bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tryp: a dataset of microscopy images of unstained thick blood smears for trypanosome detection
Authors: Anzaku Esla Timothy , Mohammed Mohammed Aliy , Ozbulak Utku , Won Jongbum , Hong Hyesoo , Krishnamoorthy Janarthanan , Van Hoecke Sofie , Magez Stefan , Van Messem Arnout , De Neve Wesley 
Published: October 2023

AbstractTrypanosomiasis, a neglected tropical disease (NTD), challenges communities in sub-Saharan Africa and Latin America. The World Health Organization underscores the need for practical, field-adaptable diagnostics and rapid screening tools to address the negative impact of NTDs. While artificial intelligence has shown promising results in disease screening, the lack of curated datasets impedes progress. In response to this challenge, we developed the Tryp dataset, comprising microscopy images of unstained thick blood smears containing the Trypanosoma brucei brucei parasite. The Tryp dataset provides bounding box annotations for tightly enclosed regions containing the parasite for 3,085 positive images, and 93 images collected from negative blood samples. The Tryp dataset represents the largest of its kind. Furthermore, we provide a benchmark on three leading deep learning-based object detection techniques that demonstrate the feasibility of AI for this task. Overall, the availability of the Tryp dataset is expected to facilitate research advancements in diagnostic screening for this disease, which may lead to improved healthcare outcomes for the communities impacted.
Context reexposure to bolster contextual dependency of emotional episodic memory
Authors: Cox Wouter R. , Woelk Mandy , de Vries Olivier T. , Krypotos Angelos-Miltiadis , Kindt Merel , Engelhard Iris M. , Sevenster Dieuwke , van Ast Vanessa A. 
Published: October 2023

AbstractContextual overgeneralization of emotional memory is a core aspect of anxiety disorders. Identifying methods to enhance contextual dependency of emotional memory is therefore of significant clinical interest. Animal research points to a promising approach: reexposure to the context in which fear is acquired reduces generalization to other contexts. However, the exact conditions for this effect are unknown, complicating translation to effective interventions. Most notably, exposure to a context that resembles—but is not identical to—the learning context may diminish contextual dependency of memory by integration of additional contextual cues. Here, we therefore assessed in a large-scale study (N = 180) whether context reexposure enhances contextual dependency of emotional episodic memory whereas exposure to a similar context impairs it. We also tested whether relatively strong memory retrieval during context (re)exposure amplifies these effects. We replicated prior research showing that correct recognition depends on context and contextual dependency is lower for emotional than neutral memories. However, exposure to the encoding context or a similar context did not affect contextual dependency of memory, and retrieval strength did not interact with such effects. Thorough insight into factors underlying the effects of context (re)exposure on contextual dependency seems key to eventually attain a memory recontextualization intervention.
Pulmonary and chest wall function in obese adults
Authors: Lo Mauro Antonella , Tringali Gabriella , Codecasa Franco , Abbruzzese Laura , Sartorio Alessandro , Aliverti Andrea 
Published: October 2023

AbstractObesity is frequently associated with breathing disorders. To investigate if and how the highest levels of obesity impact respiratory function, 17 subjects with obesity (median age: 49 years; BMI: 39.7 kg/m2, 8 females) and 10 normal-weighted subjects (49 years; 23.9 kg/m2, 5 females) were studied. The abdominal volume occupied 41% in the obese group, being higher (p < 0.001) than the normal-weighted group (31%), indicating accumulation of abdominal fat. Restrictive lung defect was present in 17% of subjects with obesity. At rest in the supine position, subjects with obesity breathed with higher minute ventilation (11.9 L/min) and lower ribcage contribution (5.7%) than normal weighted subjects (7.5 L/min, p = 0.001 and 31.1%, p = 0.003, respectively), thus indicating thoracic restriction. Otherwise healthy obesity might not be characterized by a systematic restrictive lung pattern. Despite this, another sign of restriction could be poor thoracic expansion at rest in the supine position, resulting in increased ventilation. Class 3 obesity made respiratory rate further increased. Opto-electronic plethysmography and its thoraco-abdominal analysis of awake breathing add viable and interesting information in subjects with obesity that were complementary to pulmonary function tests. In addition, OEP is able to localize the restrictive effect of obesity.
Phylogenomic insights into the polyphyletic nature of Altai falcons within eastern sakers (Falco cherrug) and the origins of gyrfalcons (Falco rusticolus)
Authors: Zinevich Liudmila , Prommer Mátyás , Laczkó Levente , Rozhkova Daria , Sorokin Alexander , Karyakin Igor , Bagyura János , Cserkész Tamás , Sramkó Gábor 
Published: October 2023

