bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advances in Diagnosis and Treatment of Basal Cell Carcinoma
Authors: Khalil Afrah A. , Enezei Hamid H. , Aldelaimi Tahrir N. , Mohammed Khalil Abdullah 
Published: January 2024

Basal cell carcinoma (BCC) is one among the most prevalent malignant neoplasms that has exhibited a notable surge in global incidence over recent decades. This slow-growing malignancy is typified by its localized invasiveness while demonstrating an exceedingly rare metastatic proclivity. It predominantly afflicts the sun-exposed skin of aging individuals, with a heightened predilection for the maxillofacial region. Scraping cytology offers numerous benefits, including the potential for an earlier diagnosis and the absence of scarring, as opposed to a biopsy. The cytodiagnosis of BCC proves to be straightforward with various techniques, making it highly advantageous in an outpatient environment as a swift diagnostic method when planning a surgical excision. Our study sought to scrutinize the clinicopathological facets of BCC within the maxillofacial region. We compared advanced cytological techniques for diagnosis, including scraping, scratching, and imprinting using Papanicolau and Diff-Quick stains. In addition, we evaluated the therapeutic effectiveness of diode lasers operating at wavelengths of 940nm and 980n. A retrospective analysis was undertaken, encompassing facial BCC lesions smaller than 2.5 cm in diameter that underwent treatment through diode laser ablation between September 2021 and August 2023 at Ramadi Teaching Hospital and a private clinic in Ramadi City, Iraq. Among the cohort of 48 patients with BCC, a majority (58%) were 50 years of age or older, with a predominance of males (62%). The mean duration of lesion existence exceeded 4 months. The anatomical region most commonly involved was the middle 1/3 of the face, accounting for 34% of cases. Intriguingly, the therapeutic approach of diode laser ablation yielded exceptional esthetic and functional outcomes, which were consistently observed throughout the follow-up period post-healing. The occurrence of complications following diode laser ablation was relatively infrequent. This investigation revealed that cytological examination is easily conducted, eliminating the need for local anesthesia, saving time, being more cost-effective than a conventional biopsy, and delivering swift diagnoses. The process of smear-taking for cytology is well-tolerated, inflicting minimal trauma or discomfort on the patient. BCC predominantly afflicts elderly males and most frequently affects the middle third of the face. Notably, nodular BCC emerged as the prevailing histological subtype. The use of diode laser ablation exhibited a commendable track record, producing exemplary functional and esthetic outcomes over a 6-month follow-up period.
Clinical Impact of an Enhanced Recovery Program for Lower Extremity Bypass
Authors: Tariq Marvi , Novak Zdenek , Spangler Emily L. , Passman Marc A. , Patterson Mark A. , Pearce Benjamin J. , Sutzko Danielle C. , Brokus S. Danielle , Busby Courtney , Beck Adam W. 
Published: January 2024

Objective:
To determine the association of Enhanced Recovery Program (ERP) implementation with length of stay (LOS) and perioperative outcomes after lower extremity bypass (LEB).

Background:
ERPs have been shown to decrease hospital LOS and improve perioperative outcomes, but their impact on patients undergoing vascular surgery remains unknown.

Methods:
Patients undergoing LEB who received or did not receive care under the ERP were included: pre-ERP (1/1/2016–05/13/2018) and ERP (05/14/2018–7/31/2022). Clinicopathologic characteristics and perioperative outcomes were analyzed.

