bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining intermediate-mass black holes from the stellar disc of SgrA*
Authors: Fouvry Jean-Baptiste , Bustamante-Rosell María José , Zimmerman Aaron 
Published: September 2023

ABSTRACT
Stars evolving around a supermassive black hole see their orbital orientations diffuse efficiently, a process called ‘vector resonant relaxation’. In particular, stars within the same disc, i.e. neighbours in orientations, will slowly diffuse away from one another through this stochastic process. We use jointly (i) detailed kinetic predictions for the efficiency of this dilution and (ii) the recent observation of a stellar disc around SgrA*, the supermassive black hole at the centre of the Milky Way, to constrain SgrA*’s unobserved stellar cluster. Notably, we investigate quantitatively the impact of a population of intermediate-mass black holes on the survivability of the stellar disc.
When will RNA get its AlphaFold moment?
Authors: Schneider Bohdan , Sweeney Blake Alexander , Bateman Alex , Cerny Jiri , Zok Tomasz , Szachniuk Marta 
Published: September 2023

AbstractThe protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches. We believe that there are challenges preventing the successful development of deep learning-based methods like AlphaFold for RNA in the short term. Broadly speaking, the challenges are the limited number of structures and alignments making data-hungry deep learning methods unlikely to succeed. Additionally, there are several issues with the existing structure and sequence data, as they are often of insufficient quality, highly biased and missing key information. Here, we discuss these challenges in detail and suggest some steps to remedy the situation. We believe that it is possible to create an accurate RNA structure prediction method, but it will require solving several data quality and volume issues, usage of data beyond simple sequence alignments, or the development of new less data-hungry machine learning methods.
TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization
Authors: Cao Xuewei , Zhang Ling , Islam Md Khairul , Zhao Mingxia , He Cheng , Zhang Kui , Liu Sanzhen , Sha Qiuying , Wei Hairong 
Published: September 2023

Abstract
Four statistical selection methods for inferring transcription factor (TF)–target gene (TG) pairs were developed by coupling mean squared error (MSE) or Huber loss function, with elastic net (ENET) or least absolute shrinkage and selection operator (Lasso) penalty. Two methods were also developed for inferring pathway gene regulatory networks (GRNs) by combining Huber or MSE loss function with a network (Net)-based penalty. To solve these regressions, we ameliorated an accelerated proximal gradient descent (APGD) algorithm to optimize parameter selection processes, resulting in an equally effective but much faster algorithm than the commonly used convex optimization solver. The synthetic data generated in a general setting was used to test four TF–TG identification methods, ENET-based methods performed better than Lasso-based methods. Synthetic data generated from two network settings was used to test Huber-Net and MSE-Net, which outperformed all other methods. The TF–TG identification methods were also tested with SND1 and gl3 overexpression transcriptomic data, Huber-ENET and MSE-ENET outperformed all other methods when genome-wide predictions were performed. The TF–TG identification methods fill the gap of lacking a method for genome-wide TG prediction of a TF, and potential for validating ChIP/DAP-seq results, while the two Net-based methods are instrumental for predicting pathway GRNs.
Roles of citrus fruits on energy expenditure, body weight management, and metabolic biomarkers: a comprehensive review
Authors: Aslan Merve Nur , Sukan-Karaçağıl Betül , Acar-Tek Nilüfer 
Published: September 2023