AbstractThe Altai falcon from Central Asia always attracted the attention of humans. Long considered a totemic bird in its native area, modern falconers still much appreciated this large-bodied and mighty bird of prey due to its rarity and unique look. The peculiar body characteristics halfway between the saker falcon (Falco cherrug) and the gyrfalcon (F. rusticolus) triggered debates about its contentious taxonomy. The weak phylogenetic signal associated with traditional genetic methods could not resolve this uncertainty. Here, we address the controversial evolutionary origin of Altai falcons by means of a genome-wide approach, Restriction-site Associated DNA sequencing, using sympatric eastern sakers falcons, allopatric western saker falcons and gyrfalcons as outgroup. This approach provided an unprecedented insight into the phylogenetic relationships of the studied populations by delivering 17,095 unlinked SNPs shedding light on the polyphyletic nature of Altai falcons within eastern sakers. Thus we concluded that the former must correspond to a low taxonomic rank, probably an ecotype or form of the latter. Also, we found that eastern sakers are paraphyletic without gyrfalcons, thus, these latter birds are best regarded as the direct sister lineage of the eastern sakers. This evolutionary relationship, corroborated also by re-analyzing the dataset with the inclusion of outgroup samples (F. biarmicus and F. peregrinus), put eastern sakers into a new light as the potential ancestral genetic source of high latitude and altitude adaptation in descendent populations. Finally, conservation genomic values hint at the stable genetic background of the studied saker populations.
Correlation between cognitive ability and educational attainment weakens over birth cohorts
Authors: Van Hootegem Arno , Røgeberg Ole , Bratsberg Bernt , Lyngstad Torkild Hovde 
Published: October 2023

AbstractEducational attainment is a key indicator of status and opportunity in meritocratic societies. However, it is unclear how educational expansion has affected the link between cognitive abilities and educational attainment. As a result, this study examines the correlation between cognitive ability and educational attainment across male birth cohorts in Norway. Utilizing administrative register data covering more than four decades, we investigate multiple measures of educational attainment and their connection to cognitive abilities. Our findings reveal a consistent decline in the correlation over time. These findings question the assumed shift towards meritocracy in educational systems and highlight a more complex relationship between cognitive ability and educational attainment.
GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads
Authors: Pajuste Fanny-Dhelia , Remm Maido 
Published: October 2023

AbstractGenomes exhibit large regions with segmental copy number variation, many of which include entire genes and are multiallelic. We have developed a computational method GeneToCN that counts the frequencies of gene-specific k-mers in FASTQ files and uses this information to infer copy number of the gene. We validated the copy number predictions for amylase genes (AMY1, AMY2A, AMY2B) using experimental data from digital droplet PCR (ddPCR) on 39 individuals and observed a strong correlation (R = 0.99) between GeneToCN predictions and experimentally determined copy numbers. An additional validation on FCGR3 genes showed a higher concordance for FCGR3A compared to two other methods, but reduced accuracy for FCGR3B. We further tested the method on three different genomic regions (SMN, NPY4R, and LPA Kringle IV-2 domain). Predicted copy number distributions of these genes in a set of 500 individuals from the Estonian Biobank were in good agreement with the previously published studies. In addition, we investigated the possibility to use GeneToCN on sequencing data generated by different technologies by comparing copy number predictions from Illumina, PacBio, and Oxford Nanopore data of the same sample. Despite the differences in variability of k-mer frequencies, all three sequencing technologies give similar predictions with GeneToCN.
Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq
Authors: Heimli Marte , Tennebø Flåm Siri , Sagsveen Hjorthaug Hanne , Bjørnstad Pål Marius , Chernigovskaya Maria , Le Quy Khang , Tekpli Xavier , Greiff Victor , Lie Benedicte Alexandra 
Published: October 2023