Results:
Of 393 patients who underwent LEB (pre-ERP, n=161 (41%); ERP, n=232 (59%)), most were male (n=254, 64.6%), white (n=236, 60%), and government-insured (n=265, 67.4%). Pre-ERP patients had higher BMI (28.8±6.0 vs. 27.4±5.7, P=0.03) and rates of diabetes (52% vs. 36%, P=0.002). ERP patients had shorter total (6 (3-13) vs. 7 (5-14) days, P=0.01) and postoperative LOS (5 (3-8) vs. 6 (4-8) days, P<0.001). Stratified by indication, postoperative LOS was shorter in ERP patients with claudication (3 vs. 5 d, P=0.01), rest pain (5 vs. 6 d, P=0.02) and tissue loss (6 vs. 7 d, P=0.03). ERP patients with rest pain also had a shorter total LOS (6 vs. 7 d, P=0.04) and lower 30-day readmission rates (32% to 17%, P=0.02). After ERP implementation, the average daily oral morphine equivalents (OMEs) decreased (median (IQR) 52.5 (26.6-105.0) vs. 44.12 (22.2-74.4), P=0.019), while the rates of direct discharge to home increased (83% vs. 69%, P=0.002).

Conclusions:
This is the largest single center cohort study evaluating ERP in LEB, showing that ERP implementation is associated with shorter LOS and improved perioperative outcomes.
LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer
Authors: Mandl A , Jasmine S , Krueger TEG , Kumar R , Coleman IM , Dalrymple SL , Antony L , Rosen DM , Jing Y , Hanratty B , Patel RA , Jin-Yih L , Dias J , Celatka CA , Tapper AE , Kleppe M , Kanayama M , Speranzini V , Wang YZ , Luo J , Corey E , Sena LA , Casero RA , Lotan T , Trock BJ , Kachhap SK , Denmeade SR , Carducci MA , Mattevi A , Haffner MC , Nelson PS , Rienhoff HY , Isaacs JT , Brennen WN 
Published: January 2024

AbstractLysine-specific demethylase 1 (LSD1 orKDM1A) has emerged as a critical mediator of tumor progression in metastatic castration-resistant prostate cancer (mCRPC). Among mCRPC subtypes, neuroendocrine prostate cancer (NEPC) is an exceptionally aggressive variant driven by lineage plasticity, an adaptive resistance mechanism to androgen receptor axis-targeted therapies. Our study shows that LSD1 expression is elevated in NEPC and associated with unfavorable clinical outcomes. Using genetic approaches, we validated the on-target effects of LSD1 inhibition across various models. We investigated the therapeutic potential of bomedemstat, an orally bioavailable, irreversible LSD1 inhibitor with low nanomolar potency. Our findings demonstrate potent antitumor activity against CRPC models, including tumor regressions in NEPC patient-derived xenografts. Mechanistically, our study uncovers that LSD1 inhibition suppresses the neuronal transcriptional program by downregulating ASCL1 through disrupting LSD1:INSM1 interactions and de-repressing YAP1 silencing. Our data support the clinical development of LSD1 inhibitors for treating CRPC – especially the aggressive NE phenotype.Statement of SignificanceNeuroendocrine prostate cancer presents a clinical challenge due to the lack of effective treatments. Our research demonstrates that bomedemstat, a potent and selective LSD1 inhibitor, effectively combats neuroendocrine prostate cancer by downregulating the ASCL1- dependent NE transcriptional program and re-expressing YAP1.
Evaluation of genetic associations with clinical phenotypes of kidney stone disease
Authors: Hsi Ryan S , Zhang Siwei , Triozzi Jefferson L , Hung Adriana M , Xu Yaomin , Bejan Cosmin A 
Published: January 2024