Abstract
Citrus fruits are widely consumed for their nutritional and health benefits. They belong to the Rutaceae and have many varieties, such as sweet orange (Citrus sinensis), which is the most popular. Citrus fruits are rich in water (&gt;80%), dietary fiber, and vitamins. They also contain bioactive components, which may modulate energy metabolism and lipid oxidation through various mechanisms. These mechanisms include stimulating β3-adrenergic receptors, increasing mitochondrial biogenesis and thermogenesis, activating AMP kinase and peroxisome proliferator-activated receptor-gamma coactivator-1α pathways, inhibiting lipogenesis and lipid accumulation, and inducing browning of white adipose tissue. This review summarizes the mechanisms and outcomes of citrus fruits and their metabolites on energy metabolism and body weight in different experimental models. The literature was searched for in vitro and in vivo animal and human studies that investigated the effects of citrus consumption on energy expenditure, thermogenesis, adipogenesis, and lipid accumulation. Citrus fruits and their metabolites have shown promising effects on energy metabolism and lipid oxidation in in vitro and in vivo animal studies. However, the evidence from human studies is limited and inconsistent. Possible reasons for the discrepancy are briefly discussed, and knowledge gaps and research needs are identified for future studies. Citrus fruits may have beneficial effects on energy metabolism and body weight, but more rigorous and well-designed human trials are needed to confirm their efficacy and safety.
Root Primordium Defective 1 Encodes an Essential PORR Protein Required for the Splicing of Mitochondria-Encoded Group II Introns and for Respiratory Complex I Biogenesis
Authors: Edris Rana , Sultan Laure D , Best Corinne , Mizrahi Ron , Weinstein Ofir , Chen Stav , Kamennaya Nina A , Keren Nir , Zer Hagit , Zhu Hongliang , Ostersetzer-Biran Oren 
Published: September 2023

Abstract
Cellular respiration involves complex organellar metabolic activities that are pivotal for plant growth and development. Mitochondria contain their own genetic system (mitogenome, mtDNA), which encodes key elements of the respiratory machinery. Plant mtDNAs are notably larger than their counterparts in Animalia, with complex genome organization and gene expression characteristics. The maturation of the plant mitochondrial transcripts involves extensive RNA editing, trimming and splicing events. These essential processing steps rely on the activities of numerous nuclear-encoded cofactors, which may also play key regulatory roles in mitochondrial biogenesis and function and hence in plant physiology. Proteins that harbor the plant organelle RNA recognition (PORR) domain are represented in a small gene family in plants. Several PORR members, including WTF1, WTF9 and LEFKOTHEA, are known to act in the splicing of organellar group II introns in angiosperms. The AT4G33495 gene locus encodes an essential PORR protein in Arabidopsis, termed ROOT PRIMORDIUM DEFECTIVE 1 (RPD1). A null mutation of At.RPD1 causes arrest in early embryogenesis, while the missense mutant lines, rpd1.1 and rpd1.2, exhibit a strong impairment in root development and retarded growth phenotypes, especially under high-temperature conditions. Here, we further show that RPD1 functions in the splicing of introns that reside in the coding regions of various complex I (CI) subunits (i.e. nad2, nad4, nad5 and nad7), as well as in the maturation of the ribosomal rps3 pre-RNA in Arabidopsis mitochondria. The altered growth and developmental phenotypes and modified respiration activities are tightly correlated with respiratory chain CI defects in rpd1 mutants.
Physiological Functions of Phospholipid:Diacylglycerol Acyltransferases
Authors: Sah Saroj Kumar , Fan Jilian , Blanford Jantana , Shanklin John , Xu Changcheng 
Published: September 2023

Abstract
Triacylglycerol (TAG) is among the most energy dense storage forms of reduced carbon in living systems. TAG metabolism plays critical roles in cellular energy balance, lipid homeostasis, cell growth and stress responses. In higher plants, microalgae and fungi, TAG is assembled by acyl-CoA-dependent and acyl-CoA-independent pathways catalyzed by diacylglycerol (DAG) acyltransferase and phospholipid:DAG acyltransferase (PDAT), respectively. This review contains a summary of the current understanding of the physiological functions of PDATs. Emphasis is placed on their role in lipid remodeling and lipid homeostasis in response to abiotic stress or perturbations in lipid metabolism.
The Procedural Politicking Tug of War: Law-Versus-Management Disputes in Contexts of Democratic Backsliding
Authors: Spanghero Lotta Gabriela , Alves de Lima Iana , Costa Silveira Mariana , Fernandez Michelle , Paschoal Pedote João , Landi Corrales Guaranha Olívia 
Published: September 2023

