bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fossil pollen resolves origin of the South African Proteaceae as transcontinental not transoceanic
Authors: Lamont Byron B , He Tianhua , Cowling Richard M 
Published: April 2023

Abstract

Background and Aims
The prevailing view from the areocladogenesis of molecular phylogenies is that the iconic South African Cape Proteaceae (subfamily Proteoideae) arrived from Australia across the Indian Ocean during the Late Cretaceous (100–65 million years ago, Ma). Since fossil pollen indicates that the family probably arose in North-West Africa during the Early Cretaceous, an alternative view is that it migrated to the Cape from North-West-Central Africa. The plan therefore was to collate fossil pollen records throughout Africa to determine if they are consistent with an African (para-autochthonous) origin for the Cape Proteaceae, and to seek further support from other palaeo-disciplines.

Methods
We used palynology (identity, date and location of records), molecular phylogeny and chronogram preparation, biogeography of plate tectonics, and palaeo-atmospheric and ocean circulation models.

Key Results
Our collation of the rich assemblage of Proteaceae palynomorphs stretching back to 107 Ma (Triorites africaensis) in North-West Africa showed its progressive overland migration to the Cape by 75–65 Ma. No key palynomorphs recorded in Australia–Antarctica have morphological affinities with African fossils but specific clade assignment of the pre-Miocene records is not currently possible. The Cape Proteaceae encompass three molecular-based clades (tribes) whose most recent apparent ancestors are sisters to those in Australia. However, our chronogram shows that the major Adenanthos/Leucadendron-related clade, originating 54–34 Ma, would have ‘arrived’ too late as species with Proteaceae affinities were already present ~20 million years earlier. The Franklandia/Protea-related clade arose 118–81 Ma so its distinctive pollen should have been the foundation for the scores of palynomorphs recorded at 100–80 Ma, but it was not. Also, the prevailing winds and ocean currents trended away from South Africa rather than towards, as the ‘out-of-Australia’ hypothesis requires. Based on the evidence assembled here, we list three points favouring an Australian origin and nine against; four points favouring an Antarctic origin and seven against; and nine points favouring a North-West-Central African origin and three against.

Conclusions
We conclude that a gradual migration of the Proteaceae from North-West-Central Africa southeast→south→southwest to the Cape and its surroundings occurred via adaptation and speciation during the period 95–70 Ma. We caution that incorrect conclusions may be drawn from literal interpretations of molecular phylogenies that neglect the fossil record and do not recognize the possible confounding effects of selection under matched environments leading to parallel evolution and extinction of bona fide sister clades.
The Effect of Female Genital Cosmetic and Reconstructive Procedures on Body and Genital Self-Image: A Systematic Review and Meta-Analysis
Authors: Alavi-Arjas Fatemeh , Goodman Michael P , Simbar Masoumeh , Majd Hamid Alavi , Sharp Gemma , Nahidi Fatemeh 
Published: April 2023

Abstract

Performance of female genital cosmetic and reconstructive procedures (FGCRP) has been increasing over past decades. Appearance and functional concerns are the most common reasons for seeking FGCRP. Poor body and genital self-image may contribute to the increase in demand for surgery. The aim of this systematic review is to explore outcomes of FGCRP in the domains of body and genital self-image. A systematic literature review of PubMed, Web of Science, Scopus, PsycINFO, Embase, and the Cochrane Library was conducted to identify articles that measured body and genital self-image in females after FGCRP. The authors identified 5 articles for a systematic review of body image and 8 studies for a systematic review of genital self-image. The most common procedure performed was labia minora labiaplasty. Instruments for body image evaluation were the Yale–Brown Obsessive-Compulsive Scale Modified for Body Dysmorphic Disorder and the Body Image Quality of Life Inventory. Genital image was assessed with the Female Genital Self-Image Scale and Genital Appearance Satisfaction (GAS) scale. Most of the studies indicated that FGCRP can improve both body image and genital self-image; meta-analysis revealed that FGCRP improved GAS scores by 17.96 (range: 0-33; P &lt; .001). It appears that FGCRP leads to improvements in females’ body and genital self-image. Inconsistencies in study design and measures, however, limit this conclusion. Future research should involve more rigorous study designs (for example randomized clinical trials with large sample sizes) for a more accurate assessment of FGCRP's consequences.