ABSTRACTIntroduction and ObjectiveWe sought to replicate and discover genetic associations of kidney stone disease within a large-scale electronic health record (EHR) system.MethodsWe performed genome-wide association studies (GWASs) for nephrolithiasis from genotyped samples of 5,571 cases and 83,692 controls. Among the significant risk variants, we performed association analyses of stone composition and first-time 24-hour urine parameters. To assess disease severity, we investigated the associations of risk variants with age at first stone diagnosis, age at first procedure, and time from first to second procedure.ResultsThe main GWAS analysis identified 10 significant loci, each located on chromosome 16 within coding regions of theUMODgene, which codes for uromodulin, a urine protein with inhibitory activity for calcium crystallization. The strongest signal was from SNP 16:20359633-C-T (odds ratio [OR] 1.17, 95% CI 1.11-1.23), with the remaining significant SNPs having similar effect sizes. In subgroup GWASs by stone composition, 19 significant loci were identified, of which two loci were located in coding regions (brushite;NXPH1, rs79970906 and rs4725104). TheUMODSNP 16:20359633-C-T was associated with differences in 24-hour excretion of urinary calcium, uric acid, phosphorus, sulfate; and the minor allele was positively associated with calcium oxalate dihydrate stone composition (p<0.05). No associations were found betweenUMODvariants and disease severity.ConclusionsWe replicated germline variants associated with kidney stone disease risk atUMODand reported novel variants associated with stone composition. Genetic variants ofUMODare associated with differences in 24-hour urine parameters and stone composition, but not disease severity.
Noncaloric monosaccharides induce excessive sprouting angiogenesis in zebrafish via foxo1a-marcksl1a signal
Authors: Wang Xiaoning , Zhao Jinxiang , Xu Jiehuan , Li Bowen , Liu Xia , Xie Gangcai , Duan Xuchu , Liu Dong 
Published: January 2024

AbstractArtificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. We have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose, resembling the hyperangiogenic characteristics observed in proliferative diabetic retinopathy (PDR). Utilizing this model, we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels, especially intersegmental vessels (ISVs). The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells (ECs) into tip cells. Single-cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs, proliferating ECs, and a series of upregulated proangiogenic genes. Further analysis and experiments validated that reducedfoxo1amediated the excessive angiogenesis induced by monosaccharides via up-regulating the expression ofmarcksl1a. This study has provided new evidence showing the negative effects of noncaloric monosaccharides on the vascular system and the underlying mechanisms.
Exploring athlete pain assessment experiences and priorities; A two-part qualitative series of athlete and physiotherapist interactions. Part Two. “Forging Our Future” - Athlete and physiotherapists’ priorities for pain assessment and beyond
Authors: Purcell Ciarán , Walsh Caoimhe Barry , Van Oirschot Garett , Fullen Brona M , Ward Tomás , Caulfield Brian M 
Published: January 2024

AbstractObjectivesTo explore the priorities and directions of athlete upper and lower limb pain assessment by facilitating shared understandings of athletes and sports physiotherapists.DesignQualitative Research using a hermeneutic phenomenological approach.MethodsWe carried out focus groups using a deliberate criterion sample and a constructivist perspective. At the end of each focus group, we used the nominal group technique method to generate a list of consensus-based priorities for future pain assessment. Our paper follows the consolidated criteria for reporting qualitative research (COREQ) guidelines.ResultsWe completed five focus groups, comprising twelve athletes (female, n=5, male n=7) and four sports physiotherapists (male, n=4) Two final themes (and six subthemes) were developed; (i) Enhanced Communication and Pain Descriptions (describing and representing pain, better communication, the role of technology, providing direction and setting the pace), (ii) Integrating Sport Specific and Multidimensional Assessments (broadening the pain assessment toolkit, the role of technology). We developed a set of thirteen practical priorities for pain assessment that span the subjective, objective, and general aspects of the athlete pain assessment.ConclusionWe have presented stakeholder-generated perspectives, directions, and priorities for athlete pain assessment. Athletes and Physiotherapists must continue to work together to achieve a comprehensive sport-specific multidimensional pain assessment experience alongside their wider support networks to ensure optimal representation and communication. We have highlighted some available pain assessment tools and strategies and outlined how novel tools may address certain gaps in the assessment process. Researchers, clinicians, and athletes can consider the practical guidance we have provided to address these priorities.
IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency
Authors: Flores-Mendez Marco , Ohl Laura , Roule Thomas , Zhou Yijing , Tintos-Hernández Jesus A , Walsh Kelsey , Ortiz-González Xilma R , Akizu Naiara 
Published: January 2024

AbstractMetabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use mouse models of AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that AMPD deficiency in mice primarily leads to hippocampal dentate gyrus degeneration despite causing a generalized reduction of brain GTP levels. Remarkably, we found that neurodegeneration resistant regions accumulate micron sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis. In contrast, IMPDH2 filaments are barely detectable in the hippocampal dentate gyrus, which shows a progressive neuroinflammation and neurodegeneration. Furthermore, using a human AMPD2 deficient neural cell culture model, we show that blocking IMPDH2 polymerization with a dominant negativeIMPDH2variant, impairs AMPD2 deficient neural progenitor growth. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation in neurons with available GTP precursor molecules, providing resistance to neurodegeneration. Our findings open the possibility of exploring the involvement of IMPDH2 assembly as a therapeutic intervention for neurodegeneration.
Individual variability in neural representations of mind-wandering
Authors: Kucyi Aaron , Anderson Nathan , Bounyarith Tiara , Braun David , Shareef-Trudeau Lotus , Treves Isaac , Braga Rodrigo M. , Hsieh Po-Jang , Hung Shao-Min 
Published: January 2024

AbstractMind-wandering is a frequent, daily mental activity, experienced in unique ways in each person. Yet neuroimaging evidence relating mind-wandering to brain activity, for example in the default mode network (DMN), has relied on population-rather than individual-based inferences due to limited within-individual sampling. Here, three densely-sampled individuals each reported hundreds of mind-wandering episodes while undergoing multi-session functional magnetic resonance imaging. We found reliable associations between mind-wandering and DMN activation when estimating brain networks within individuals using precision functional mapping. However, the timing of spontaneous DMN activity relative to subjective reports, and the networks beyond DMN that were activated and deactivated during mind-wandering, were distinct across individuals. Connectome-based predictive modeling further revealed idiosyncratic, whole-brain functional connectivity patterns that consistently predicted mind-wandering within individuals but did not fully generalize across individuals. Predictive models of mind-wandering and attention that were derived from larger-scale neuroimaging datasets largely failed when applied to densely-sampled individuals, further highlighting the need for personalized models. Our work offers novel evidence for both conserved and variable neural representations of self-reported mind-wandering in different individuals. The previously-unrecognized inter-individual variations reported here underscore the broader scientific value and potential clinical utility of idiographic approaches to brain-experience associations.
A complexPlasmodium falciparumcryptotype circulating at low frequency across the African continent
Authors: Miotto Olivo , Amambua-Ngwa Alfred , Amenga-Etego Lucas , Abdel Hamid Muzamil M , Adam Ishag , Aninagyei Enoch , Apinjoh Tobias , Awandare Gordon A , Bejon Philip , Bertin Gwladys I , Bouyou-Akotet Marielle , Claessens Antoine , Conway David J , D’Alessandro Umberto , Diakite Mahamadou , Djimdé Abdoulaye , Dondorp Arjen M , Duffy Patrick , Fairhurst Rick M , Fanello Caterina I , Ghansah Anita , Ishengoma Deus , Lawniczak Mara , Maïga-Ascofaré Oumou , Auburn Sarah , Rosanas-Urgell Anna , Wasakul Varanya , White Nina FD , Almagro-Garcia Jacob , Pearson Richard D , Goncalves Sonia , Ariani Cristina , Bozdech Zbynek , Hamilton William , Simpson Victoria , Kwiatkowski Dominic P 
Published: January 2024