Abstract
The legitimacy of democracy and civil rights is based upon laws and administrative procedures. The presence of a legal framework and its application by bureaucrats in their daily decisions are prerequisites for the democratic rule of law. This explains why, in contexts of democratic backsliding, legal frameworks are under attack. Scholars observed the role of public administration in processes of democratic backsliding, but there is still a gap in understanding the disputes around the legal framework. Here, we analyze the conflicts between politicians and bureaucrats around the legal framework in a context of democratic backsliding. Analyzing the case of Brazil under Bolsonaro’s Government, we draw on 164 interviews with bureaucrats to understand how both bureaucrats and politicians dispute the legitimacy, uses, and interpretations of the legal framework to attack or protect democratic institutions and civil rights. On one side, bureaucrats defend themselves and their legitimacy through existing rules and procedures. On the other side, politicians change or reinterpret the rules to fragilize bureaucrats’ decisions. In this process, both politicians and bureaucrats learn how to improve their strategies around the uses of legal frameworks. These findings contribute to understanding how the dynamics around the legal framework explain processes of democratic backsliding.
Exacerbating inequality over the life-course: examining race differences in the reciprocal effects between incarceration and income
Authors: Silver Ian A , D’Amato Christopher , Wooldredge John 
Published: September 2023

Abstract
Relative to Whites, Blacks face lower odds of gaining employment with notable wages while also facing longer terms of incarceration when sent to jail or prison for criminal offenses. Although a variety of factors contribute to these patterns, the time a Black individual spends incarcerated could decrease future earnings, whereas lower earnings could increase the time spent incarcerated. Nevertheless, prior research has yet to consider—or evaluate—the reciprocal association between income and incarceration, limiting our ability to discern how involvement in the criminal justice system contributes to the racial gap in income between Black and Whites. Using the National Longitudinal Survey of Youth 1997, the current study evaluated the influence of time spent incarcerated and income on future time spent incarcerated and income of Blacks and Whites. A lagged Latent Curve Model with Structured Residuals was estimated to examine the between- and within-individual reciprocal effects of months incarcerated and income. The findings suggested that a 1 month increase in time spent incarcerated for Blacks resulted in a 300–600 dollar decrease in income during the subsequent measurement period, an effect that was not observed for Whites. It appears that time spent incarcerated reduces future earnings for justice-involved Blacks. Overall, findings suggest that the criminal justice system contributes to the income gap that exists more generally between Blacks and Whites in the United States.
ROS1 Fusion Angiomatoid Spitz Nevus With Eccrine Duct Fibroadenomatosis and Syringoid Features
Authors: Daruish Maged , Stefanato Catherine M. 
Published: September 2023

Abstract:
Eccrine duct fibroadenomatosis is a reactive histological phenomenon observed in a variety of inflammatory and neoplastic pathologies. We report a case of a ROS1 fusion angiomatoid Spitz nevus with associated acrosyringeal hyperplasia and a syringoma-like ductal proliferation in a young female patient.
A Network Pharmacology Approach to Understand the Action Mechanisms of the TangShenKangPing Decoction for Diabetic Nephropathy Treatment
Authors: Chang Jingsheng , Li Xueling , Wang Jue , Zhong Yifei 
Published: September 2023

ABSTRACT

Background:
TangShenKangPing decoction (TSKPD) has been used to treat patients with diabetic nephropathy (DN) for more than 10 years. However, its active ingredients and their pharmacological mechanisms of action remain unclear. In this study, we aimed to identify the key targets, major active ingredients, and pathways of TSKPD using network pharmacology.