AbstractThymic T cell development comprises T cell receptor (TCR) recombination and assessment of TCR avidity towards self-peptide-MHC complexes presented by antigen-presenting cells. Self-reactivity may lead to negative selection, or to agonist selection and differentiation into unconventional lineages such as regulatory T cells and CD8$$\mathrm{\alpha \alpha }$$

α
α

T cells. To explore the effect of the adaptive immune receptor repertoire on thymocyte developmental decisions, we performed single cell adaptive immune receptor repertoire sequencing (scAIRR-seq) of thymocytes from human young paediatric thymi and blood. Thymic PDCD1+ cells, a putative CD8$$\mathrm{\alpha \alpha }$$

α
α

T cell precursor population, exhibited several TCR features previously associated with thymic and peripheral ZNF683+ CD8$$\mathrm{\alpha \alpha }$$

α
α

T cells, including enrichment of large and positively charged complementarity-determining region 3 (CDR3) amino acids. Thus, the TCR repertoire may partially explain the decision between conventional vs. agonist selected thymocyte differentiation, an aspect of importance for the development of therapies for patients with immune-mediated diseases.
Quantitative analysis of prion disease using an AI-powered digital pathology framework
Authors: Salvi Massimo , Molinari Filippo , Ciccarelli Mario , Testi Roberto , Taraglio Stefano , Imperiale Daniele 
Published: October 2023

AbstractPrion disease is a fatal neurodegenerative disorder characterized by accumulation of an abnormal prion protein (PrPSc) in the central nervous system. To identify PrPSc aggregates for diagnostic purposes, pathologists use immunohistochemical staining of prion protein antibodies on tissue samples. With digital pathology, artificial intelligence can now analyze stained slides. In this study, we developed an automated pipeline for the identification of PrPSc aggregates in tissue samples from the cerebellar and occipital cortex. To the best of our knowledge, this is the first framework to evaluate PrPSc deposition in digital images. We used two strategies: a deep learning segmentation approach using a vision transformer, and a machine learning classification approach with traditional classifiers. Our method was developed and tested on 64 whole slide images from 41 patients definitively diagnosed with prion disease. The results of our study demonstrated that our proposed framework can accurately classify WSIs from a blind test set. Moreover, it can quantify PrPSc distribution and localization throughout the brain. This could potentially be extended to evaluate protein expression in other neurodegenerative diseases like Alzheimer's and Parkinson's. Overall, our pipeline highlights the potential of AI-assisted pathology to provide valuable insights, leading to improved diagnostic accuracy and efficiency.
Development and validation of a nomogram to predict cancer-specific survival in nonsurgically treated elderly patients with prostate cancer
Authors: Zhang Zhaoxia , Cai Qian , Wang Jinkui , Yao Zhigang , Ji Fengming , Hang Yu , Ma Jing , Jiang Hongchao , Yan Bing , Zhanghuang Chenghao 
Published: October 2023

AbstractProstate Cancer (PC) is the most common male nonskin tumour in the world, and most diagnosed patients are over 65 years old. The main treatment for PC includes surgical treatment and nonsurgical treatment. Currently, for nonsurgically treated elderly patients, few studies have evaluated their prognostic factors. Our aim was to construct a nomogram that could predict cancer-specific survival (CSS) in nonsurgically treated elderly PC patients to assess their prognosis-related independent risk factors. Patient information was obtained from the Surveillance, Epidemiology and End Results (SEER) database, and our target population was nonsurgically treated PC patients who were over 65 years old. Independent risk factors were determined using both univariate and multivariate Cox regression models. A nomogram was built using a multivariate Cox regression model. The accuracy and discrimination of the prediction model were tested using the consistency index (C-index), the area under the subject operating characteristic curve (AUC), and the calibration curve. Decision curve analysis (DCA) was used to examine the potential clinical value of this model. A total of 87,831 elderly PC patients with nonsurgical treatment in 2010–2018 were included in the study and were randomly assigned to the training set (N = 61,595) and the validation set (N = 26,236). Univariate and multivariate Cox regression model analyses showed that age, race, marital status, TNM stage, chemotherapy, radiotherapy modality, PSA and GS were independent risk factors for predicting CSS in nonsurgically treated elderly PC patients. The C-index of the training set and the validation set was 0.894 (95% CI 0.888–0.900) and 0.897 (95% CI 0.887–0.907), respectively, indicating the good discrimination ability of the nomogram. The AUC and the calibration curves also show good accuracy and discriminability. We developed a new nomogram to predict CSS in elderly PC patients with nonsurgical treatment. The model is internally validated with good accuracy and reliability, as well as potential clinical value, and can be used for clinical aid in decision-making.
Numerical simulation and experiment of double chamber brake based on CFD
Authors: Yuhao Liu , Pu Qu , Qiang Li 
Published: October 2023