Level of Evidence: 4
NSRGRN: a network structure refinement method for gene regulatory network inference
Authors: Liu Wei , Yang Yu , Lu Xu , Fu Xiangzheng , Sun Ruiqing , Yang Li , Peng Li 
Published: April 2023

Abstract
The elucidation of gene regulatory networks (GRNs) is one of the central challenges of systems biology, which is crucial for understanding pathogenesis and curing diseases. Various computational methods have been developed for GRN inference, but identifying redundant regulation remains a fundamental problem. Although considering topological properties and edge importance measures simultaneously can identify and reduce redundant regulations, how to address their respective weaknesses whilst leveraging their strengths is a critical problem faced by researchers. Here, we propose a network structure refinement method for GRN (NSRGRN) that effectively combines the topological properties and edge importance measures during GRN inference. NSRGRN has two major parts. The first part constructs a preliminary ranking list of gene regulations to avoid starting the GRN inference from a directed complete graph. The second part develops a novel network structure refinement (NSR) algorithm to refine the network structure from local and global topology perspectives. Specifically, the Conditional Mutual Information with Directionality and network motifs are applied to optimise the local topology, and the lower and upper networks are used to balance the bilateral relationship between the local topology’s optimisation and the global topology’s maintenance. NSRGRN is compared with six state-of-the-art methods on three datasets (26 networks in total), and it shows the best all-round performance. Furthermore, when acting as a post-processing step, the NSR algorithm can improve the results of other methods in most datasets.
LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data
Authors: Li Lingyu , Sun Liangjie , Chen Guangyi , Wong Chi-Wing , Ching Wai-Ki , Liu Zhi-Ping 
Published: April 2023

AbstractMotivationFrom a systematic perspective, it is crucial to infer and analyze gene regulatory network (GRN) from high-throughput single-cell RNA sequencing data. However, most existing GRN inference methods mainly focus on the network topology, only few of them consider how to explicitly describe the updated logic rules of regulation in GRNs to obtain their dynamics. Moreover, some inference methods also fail to deal with the over-fitting problem caused by the noise in time series data.ResultsIn this article, we propose a novel embedded Boolean threshold network method called LogBTF, which effectively infers GRN by integrating regularized logistic regression and Boolean threshold function. First, the continuous gene expression values are converted into Boolean values and the elastic net regression model is adopted to fit the binarized time series data. Then, the estimated regression coefficients are applied to represent the unknown Boolean threshold function of the candidate Boolean threshold network as the dynamical equations. To overcome the multi-collinearity and over-fitting problems, a new and effective approach is designed to optimize the network topology by adding a perturbation design matrix to the input data and thereafter setting sufficiently small elements of the output coefficient vector to zeros. In addition, the cross-validation procedure is implemented into the Boolean threshold network model framework to strengthen the inference capability. Finally, extensive experiments on one simulated Boolean value dataset, dozens of simulation datasets, and three real single-cell RNA sequencing datasets demonstrate that the LogBTF method can infer GRNs from time series data more accurately than some other alternative methods for GRN inference.Availability and implementationThe source data and code are available at https://github.com/zpliulab/LogBTF.
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
Authors: Del Conte Alessio , Monzon Alexander Miguel , Clementel Damiano , Camagni Giorgia F , Minervini Giovanni , Tosatto Silvio C E , Piovesan Damiano 
Published: April 2023

Abstract

RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites, and structural heterogeneity connected with molecular function. It is easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output files for use with external tools. The underlying RING software has been improved extensively. It is 10 times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids.

Availability and implementation
https://github.com/BioComputingUP/ring-pymol
A parahippocampal-sensory Bayesian vicious circle generates pain or tinnitus: a source-localized EEG study
Authors: De Ridder Dirk , Friston Karl , Sedley William , Vanneste Sven 
Published: April 2023