Methods:
Human phenotypic disease, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and 37 candidates targets of 40 active TSKPD ingredients were identified. Enrichment analyses revealed that TSKPD reduced podocyte apoptosis via vitamin metabolic processes, regulated the inflammatory response via the advanced glycation end product–receptor for AGE (AGE-RAGE) signaling, and reduced abnormal angiogenesis via vascular endothelial growth factor (VEGF) signaling in patients with DN. Furthermore, we verified the therapeutic roles and action mechanism of TSKPD in db/db mice with DN. The medicine was administered via gavage for 12 weeks. Fasting blood glucose, blood lipid, pro-inflammatory cytokine, and 24 h urinary albumin levels and pathological alterations in the renal tissues were evaluated. KHDRBS1, NLRP3 and VEGF relative mRNA and protein expression levels in renal tissues were determined using reverse transcription-quantitative olymerase chain reaction (RT-qPCR) and western blotting, respectively.

Results:
Treatment with TSKPD decreased proteinuria and lipid levels in the serum, significantly decreased the kidney weight, ameliorated renal histopathological alterations, and reduced pro-inflammatory cytokine expression and oxidative stress in db/db mice.

Conclusion:
TSKPD exerts therapeutic effects by regulating multiple factors, reducing oxidative stress and inflammation, and protecting the podocytes.
Influence of Nd:YAG laser capsulotomy on toric intraocular lens rotation and change in cylinder power
Authors: Cinar Esat , Yuce Berna , Aslan Fatih , Erbakan Gökhan 
Published: September 2023

Purpose:
To investigate toric monofocal intraocular lens (TIOL) rotation and associated changes in cylinder power caused by Nd:YAG laser capsulotomy performed due to posterior capsule opacification (PCO).

Setting:
Ekol Eye Hospital, Izmir, Turkey.

Design:
Prospective case series.

Methods:
41 eyes of 20 women and 21 men were included in the study. Before and 1 month after Nd:YAG laser capsulotomy, TIOL tilt and decentration were determined with Scheimpflug camera, and TIOL axial rotation and the change in cylinder power induced by this rotation were measured by ray tracing aberrometry. The time interval between cataract surgery and Nd:YAG laser capsulotomy was noted.

Results:
Rotational misalignment of the TIOL was measured as 4.65 ± 2.75 degrees (range 0 to 11 degrees) before vs 6.97 ± 2.92 degrees (range 0 to 13 degrees) after capsulotomy, and absolute rotation was 2.75 ± 1.94 degrees (range 0 to 7 degrees, P = .028). Before and after Nd:YAG laser capsulotomy, cylinder power was 0.24 ± 0.70 diopter (D) (range 0.00 to 0.63 D) vs 0.56 ± 0.77 D (range 0.02 to 0.91 D), respectively, with an absolute change in cylinder power of 0.34 ± 0.22 D (range 0.01 to 0.90 D, P = .001). After capsulotomy, there was a significant decrease in IOL tilt in the horizontal and vertical planes and an increase in decentration (P < .05). Time interval (33.02 ± 12.9 months) and IOL horizontal decentration were independent factors affecting IOL rotation after capsulotomy (P < .05).

Conclusions:
Nd:YAG laser capsulotomy may cause TIOL rotation as well as tilt and decentration, resulting in a change in the TIOL's corrective effect on corneal astigmatism. Although this change was clinically insignificant, it may be beneficial to consider that TIOL rotational misalignment may occur in patients undergoing early capsulotomy.
Bradykinin receptor expression and bradykinin-mediated sensitization of human sensory neurons
Authors: Yi Jiwon , Bertels Zachariah , Del Rosario John Smith , Widman Allie J. , Slivicki Richard A. , Payne Maria , Susser Henry M. , Copits Bryan A. , Gereau Robert W. 
Published: September 2023

