bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene regulation by convergent promoters
Authors: Wiechens Elina , Vigliotti Flavia , Siniuk Kanstantsin , Schwarz Robert , Schwab Katjana , Riege Konstantin , van Bömmel Alena , Görlich Ivonne , Bens Martin , Sahm Arne , Groth Marco , Sammons Morgan A. , Loewer Alexander , Hoffmann Steve , Fischer Martin 
Published: January 2025

Abstract
Convergent transcription, that is, the collision of sense and antisense transcription, is ubiquitous in mammalian genomes and believed to diminish RNA expression. Recently, antisense transcription downstream of promoters was found to be surprisingly prevalent. However, functional characteristics of affected promoters are poorly investigated. Here we show that convergent transcription marks an unexpected positively co-regulated promoter constellation. By assessing transcriptional dynamic systems, we identified co-regulated constituent promoters connected through a distinct chromatin structure. Within these cis-regulatory domains, transcription factors can regulate both constituting promoters by binding to only one of them. Convergent promoters comprise about a quarter of all active transcript start sites and initiate 5′-overlapping antisense RNAs—an RNA class believed previously to be rare. Visualization of nascent RNA molecules reveals convergent cotranscription at these loci. Together, our results demonstrate that co-regulated convergent promoters substantially expand the cis-regulatory repertoire, reveal limitations of the transcription interference model and call for adjusting the promoter concept.
Structural polymorphism and diversity of human segmental duplications
Authors: Jeong Hyeonsoo , Dishuck Philip C. , Yoo DongAhn , Harvey William T. , Munson Katherine M. , Lewis Alexandra P. , Kordosky Jennifer , Garcia Gage H. ,   Human Genome Structural Variation Consortium (HGSVC), Yilmaz Feyza , Hallast Pille , Lee Charles , Pastinen Tomi , Eichler Evan E. 
Published: January 2025

Abstract
Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies (from 85 samples representing 38 Africans and 47 non-Africans) in which the majority of autosomal SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms and sex chromosomes, we identify 173.2 Mb of duplicated sequence (47.4 Mb not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable, with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy numbers than non-African samples. Comparison to a resource of 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
The stability and modulation of if-then rules versus prospective planning in movement selection under dual-tasking conditions
Authors: Stoll S. E. M. , Wenzel A. , Hitzler B. , Randerath J. 
Published: January 2025

AbstractTwo approaches to movement selection, if-then rules versus prospective planning, were investigated. Studies have shown that the rule-based approach leads to more efficient movement selection than the plan-based approach, though the resulting movements are the same. This dual-tasking study investigates two hypotheses explaining this discrepancy: The efficiency hypothesis states that the rule-based approach to movement selection is more efficient, and its advantage over the plan-based approach increases under any kind of enhanced task demands. The dual-mechanisms hypothesis states that the two approaches to movement selection are based on distinct mechanisms and that they can be differentially affected by secondary tasks. Forty-eight participants selected a grip in order to comfortably rotate a dowel to a target position using the rule- or the plan-based approach. Four dual-tasking conditions were added: Identifying the activity underlying an object-interaction sound, identifying and categorizing the object underlying an object-interaction sound, identifying one of four words that does not match the others semantically, and solving calculations. The rule-based approach led to more efficient movement selection in most dual-tasking conditions. However, its advantage disappeared when the secondary task was to identify and categorize objects. These results strengthen the dual-mechanisms hypothesis, and possible factors distinguishing the approaches are discussed.
Ribitol and ribose treatments differentially affect metabolism of muscle tissue in FKRP mutant mice
Authors: Cataldi Marcela P. , Lu Qi L. 
Published: January 2025