AbstractPain and tinnitus share common pathophysiological mechanisms, clinical features, and treatment approaches. A source-localized resting-state EEG study was conducted in 150 participants: 50 healthy controls, 50 pain, and 50 tinnitus patients. Resting-state activity as well as functional and effective connectivity was computed in source space. Pain and tinnitus were characterized by increased theta activity in the pregenual anterior cingulate cortex, extending to the lateral prefrontal cortex and medial anterior temporal lobe. Gamma-band activity was increased in both auditory and somatosensory cortex, irrespective of the pathology, and extended to the dorsal anterior cingulate cortex and parahippocampus. Functional and effective connectivity were largely similar in pain and tinnitus, except for a parahippocampal-sensory loop that distinguished pain from tinnitus. In tinnitus, the effective connectivity between parahippocampus and auditory cortex is bidirectional, whereas the effective connectivity between parahippocampus and somatosensory cortex is unidirectional. In pain, the parahippocampal-somatosensory cortex is bidirectional, but parahippocampal auditory cortex unidirectional. These modality-specific loops exhibited theta–gamma nesting. Applying a Bayesian brain model of brain functioning, these findings suggest that the phenomenological difference between auditory and somatosensory phantom percepts result from a vicious circle of belief updating in the context of missing sensory information. This finding may further our understanding of multisensory integration and speaks to a universal treatment for pain and tinnitus—by selectively disrupting parahippocampal-somatosensory and parahippocampal-auditory theta–gamma activity and connectivity.
Therapy With Allogeneic Severe Acute Respiratory Syndrome Coronavirus-2–Specific T Cells for Persistent Coronavirus Disease 2019 in Immunocompromised Patients
Authors: Haidar Ghady , Jacobs Jana L , Kramer Kailey Hughes , Naqvi Asma , Heaps Amy , Parikh Urvi , McCormick Kevin D , Sobolewski Michele D , Agha Mounzer , Bogdanovich Tatiana , Bushunow Vasilii , Farah Rafic , Hensley Matthew , Hsu Yen-Michael S , Johnson Bruce , Klamar-Blain Cynthia , Kozar Jennifer , Lendermon Elizabeth , Macatangay Bernard J C , Marino Christopher C , Raptis Anastasios , Salese Erin , Silveira Fernanda P , Leen Ann M , Marshall William L , Miller Michael , Patel Badrish , Atillasoy Ercem , Mellors John W 
Published: April 2023

Abstract
We administered severe acute respiratory syndrome coronavirus-2 viral-specific T cells (VSTs) under emergency investigational new drug applications to 6 immunocompromised patients with persistent coronavirus disease 2019 (COVID-19) and characterized clinical and virologic responses. Three patients had partial responses after failing other therapies but then died. Two patients completely recovered, but the role of VSTs in recovery was unclear due to concomitant use of other antivirals. One patient had not responded to 2 courses of remdesivir and experienced sustained recovery after VST administration. The use of VSTs in immunocompromised patients with persistent COVID-19 requires further study.
Economic Burden of Fatigue in Inflammatory Bowel Disease
Authors: Ananthakrishnan Ashwin N , Desai Raj , Lee Wan-Ju , Griffith Jenny , Chen Naijun , Loftus Edward V 
Published: April 2023

AbstractBackgroundThis retrospective study gathered medical/pharmacy claims data on patients with inflammatory bowel disease (IBD) between January 01, 2000 and March 31, 2019 from the IBM MarketScan commercial claims database to assess the real-world impact of fatigue on healthcare costs in patients newly diagnosed with IBD.MethodsEligible participants were ≥18 years, newly diagnosed with IBD (≥2 separate claims), and had ≥12 months of continuous database enrollment before and after fatigue diagnosis. The date of fatigue diagnosis was the index date; participants were followed for 12 months post-index. Patients with (cases) or without (controls) fatigue were matched 1:1 by propensity score matching. Patients with evidence of prior IBD diagnosis/treatment, or those with a chronic disease other than IBD wherein fatigue is the primary symptom, were excluded. Healthcare resource utilization (HCRU), including hospitalizations, inpatient and outpatient visits, and associated costs were compared between cases and controls.ResultsMatched IBD cohorts (21 321 cases/21 321 controls) were identified (42% Crohn’s disease [CD] and 58% ulcerative colitis [UC]) with similar baseline characteristics (average age: 46 years; 60% female). Cases versus controls had significantly more all-cause outpatient visits (incidence rate ratio [IRR], 95% confidence intervals [95% CI]: 1.64 [1.61, 1.67], P &lt; .001) and all-cause hospitalizations (IRR [95% CI]: 1.92 [1.81, 2.04], P &lt; .001); as well as significantly higher all-cause total direct healthcare costs (mean: $24 620 vs. $15 324; P &lt; .001). Similar findings were observed for IBD-related outcomes, as well as in CD- and UC-specific subgroups.ConclusionsPresence of fatigue is associated with an increase in HCRU and total medical costs among patients newly diagnosed with IBD.
Lipoprotein(a) and calcific aortic valve disease initiation and progression: a systematic review and meta-analysis
Authors: Pantelidis Panteleimon , Oikonomou Evangelos , Lampsas Stamatios , Zakynthinos Georgios E , Lysandrou Antonios , Kalogeras Konstantinos , Katsianos Efstratios , Theofilis Panagiotis , Siasos Gerasimos , Vavuranakis Michael Andrew , Antonopoulos Alexios S , Tousoulis Dimitris , Vavouranakis Manolis 
Published: April 2023

