to the movement, (2) suppressed spatial and temporal synchronization at pre-motor areas contra-lateral to the responding hand, (2) inhibited connections between the medial frontal cortex and sensorimotor areas, and (3) suppressed connectivity and temporal phase-synchronization of motor theta networks in the posterior left hemisphere, irrespective of the hand, left, or right, with which the error was made.These findings reveal distributed effects of errors on motor theta oscillations in older subjects and support the hypothesis that error processing operates on a network level. They confirm the presence of aging-dependent functional disengagement of the medial frontal region and suggest that difficulties in controlling the focus of motor attention and response selection contribute to performance impairment in old individuals.
LRRK2 G2019S promotes the development of colon cancer via modulating intestinal inflammation
Authors: Wang Yuhang , Gao Joyce Z , Sakaguchi Taylor , Maretzky Thorsten , Gurung Prajwal , Short Sarah , Xiong Yiqin , Kang Zizhen 
Published: July 2023

AbstractLRRK2 G2019S is the most prevalent variant associated with Parkinson’s disease (PD), found in 1-3% of sporadic and 4-8% of familial PD cases. Intriguingly, emerging clinical studies have suggested that LRRK2 G2019S carriers have an increased risk of cancers including colorectal cancer. However, the underlying mechanisms of the positive correlation between LRRK2-G2019S and colorectal cancer remain unknown. Using a mouse model of colitis-associated cancer (CAC) and LRRK2 G2019S knockin (KI) mice, here we report that LRRK2 G2019S promotes the pathogenesis of colon cancer as evidenced by increased tumor number and tumor size in LRRK2 G2019S KI mice. LRRK2 G2019S promoted intestinal epithelial cell proliferation and inflammation within the tumor microenvironment. Mechanistically, we found that LRRK2 G2019S KI mice are more susceptible to dextran sulfate sodium (DSS)-induced colitis. Suppressing the kinase activity of LRRK2 ameliorated the severity of colitis in both LRRK2 G2019S KI and WT mice. At the molecular level, our investigation unveiled that LRRK2 G2019S promotes the production of reactive oxygen species, triggers inflammasome activation, and induces cell necrosis in the gut epithelium in a mouse model of colitis. Collectively, our data provide direct evidence that gain-of-kinase activity in LRRK2 promotes colorectal tumorigenesis, implicating LRRK2 as a potential target in colon cancer patients with hyper LRRK2 kinase activity.
Hippocampal contributions to novel spatial learning are both age-related and age-invariant
Authors: Zheng Li , Gao Zhiyao , Doner Stephanie , Oyao Alexis , Forloines Martha , Grilli Matthew D. , Barnes Carol A. , Ekstrom Arne D. 
Published: July 2023

AbstractOlder adults show declines in spatial memory, although the extent of these alterations is not uniform across the healthy older population. Here, we investigate the stability of neural representations for the same and different spatial environments in a sample of younger and older adults using high-resolution functional magnetic resonance imaging (fMRI) of the medial temporal lobe. Older adults showed, on average, lower neural pattern similarity for retrieving the same environment and more variable neural patterns compared to young adults. We also found a positive association between spatial distance discrimination and the distinctiveness of neural patterns between environments. Our analyses suggested that one source for this association was the extent of informational connectivity to CA1 from other subfields, which was dependent on age, while another source was the fidelity of signals within CA1 itself, which was independent of age. Together, our findings suggest both age-dependent and independent neural contributions to spatial memory performance.Significance StatementSpatial memory declines with age, although some older adults show little cognitive decline, even into their 80s. One important lead for age-related changes comes from electrophysiological studies of older rats, who have less stable neural representations for a spatial environment, termed “place cells.” Using high-resolution fMRI targeting the human hippocampus, we demonstrate that older adults also have less stable neural representations within the same environment. Our results reveal, however, that there are both age and performance dependent differences driving these effects. While older adults, on average, showed alterations in information flow within the hippocampal circuit, better performing individuals showed more differentiated neural representations regardless of age. Together, these findings provide novel insight into the impact of age on spatial memory.