AbstractDystroglycanopathy is characterized by reduced or lack of matriglycan, a cellular receptor for laminin as well as other extracellular matrix proteins. Recent studies have delineated the glycan chain structure of the matriglycan and the pathway with key components identified. FKRP functions as ribitol-5-phosphate transferase with CDP-ribitol as the substrate for the extension of the glycan chain. Supplement of ribitol and ribose have been reported to increase the levels of CDP-ribitol in both cells and in muscles in vivo. Clinical trials with both ribitol and ribose have been reported for treating LGMD2I caused by mutations in the FKRP gene. Here we compared the comprehensive metabolite profiles of the skeletal muscle between ribitol-treated and ribose-treated FKRP mutant mice. The closely related pentose and pentitol show clearly differential impacts on metabolisms despite their similarity in enhancing the levels of CDP-ribitol and matriglycan synthesis. Supplement of ribitol changes lysophospholipid sub-pathway metabolite profiling with a trend towards normalization as reported in the muscle after AAV9-FKRP gene therapy. Ribose treatment significantly increases level of ribonate and elevates levels of advanced glycation end products. Further analysis is required to determine which metabolite is prudent to use for long-term daily treatment of dystroglycanopathies.
Observer- and sequence variability in personalized 4D flow MRI-based cardiovascular models
Authors: Casas Garcia Belén , Tunedal Kajsa , Viola Federica , Cedersund Gunnar , Carlhäll Carl-Johan , Karlsson Matts , Ebbers Tino 
Published: January 2025

AbstractSubject-specific parameters in lumped hemodynamic models of the cardiovascular system can be estimated using data from experimental measurements, but the parameter estimation may be hampered by the variability in the input data. In this study, we investigate the influence of inter-sequence, intra-observer, and inter-observer variability in input parameters on estimation of subject-specific model parameters using a previously developed approach for model-based analysis of data from 4D Flow MRI acquisitions and cuff pressure measurements. The investigated parameters describe left ventricular time-varying elastance and aortic compliance. Parameter reproducibility with respect to variability in the MRI input measurements was assessed in a group of ten healthy subjects. The subject-specific parameters had coefficient of variations between 2.6 and 35% in the intra- and inter-observer analysis. In comparing parameters estimated using data from the two MRI sequences, the coefficients of variation ranged between 3.3 and 41%. The diastolic time constant of the left ventricle and the compliance of the ascending aorta were the parameters with the lowest and the highest variability, respectively. In conclusion, the modeling approach allows for estimating left ventricular elastance parameters and aortic compliance from non-invasive measurements with good to moderate reproducibility concerning intra-user, inter-user, and inter-sequence variability in healthy subjects.
Evaluation of Swallowing Dysfunction With Flexible Endoscopic Evaluation of Swallowing in the Neonatal Unit
Authors: Heston Aaron , Patel Anjali , Ahn Kevin , Wresch Delaney , Ridgway Lauren , Shipman Bethany , Graf Katrina , Elkhwad Mohammed , Muniraman Hemananda 
Published: January 2025

Background:
Preterm and low-birth-weight infants often experience discoordination of the suck–swallow–breathe pattern, leading to dysrhythmic feeding, inefficient feeding skills, and swallowing dysfunction, increasing the risk of aspiration and respiratory morbidity. While videofluoroscopic swallowing study is commonly utilized to assess swallow function in neonates, flexible endoscopic evaluation of swallowing (FEES) has been an emerging modality and has been utilized routinely at our institution since 2018.

Method:
A single-center, retrospective study including 90 infants admitted to the neonatal unit between 2018–2023 who underwent FEES procedure. Our objective was to evaluate the utility of FEES for evaluating functional and anatomical abnormalities, secretions, penetration/aspiration, and residue in infants in the Neonatal Intensive Care Unit. Our secondary objective was to observe whether clinical feeding decisions were changed based on FEES and describe progress in oral feeding.

Results:
A majority of infants (85.5%) were reported to have abnormal FEES findings, with aspiration below the vocal cords noted in 37.7% and laryngeal penetration reported in 34.5% of the infants. Anatomical abnormalities were reported in 39% of infants including predominantly laryngomalacia (27.7%). Ten infants were noted to have unanticipated anatomical abnormalities, of which four went on to require surgical interventions. Changes in nipple or bottle were the most frequent recommendations (68.8%) with thickening of feeds recommended in 35% of infants. The percentage of oral feedings increased from median of 45% to 75% with a decrease in infants with apneic, bradycardic, and desaturation events in the 7 days after FEES guided interventions were introduced.