AbstractThe artillery firing process will instantly produce high-temperature and high-pressure gunpowder gas, this process will produce shock waves. The gunpowder gas has a limited effect on the projectile during the firing and ballistic after-effects period, however, it has a very obvious effect on the stability of the gun body, and the reduction of the stability of the gun body directly affects the firing accuracy and the safety of the firing personnel. Based on the method of Computational Fluid Dynamics (CFD), numerical simulation is carried out, and the structure and flow parameters of the muzzle flow field are obtained by using three-dimensional Euler's control equation, gas equation of state, and k-epsilon model, as well as dynamic mesh technology. By comparing the flow parameters of the brake before and after optimization, and analyzing the results obtained from the 8-round firing experiments, the efficiency of the optimized brake is increased by 8.2%, and the deviation between the experimental data and the simulation results is only 10.5%, which not only verifies the accuracy of the numerical simulation calculations but also verifies the optimized brake's good retracting effect. The results of the study can provide a reference for the optimization and design of the double-chamber brake.
Comparative and phylogenetic analyses of the chloroplast genomes of Filipendula species (Rosoideae, Rosaceae)
Authors: Zhang Shu-Dong , Ling Li-Zhen 
Published: October 2023

AbstractGenus Filipendula (Rosoideae, Rosaceae) comprises about 15 species and mainly distributed in Northern Hemisphere. The phylogenetic relationships based on the nrITS marker are not consistent with the traditional taxonomic systems of the genus. Here, we first analysed the complete chloroplast (cp) genomes of seven Filipendula species (including two varieties of F. palmate). Our results indicated that the cp genomes of Filipendula species had few changes in size, ranging from 154,205 bp to 154,633 bp and the average of 36.63% GC content. A total of 126 annotated genes had the identical order and orientation, implying that the cp genome structure of Filipendula species was rather conserved. However, the cp genomes of Filipendula species exhibited structural differences, including gene loss, transposition and inversion when compared to those of other genera of Rosoideae. Moreover, SSRs with the different number were observed in the cp genome of each Filipendula species and sequence divergence mainly occurred in noncoding regions, in which four mutational hotspots were identified. In contrast, only two positive selection genes (matK and rps8) were found. Phylogenetic and molecular-dating analysis indicated that Filipendula species were divergent from other genera of Rosoideae at about 82.88 Ma. Additionally, Filipendula species from East Asia were split at about 9.64 Ma into two major clades. These results provide a basis for further studying the infrageneric classification of Filipendula.
High-frequency ultrasound in anti-aging skin therapy monitoring
Authors: Czajkowska Joanna , Juszczyk Jan , Bugdol Monika Natalia , Glenc-Ambroży Małgorzata , Polak Anna , Piejko Laura , Pietka Ewa 
Published: October 2023