Abstract
Although evidence indicates the association of lipoprotein(a) [Lp(a)] with atherosclerosis, the link with calcific aortic valve disease (CAVD) is unclear. This systematic review and meta-analysis explores the connection between Lp(a) and aortic valve calcification and stenosis (AVS). We included all relevant studies, indexed in eight databases, up to February 2023. A total of 44 studies (163 139 subjects) were included, with 16 of them being further meta-analysed. Despite considerable heterogeneity, most studies support the relationship between Lp(a) and CAVD, especially in younger populations, with evidence of early aortic valve micro-calcification in elevated-Lp(a) populations. The quantitative synthesis showed higher Lp(a) levels, by 22.63 nmol/L (95% CI: 9.98–35.27), for patients with AVS, while meta-regressing the data revealed smaller Lp(a) differences for older populations with a higher proportion of females. The meta-analysis of eight studies providing genetic data, revealed that the minor alleles of both rs10455872 and rs3798220 LPA gene loci were associated with higher risk for AVS (pooled odds ratio 1.42; 95% CI: 1.34–1.50 and 1.27; 95% CI: 1.09–1.48, respectively). Importantly, high-Lp(a) individuals displayed not only faster AVS progression, by a mean difference of 0.09 m/s/year (95% CI: 0.09–0.09), but also a higher risk of serious adverse outcomes, including death (pooled hazard ratio 1.39; 95% CI: 1.01–1.90). These summary findings highlight the effect of Lp(a) on CAVD initiation, progression and outcomes, and support the early onset of Lp(a)-related subclinical lesions before clinical evidence.
Stochastic processes shape the functional and phylogenetic structure of bird assemblages at the mine area in southwest China
Authors: Liu Shilong , Zhou Tianlong , Tan Xiaocai , Mtemi Wambura M , Jiang Aiwu 
Published: April 2023

Abstract
Understanding the mechanisms of community assembly is a key question in ecology. Metal pollution may result in significant changes in bird community structure and diversity, with implications for ecosystem processes and function. However, the relative importance of these processes in shaping the bird community at the polluted area is still not clear. Here, we explored bird species richness, functional, and phylogenetic diversity, and the assembly processes of community at the mine region of southwest China. Our results showed that the 3 dimensions of diversity at the mine area were lower than that at the reference sites. In the community assembly, the result was 0 &lt; NRI/ NFRI &lt; 1.96, which indicated deterministic processes (environmental filtering) might drive community clustering. The results of the neutral community model, and normalized stochasticity ratio, showed the dominant role of stochastic processes in shaping the bird community assembly. We further quantified the community-level habitat niche breadth (Bcom), and we found that there was no difference in Bcom-value between the mine area and reference sites. This indicates that the bird communities at the mine area and 3 reference sites were not subjected to extreme environmental selection (same or different resource allocation) to form a highly specialized niche. These findings provide insights into the distribution patterns and dominant ecological processes of bird communities under metal exposure, and extend the knowledge in community assembly mechanisms of bird communities living in the mine area.
Global Type-Specific Genital Human Papillomavirus Prevalence in Men, by Sexual Orientation: A Systematic Review and Meta-Analysis
Authors: Kusters Johannes M A , Brouwer Jesca G M , van Benthem Birgit H B , Heijne Janneke C M , Schim van der Loeff Maarten F 
Published: April 2023

Abstract

Background
Knowledge on genital type-specific human papillomavirus (HPV) prevalence among men is important for prevention of HPV-related cancers and other diseases. Men who have sex with men (MSM) have higher anal prevalence than men who have sex with women only (MSW) but for genital HPV this is unclear. We performed a systematic review and meta-analysis of type-specific genital HPV prevalence among men, by sexual orientation.