Conclusions:
Majority of the infants with clinical concerns of swallow dysfunction were noted to have abnormalities on FEES, with one third of infants reported to have aspiration and anatomical abnormalities. Changes in feeding practices were recommended to majority of the infants based on FEES evaluation. Four of the five infants with anatomical abnormalities referred urgently for specialist evaluation required interventions.
Image inpainting with aggregated convolution progressive network
Authors: Li Yang , Zhai Jia , Lu Wen , Guo Haipeng , Wen JiaZheng , Liu Huanyu , Li Junbao 
Published: January 2025

AbstractImages can be corrupted during capture or transmission due to clouds, overlaps, and other interferences, deviating from their original state. Image inpainting techniques restore such images, but different types—Synthetic Aperture Radar (SAR), RGB, and infrared—require varying field‐of‐view sizes. SAR and infrared images, with less information, need a larger field of view, leading to uncorrelated interference in distant areas. RGB images, richer in information, are constrained by a limited local field of view, hindering access to full semantic details. To address these challenges, an aggregated convolution progressive network is proposed. This model employs a coarse‐grained inpainting module for initial restoration, enhanced by an aggregated convolution module to capture contextual information. Local and global details are then used to refine the output, improving restoration quality. Additionally, existing datasets predominantly focus on RGB images, lacking diversity. To bridge this gap, a comprehensive dataset covering SAR, RGB, and infrared images under cloud, overlap, and corruption conditions is constructed. This method achieves superior performance, with MAE of 0.05, SSIM of 0.95, and PSNR of 36.68 within a 20–30% mask size range, outperforming state‐of‐the‐art techniques across diverse image types and size ranges. Experimental results validate its effectiveness in advancing image inpainting.
Multiprofessionelles Clearing in einem Modellvorhaben nach § 64b SGB
V am Beispiel der Gerontopsychiatrie
Authors: Holzberger Marie-Luise , Fußer Fabian , Martin Kathrin , Stasik Eileen , Back Simone , Becker-Scharwatz Rita , Hesse Dana , Frisch Stefan 
Published: January 2025

ZusammenfassungIm Rahmen des bundesweit größten Modellvorhabens nach
§ 64b SGB V wurde in der Klinik für Gerontopsychiatrie am Pfalzklinikum ein
Clearingkonzept erarbeitet, um eine rasche und adäquate Diagnostik sowie
effektive Zuweisung in das weiterbehandelnde Setting zu
gewährleisten.Vorgestellt werden retrospektive Daten aller
Clearingfälle des ersten Jahres. Neben demografischen Daten und
Behandlungsdiagnosen wird die Verteilung der Patient*innen auf die
weiterbehandelnden Settings dargestellt. Von 1076 Fällen mit
stationärer Einweisung konnten durch das Clearing mehr als die Hälfte nach
spätestens fünf Werktagen ambulant weiterbehandelt oder entlassen werden. Die Ergebnisse heben die zentrale Rolle eines
Clearings für die Behandlungssteuerung hervor. Im Hinblick auf den
demografischen Wandel lassen sich Anregungen für die Regelversorgung ableiten,
um Patient*innen mit besonderen Diagnostik- und Behandlungsbedarfen gezielter zu
versorgen.
Comparison of adenoma detection rate between three-dimensional and standard colonoscopy: a multicenter randomized controlled trial
Authors: Chang Wei-Yuan , Liao Wei-Chih , Chang Li-Chun , Lin Hsuan-Ho , Wei Pin-Ya , Wu Hsing-Chien , Chiu Han-Mo , Wu Ming-Shiang 
Published: January 2025

AbstractImprovement in adenoma detection rates (ADRs) effectively reduces the incidence of colorectal cancer. In a simulation study, three-dimensional (3D) colonoscopy provided more anatomical details than standard two-dimensional (2D) colonoscopy and improved ADR. We compared ADRs between 2D and 3D colonoscopy.In this multicenter randomized controlled trial, participants aged ≥40 years undergoing colonoscopy for screening, surveillance, or symptoms between February 2022 and June 2023 were randomized 1:1 into 2D or 3D groups. The primary outcome was ADR. Secondary outcomes included detection rates for flat adenomas, right-sided adenomas, proximal adenomas, advanced adenomas, and sessile serrated lesions (SSLs).Of 348 participants recruited, data from 158 (2D group) and 160 (3D group) were analyzed. Mucosa inspection time was comparable between the 3D (9.8 [SD 2.6] minutes) and 2D (9.4 [SD 3.1] minutes) groups (P = 0.21). Compared with the 2D group, the 3D group had a significantly higher ADR (53.1% vs. 38.6%; difference 14.5% [95%CI 3.7 to 25.4]; P = 0.009), and higher detection rates for flat adenomas (35.0% vs. 21.5%; difference 13.5% [95%CI 3.7 to 23.3]; P = 0.008), right-sided adenomas (26.3% vs. 15.2%; difference 11.1% [95%CI 2.2 to 19.9]; P = 0.02), proximal adenomas (38.1% vs. 23.4%; difference 14.7% [95%CI 4.7 to 24.7]; P = 0.005), and adenomas sized 5–9 mm (45.0% vs. 31.0%; difference 14.0% [95%CI 3.4 to 24.5]; P = 0.01). There was no difference in detection rates for SSLs or advanced adenomas.3D colonoscopy improved adenoma detection without significantly increasing the mucosa inspection time.
Hybrid percutaneous endoscopic gastrostomy (Hybrid PEG) improves patient safety by combining pull-through technique with gastropexy
Authors: Branchi Federica , Treese Christoph , Kinzel Tobias Horst , Reich Viktoria , Schuhmacher Leonie , Bojarski Christian , Adler Andreas , Veltzke-Schlieker Wielfried , Jürgensen Christian , Tacke Frank , Siegmund Britta , Buchkremer Juliane 
Published: January 2025