AbstractOver the last few decades, high-frequency ultrasound has found multiple applications in various diagnostic fields. The fast development of this imaging technique opens up new diagnostic paths in dermatology, allergology, cosmetology, and aesthetic medicine. In this paper, being the first in this area, we discuss the usability of HFUS in anti-aging skin therapy assessment. The fully automated algorithm combining high-quality image selection and entry echo layer segmentation steps followed by the dermal parameters estimation enables qualitative and quantitative evaluation of the effectiveness of anti-aging products. Considering the parameters of subcutaneous layers, the proposed framework provides a reliable tool for TCA-peel therapy assessment; however, it can be successfully applied to other skin-condition-related problems. In this randomized controlled clinical trial, forty-six postmenopausal women were randomly assigned to the experimental and control groups. Women were treated four times at one-week intervals and applied skin cream daily between visits. The three month follow-up study enables measurement of the long-term effect of the therapy. According to the results, the TCA-based therapy increased epidermal (entry echo layer) thickness, indicating that the thinning process has slowed down and the skin’s condition has improved. An interesting outcome is the obtained growth in the intensity of the upper dermis in the experimental group, which might suggest a reduced photo-aging effect of TCA-peel and increased water content. The same conclusions connected with the anti-aging effect of TCA-peel can be drawn by observing the parameters describing the contribution of low and medium-intensity pixels in the upper dermis. The decreased share of low-intensity pixels and increased share of medium-intensity pixels in the upper dermis suggest a significant increase in local protein synthesis.
The use of tourniquet is useful in terms of blood loss and soft tissue damage in arthroscopic anterior cruciate ligament reconstruction: a retrospective study
Authors: Nagashima Masaki , Sasaki Ryo , Tanaka Kentaro , Takeshima Kenichiro 
Published: October 2023

AbstractWhether a tourniquet should be used for anterior cruciate ligament reconstruction (ACLR) when the operative field is secured remains controversial. Little is known about the influence of not using a tourniquet on total perioperative blood loss and soft tissue damage. The aim of this study was to compare total perioperative blood loss and soft tissue damage with and without tourniquet use during ACLR. Seventy-seven consecutive ACLRs in 76 patients were performed without tourniquet use at our hospital and enrolled in this study (T− group) between November 2018 and September 2021. The control group (T + group) comprised 55 historical ACLRs in 55 patients performed with tourniquet use at our hospital between April 2017 and September 2018. Total perioperative blood loss, calculated from the change in hemoglobin between that preoperatively and on postoperative day (POD) 1, and indicators of soft tissue damage including serum white blood cell (WBC) counts, creatine phosphokinase (CPK), and C-reactive protein (CRP) values measured on POD 1 and POD 7 were compared between groups. Total blood loss was significantly higher in the T− group (339 ± 216 mL) than in the T + group (258 ± 199 mL; P = 0.030). On POD 1, WBC counts were significantly higher in the T− group (9.7 ± 2.4 × 103 cells/µL) than in the T + group (9.1 ± 2.5 × 103 cells/µL; P = 0.043), CPK levels were significantly higher in the T− group (294 ± 417 U/L) than in the T + group (255 ± 88 U/L; P = 0.046), and CRP levels were also significantly higher in the T− group (1.40 ± 1.12 mg/dL) than in the T + group (0.91 ± 0.76 mg/dL; P = 0.016). No significant differences in WBC counts or CPK or CRP levels were seen between groups on POD 7. Total blood loss and soft tissue damage were significantly increased without tourniquet use during ACLR. No advantage was found for not using a tourniquet in terms of blood loss or soft tissue damage.
Repetitive small seismicity coupled with rainfall can trigger large slope instabilities on metastable volcanic edifices
Authors: Durand Virginie , Mangeney Anne , Bernard Pascal , Jia Xiaoping , Bonilla Fabian , Satriano Claudio , Saurel Jean-Marie , Aissaoui El Madani , Peltier Aline , Ferrazzini Valérie , Kowalski Philippe , Lauret Frédéric , Brunet Christophe , Hibert Clément 
Published: October 2023

AbstractQuantifying the effect of external forcings like seismicity or rain on slope destabilization is a long-standing and challenging issue. To investigate the respective roles of these forcings, we analyze an unprecedented 10-year long catalog of rockfalls occurring in the crater of the Piton de la Fournaise volcano (La Reunion Island), using statistical tools originally developed for earthquakes. Our analysis reveals the predominant effect of low amplitude repetitive seismicity in the triggering of rockfalls located at a few kilometers from the source, due to progressive damaging of the slope. Moreover, we show that the efficiency and time-delay of this dynamic triggering is controlled by the stability state of the slope, i.e. its closeness to the failure, as observed with lab-experiments on metastable granular slopes. Our results show the need to account for long-term swarm-type seismic activity that can affect the stability of geological structures like slopes and faults, but also buildings.