ABSTRACTThe population structure of the malaria parasitePlasmodium falciparumcan reveal underlying demographic and adaptive evolutionary processes. Here, we analyse population structure in 4,376P. falciparumgenomes from 21 countries across Africa. We identified a strongly differentiated cluster of parasites, comprising ∼1.2% of samples analysed, geographically distributed over 13 countries across the continent. Members of this cluster, named AF1, carry a genetic background consisting of a large number of highly differentiated variants, rarely observed outside this cluster, at a multitude of genomic loci distributed across most chromosomes. At these loci, the AF1 haplotypes appear to have common ancestry, irrespective of the sampling location; outside the shared loci, however, AF1 members are genetically similar to their sympatric parasites. AF1 parasites sharing up to 23 genomic co-inherited regions were found in all major regions of Africa, at locations over 7,000 km apart. We coined the termcryptotypeto describe a complex common background which is geographically widespread, but concealed by genomic regions of local origin. Most AF1 differentiated variants are functionally related, comprising structural variations and single nucleotide polymorphisms in components of the MSP1 complex and several other genes involved in interactions with red blood cells, including invasion and erythrocyte antigen export. We propose that AF1 parasites have adapted to some as yet unidentified evolutionary niche, by acquiring a complex compendium of interacting variants that rarely circulate separately in Africa. As the cryptotype spread across the continent, it appears to have been maintained mostly intact in spite of recombination events, suggesting a selective advantage. It is possible that other cryptotypes circulate in Africa, and new analysis methods may be needed to identify them.
Don’t put words in my mouth: Speech perception can generate False Positive activation of a speech BCI
Authors: Schippers A. , Vansteensel M.J. , Freudenburg Z.V. , Ramsey N.F. 
Published: January 2024

AbstractRecent studies have demonstrated that speech can be decoded from brain activity and used for brain-computer interface (BCI)-based communication. It is however also known that the area often used as a signal source for speech decoding BCIs, the sensorimotor cortex (SMC), is also engaged when people perceive speech, thus making speech perception a potential source of false positive activation of the BCI. The current study investigated if and how speech perception may interfere with reliable speech BCI control. We recorded high-density electrocorticography (HD-ECoG) data from five subjects while they performed a speech perception and speech production task and trained a support-vector machine (SVM) on the produced speech data. Our results show that decoders that are highly reliable at detecting self-produced speech from brain signals also generate false positives during the perception of speech. We conclude that speech perception interferes with reliable BCI control, and that efforts to limit the occurrence of false positives during daily-life BCI use should be implemented in BCI design to increase the likelihood of successful adaptation by end users.
DODGE: Automated point source bacterial outbreak detection using cumulative long term genomic surveillance
Authors: Payne Michael , Hu Dalong , Wang Qinning , Sullivan Geraldine , Graham Rikki M , Rathnayake Irani U , Jennison Amy V , Sintchenko Vitali , Lan Ruiting 
Published: January 2024

AbstractSummaryThe reliable and timely recognition of outbreaks is a key component of public health surveillance for foodborne diseases. Whole genome sequencing (WGS) offers high resolution typing of foodborne bacterial pathogens and facilitates the accurate detection of outbreaks. This detection relies on grouping WGS data into clusters at an appropriate genetic threshold, however, methods and tools for selecting and adjusting such thresholds according to the required resolution of surveillance and epidemiological context are lacking. Here we present DODGE (Dynamic Outbreak Detection for Genomic Epidemiology), an algorithm to dynamically select and compare these genetic thresholds. DODGE can analyse expanding datasets over time and clusters that are predicted to correspond to outbreaks (or ‘investigation clusters’) can be named with the established genomic nomenclature systems to facilitate integrated analysis across jurisdictions. DODGE was tested in two real-world genomic surveillance datasets of different duration, two months from Australia and nine years from the UK. In both cases only a minority of isolates were identified as investigation clusters. Two known outbreaks in the UK dataset were detected by DODGE and were recognised at an earlier timepoint than the outbreaks were reported. These findings demonstrated the potential of the DODGE approach to improve the effectiveness and timeliness of genomic surveillance for foodborne diseases and the effectiveness of the algorithm developed.Availability and implementationDODGE is freely available athttps://github.com/LanLab/dodgeand can easily be installed using Conda.Supplementary informationSupplementary Tables, Results, Figure 1 and Figure 2