Methods
MEDLINE and Embase were used for searching publications reporting on male genital HPV prevalence with data from November 2011 onwards. A random-effects meta-analysis was conducted estimating pooled type-specific and grouped external genital and urethral HPV prevalence. Subgroup analyses were conducted for sexual orientation.

Results
Twenty-nine studies were eligible. Of those, 13 studies reported prevalence among MSM, 5 among MSW, and 13 studies did not stratify by sexual orientation. The most common genotypes were HPV-6 and HPV-16 for both anatomical locations, although heterogeneity was high. HPV prevalence was similar among studies reporting on MSW, MSM, and men with unknown sexual orientation.

Conclusions
Genital HPV is common among men, with HPV-6 and HPV-16 being the most common genotypes. Type-specific HPV genital prevalence appears to be similar among MSM and MSW, which contrasts with earlier findings on anal HPV.
Rifabutin-Containing Triple Therapy Versus Bismuth Quadruple Therapy for Helicobacter pylori Rescue Treatment: A Multicenter, Randomized Controlled Trial
Authors: Chen Jinnan , Guo Yixian , Huang Yu , Ding Zhaohui , Wang Jing , Liang Xiao , Xu Ping , Han Yaohua , Lu Hong 
Published: April 2023

Abstract

Background
We compared the efficacy and safety of rifabutin-containing triple therapy with bismuth quadruple therapy for rescue treatment of Helicobacter pylori.

Methods
This was a noninferiority study trial of H. pylori treatment for subjects who had failed at least 2 prior treatments. Subjects were randomly assigned to receive rifabutin triple therapy with 14-day esomeprazole (20 mg), amoxicillin (1.0 g), and rifabutin (150 mg) twice a day; or bismuth quadruple therapy with esomeprazole (20 mg) and bismuth (220 mg) twice a day, plus metronidazole (400 mg) and tetracycline (500 mg) 4 times a day. Antimicrobial susceptibility was assessed by agar dilution and E-test.

Results
From May 2021 to October 2022, a total of 364 subjects were randomized. The eradication rates by intention-to-treat, per-protocol, and modified intention-to-treat were 89.0% (162/182; 95% confidence interval [CI], 83.6%–92.8%), 94.0% (157/167; 95% CI, 89.3%–96.7%), and 93.6% (162/173; 95% CI, 89.0%–96.4%) for rifabutin triple group. For bismuth quadruple group, they were 89.6% (163/182; 95% CI, 84.3%–93.2%), 95.3% (143/150; 95% CI, 90.7%–97.7%), and 93.7% (163/174; 95% CI, 89.0%–96.4%).

Conclusions
The rifabutin triple therapy is an alternative to classical bismuth quadruple therapy for the rescue treatment of H. pylori with fewer side effects and higher compliance.

Clinical Trials Registration
NCT04879992.
Reconstruction of Postburn Bone Exposed Defect in the Head and Face Using Two Separate Anterolateral Thigh Chimeric Flap: A Case Report
Authors: Quang Vinh Vu , Thanh Tuan Hoang , Van Anh Tran , Thanh Hai Tong , Trung Quyet Do 
Published: April 2023

AbstractReconstruction of soft-tissue defects in the head and face region requires attention to both functional and aesthetic outcomes. In general, large postburn scars are still a daunting challenge for plastic surgeons. Various types of free flaps were previously performed for head and face reconstruction, including the anterolateral thigh (ALT) flap. However, to fully cover large and complex defects, the skin pedicle needs a sufficient width. Thus, we have combined dual ALT flaps that were harvested from both the lateral thighs. In this article, we described the case of a 49-year-old female who was presented with a severe scar on the right side of the head and face and zygomatic along with the exposure of temporal bones after extensive burns. Two ALT flaps were supplied by perforators of the descending branches of lateral circumflex femoral arteries. These two source arteries were anastomosed end-to-end to merge into a chimeric flap. The 6-month follow-up revealed an acceptable aesthetic outcome. The effectiveness of the ALT chimeric flap for reconstructing head and face postburn contracture is discussed.