AbstractThe direct puncture technique has been associated with a better safety profile compared with the classical pull-through technique for insertion of a percutaneous endoscopic gastrostomy (PEG). In this study, the safety of the hybrid PEG technique, combining gastropexy with the pull-through technique, was analyzed in a large retrospective patient cohort.Clinical data from patients undergoing PEG insertion in a high-volume center for endoscopy were included retrospectively between January 2016 and December 2021. Patient characteristics and complication rates were correlated in univariate and multivariate analyses.Data from 351 patients undergoing PEG insertion with the hybrid PEG technique were compared with 145 procedures with the direct puncture technique and 1073 procedures with the pull-through technique. In the group where gastropexy was performed (hybrid PEG and direct puncture), we could not find any significant differences in frequency of major and minor complications. Comparing the pull-through technique with the gastropexy group, we detected a five-fold higher major complication rate and a doubled minor complication rate for the pull-through technique. Multivariate analysis confirmed the protective role of gastropexy, with an odds ratio of 0.166 (0.084–0.329; P < 0.001) for major complications.Hybrid PEG and direct puncture are equally safe PEG insertion techniques, with significantly better safety profiles than the pull-through technique. Despite the retrospective design of the study, these results suggest preferential use of hybrid PEG due to handling.
Synthetic Approaches toward the Batzelladine Class of Guanidinium Alkaloids
Authors: Pierce Joshua G. , Breunig Jamie L. 
Published: January 2025

AbstractPolycyclic guanidinium alkaloids (PGAs) are a class of nitrogen-containing marine natural products characterized by a vessel unit, a linker, and an anchor unit. Batzelladines, a specific subclass of PGAs, exhibit diverse biological activities and structural complexities. This short review discusses various synthetic methods developed to access batzelladine natural products, highlighting the key disconnections utilized in each synthetic strategy.1	Introduction2	Polycyclic Guanidinium Alkaloids3	Batzelladine Natural Products4	Strategies in Batzelladine Synthesis4.1	Aza-Michael Addition4.2	Biginelli Condensation4.3	1,3-Dipolar Cycloaddition4.4	[4+2] Annulation of N-Alkyl Imines and Vinyl Carbodiimides4.5	Free-Radical Cyclization4.6	Palladium-Catalyzed Carboamination4.7	Rhodium-Catalyzed [4+3] Cycloaddition4.8	A Bicyclic β-Lactam Intermediate5	Non-Total Synthesis Contributions6	Conclusion
A Case of Erosive Antral Gastritis Treated with Homeopathy
Authors: Maiti Bishnu Prasad , Khadim Azizul Islam , Chakma Abhijit 
Published: January 2025