Abstract
Bradykinin is a peptide implicated in inflammatory pain in both humans and rodents. In rodent sensory neurons, activation of B1 and B2 bradykinin receptors induces neuronal hyperexcitability. Recent evidence suggests that human and rodent dorsal root ganglia (DRG), which contain the cell bodies of sensory neurons, differ in the expression and function of key GPCRs and ion channels; whether bradykinin receptor expression and function are conserved across species has not been studied in depth. In this study, we used human DRG tissue from organ donors to provide a detailed characterization of bradykinin receptor expression and bradykinin-induced changes in the excitability of human sensory neurons. We found that B2 and, to a lesser extent, B1 receptors are expressed by human DRG neurons and satellite glial cells. B2 receptors were enriched in the nociceptor subpopulation. Using patch-clamp electrophysiology, we found that acute bradykinin increases the excitability of human sensory neurons, whereas prolonged exposure to bradykinin decreases neuronal excitability in a subpopulation of human DRG neurons. Finally, our analyses suggest that donor's history of chronic pain and age may be predictors of higher B1 receptor expression in human DRG neurons. Together, these results indicate that acute bradykinin-induced hyperexcitability, first identified in rodents, is conserved in humans and provide further evidence supporting bradykinin signaling as a potential therapeutic target for treating pain in humans.
Expectations underlie the effects of unpredictable pain: a behavioral and electroencephalogram study
Authors: Pavy Fabien , Zaman Jonas , Von Leupoldt Andreas , Torta Diana M. 
Published: September 2023

Abstract
Previous studies on the potential effects of unpredictability on pain perception and its neural correlates yielded divergent results. This study examined whether this may be explained by differences in acquired expectations. We presented 41 healthy volunteers with laser heat stimuli of different intensities. The stimuli were preceded either by predictable low, medium, or high cues or by unpredictable low–medium, medium–high, or low–high cues. We recorded self-reports of pain intensity and unpleasantness and laser-evoked potentials (LEPs). Furthermore, we investigated whether dynamic expectations that evolved throughout the experiment based on past trials were better predictors of pain ratings than fixed (nonevolving) expectations. Our results replicate previous findings that unpredictable pain is higher than predictable pain for low-intensity stimuli but lower for high-intensity stimuli. Moreover, we observed higher ratings for the medium–high unpredictable condition than the medium–low unpredictable condition, in line with an effect of expectation. We found significant interactions (N1, N2) for the LEP components between intensity and unpredictability. However, the few significant differences in LEP peak amplitudes between cue conditions did not survive correction for multiple testing. In line with predictive coding perspectives, pain ratings were best predicted by dynamic expectations. Surprisingly, expectations of reduced precision (increased variance) were associated with lower pain ratings. Our findings provide strong evidence that (dynamic) expectations contribute to the opposing effects of unpredictability on pain perception; therefore, we highlight the importance of controlling for them in pain unpredictability manipulations. We also suggest to conceptualize pain expectations more often as dynamic constructs incorporating previous experiences.
Suicide Data in Trauma Centers: Implications of Imprecision
Authors: Cronn Susan E. , Kant Jacey M. , Brandolino Amber , Kohlbeck Sara , deRoon-Cassini Terri , Emerson Nathan , Schramm Andrew 
Published: September 2023

BACKGROUND:
Trauma registries exist to provide data for evaluating the quality of care of trauma patients. These data facilitate research and can be used for outreach, planning, and improvement in trauma patient outcomes. However, the accuracy of registry data related to suicide has not been well studied.

OBJECTIVE:
This study sought to evaluate the accuracy of current trauma registry coding practices related to labeling injury as a suicide attempt among patients presenting to a Level I trauma center after self-inflicted injury.

METHODS:
We conducted a single-center, retrospective cohort analysis of a Level I trauma center trauma registry on all patients with self-inflicted injuries from 2011 to 2021. Manual chart review was used to identify cases wherein patients' injuries were categorized as suicidal despite the absence of suicidal intent.

RESULTS:
During this 11-year period, 537 patients were identified as having presented to the trauma center for traumatic self-inflicted injuries. Manual chart review revealed that 16% of these patients were incorrectly categorized as having attempted suicide despite their self-inflicted injury lacking suicidal intent (e.g., accidents, nonsuicidal self-harm).

CONCLUSION:
We found that 16% of trauma registry patients were overcategorized as having attempted suicide. Trauma registry data are an important source of information for activities related to injury prevention in trauma centers. Imprecise coding of self-inflicted injury may lead to poorly targeted programs and interventions due to incorrectly represented injury causes and patterns in trauma patient populations, including suicide prevention.