AbstractGastritis is a common gastrointestinal (GI) disorder, which commonly affects children and adult age groups. Antral gastritis is the inflammation of the inner mucosal lining in the antral part of the stomach. It can have a negative impact on health and hinder the quality of life. For the treatment of gastritis, the target should be to prevent recurrence, lessen side effects, and reduce the cost of medications. Considering these aspects, homeopathy can be one of the useful, safer therapeutic options in the treatment of gastritis. A male patient aged 31 years came with complaints of abdominal pain, nausea, vomiting, and distension of the abdomen for the last 10 months. Upper GI tract endoscopy confirmed erosive antral gastritis. He was treated with individualized homeopathic medicine Carbo vegetabilis in LM potency from 0/1 to 0/7. The patient was treated for 9 months with significant improvement both clinically and changes in diagnostic parameters. Endoscopy report revealed a normal study after 9 months of homeopathic treatment. The response of the visual analog scale for pain from +8 to 0 suggests the improvement of patient. In addition, the high score (+8) of Modified Naranjo Criteria for Homeopathy suggested that the likelihood of improvement was attributable to the homeopathic intervention. This case report suggests that a correctly chosen homeopathic medicine can be beneficial in the management of antral gastritis. Nevertheless, more extensive studies are warranted with enhanced methodology.
Upper Extremity Deep Vein Thrombosis Treated with Mechanical Thrombectomy: A Single-Center Retrospective Analysis
Authors: Pebror Travis , Davis Christopher M. , Butty Sabah D. 
Published: January 2025

Abstract
Purpose The incidence of upper extremity deep vein thrombosis (UEDVT) is rising, and few studies have assessed interventional treatment strategies. Here, we aim to evaluate outcomes following standalone mechanical thrombectomy for UEDVT.
Methods Retrospective chart review was conducted for all patients who underwent standalone mechanical thrombectomy for UEDVT between October 2019 and August 2023. Outcomes assessed included technical success (≥75% thrombus removal), intraprocedural adverse events, postprocedural hospital stay, and follow-up free from death, pulmonary embolism, and rethrombosis.
Results Mechanical thrombectomy was utilized in 14 patients during the study period. The median age was 44.0 years (interquartile range: 33.5, 57.0), and seven of the patients (50.0%) were female. All procedures were technically successful and completed in a single session with no serious adverse events. The median postprocedural stay was 2 days. At a median follow-up of 88 days, there were no mortalities, and 71.4% of patients (n = 10) were free of rethrombosis and pulmonary embolism.
Conclusion This analysis suggests that mechanical thrombectomy provides effective thrombus removal and can be safely completed in patients with UEDVT.
Structural Adaptations of the Anterolateral Complex of the Knee and Associated Tissues: A Comparative Anatomical and Histological Analysis of Knees With and Without an Anterolateral Ligament
Authors: Marchese Charles R. , Pautler Benjamin , Swancutt Makayla M. , Beutel Bryan G. 
Published: January 2025

AbstractThe anterolateral ligament (ALL) is considered a secondary stabilizer of internal rotation and, due to proximity to the lateral collateral ligament (LCL), it may contribute to anterolateral rotatory stability. This study characterized the anatomy of the ALL and associated tissues of the anterolateral complex (ALC) to determine if structural and histological compensatory adaptations exist in patients without an ALL. Forty-nine cadaveric knees were dissected from distal-to-proximal using established landmarks with the aid of internal rotation stress to localize the ALL (if present), LCL, iliotibial band (ITB), and anterolateral capsule. The width and thickness of ALL and LCL were measured with digital calipers at the origin, middle, and insertion, and cross-sectional areas were calculated. ALL and LCL length and ITB thickness were also obtained. Samples of each tissue were stained with hematoxylin and eosin and picrosirius red, and histological images were evaluated with ImageJ to quantify collagen density (mean gray value [mgv]) and quantity (percent coverage). Size measurements and collagen characteristics were compared between ALL-present and ALL-deficient knees. The ALL was identified in 63% of knees with mean cross-sectional areas of 8.9, 5.8, and 9.7 mm2 at the origin, middle, and insertion, respectively. Mean collagen density of the ALL was 106.9 mgv on a scale of 0 (black) to 255 (white), and overall collagen quantity was 40.3%. Proximal LCL width (p = 0.04), distal LCL thickness (p = 0.03), and cross-sectional area (p = 0.01), and ITB thickness (p = 0.02) were significantly greater in ALL-deficient knees. A significantly higher collagen density was found within the LCL (p = 0.04), and higher overall quantity of collagen within the LCL (p < 0.01) and ITB (p < 0.01), of ALL-deficient knees. Gross anatomical and histological alterations exist in knees without an ALL compared with those with an ALL. These may reflect adaptations in the ALC and LCL that are present to compensate for the absence of the anterolateral rotatory stability afforded by the ALL.