bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D geometry of femoral reaming for bone graft harvesting
Authors: Gehweiler Dominic , Schmitz Nina , Gueorguiev Boyko , Zderic Ivan , Grünwald Leonard , Richards Geoff , Wähnert Dirk , Raschke Michael J. 
Published: August 2021

AbstractThe reamer-irrigator-aspirator (RIA) technique allows to collect large bone graft amounts without the drawbacks of iliac crest harvesting. Nevertheless, clinical cases with occurrence of femur fractures have been reported. Therefore, this study aimed to systematically investigate the three-dimensional geometry of the reamed bone as a function of the reaming diameter and its influence on the associated potential fracture pattern. Forty-five intact fresh-frozen human cadaveric femora underwent computed tomography (CT). They were randomized to three groups (n = 15) for reaming at a diameter of either 1.5 mm (Group 1), 2.5 mm (Group 2) or 4.0 mm (Group 3) larger than their isthmus using RIA. Reaming was followed by a second CT scan, biomechanical testing until failure and a third CT scan. All CT scans of each femur were aligned via rigid registration, and fracture lines were visualized. Subsequently, a decrease in wall thickness, cross-sectional area, and harvested bone volume have been evaluated. The total volume of the bone graft was significantly higher for Group 3 (7.8 ± 2.9 ml) compared to Group 1 (2.9 ± 1.1 ml) and Group 2 (3.0 ± 1.1 ml). The maximal relative decrease of the wall thickness was located medially (72.7%) in the third (61.4%), fourth (18.2%) and second (9.1%) eighth for all groups. As the diameter of the reaming increased, an overlap of the fracture line with the maximal relative decrease in wall thickness and a maximal average relative decrease of the cross-sectional area became more frequent. This suggests that a reaming-associated fracture is most likely to occur in this region.
Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing
Authors: Biezuner Tamir , Raz Ofir , Amir Shiran , Milo Lilach , Adar Rivka , Fried Yael , Ainbinder Elena , Shapiro Ehud 
Published: August 2021

AbstractAdvances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Demand for single cell dedicated WGA kits (scWGA) has led to the development of several commercial kit. To this point, no robust comparison of all available kits was performed. Here, we benchmark an economical assay, comparing all commercially available scWGA kits. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli1 in genome coverage and of RepliG in reduced error rate. In summary, we show that no single kit is optimal across all categories, highlighting the need for a dedicated kit selection in accordance with experimental requirements.
Migrations of cancer cells through the lens of phylogenetic biogeography
Authors: Chroni Antonia , Miura Sayaka , Oladeinde Olumide , Aly Vivian , Kumar Sudhir 
Published: August 2021

AbstractMalignant cells leave their initial tumor of growth and disperse to other tissues to form metastases. Dispersals also occur in nature when individuals in a population migrate from their area of origin to colonize other habitats. In cancer, phylogenetic biogeography is concerned with the source and trajectory of cell movements. We examine the suitability of primary features of organismal biogeography, including genetic diversification, dispersal, extinction, vicariance, and founder effects, to describe and reconstruct clone migration events among tumors. We used computer-simulated data to compare fits of seven biogeographic models and evaluate models’ performance in clone migration reconstruction. Models considering founder effects and dispersals were often better fit for the clone phylogenetic patterns, especially for polyclonal seeding and reseeding of metastases. However, simpler biogeographic models produced more accurate estimates of cell migration histories. Analyses of empirical datasets of basal-like breast cancer had model fits consistent with the patterns seen in the analysis of computer-simulated datasets. Our analyses reveal the powers and pitfalls of biogeographic models for modeling and inferring clone migration histories using tumor genome variation data. We conclude that the principles of molecular evolution and organismal biogeography are useful in these endeavors but that the available models and methods need to be applied judiciously.
Biomolecular imaging of colorectal tumor lesions using a FITC-labeled scFv-Cκ fragment antibody
Authors: Kim Hyung Il , Kim Jinhyeon , Kim Hyori , Lee Hyeri , Yoon Yong Sik , Hwang Sung Wook , Park Sang Hyoung , Yang Dong-Hoon , Ye Byong Duk , Byeon Jeong-Sik , Yang Suk-Kyun , Kim Sun Young , Myung Seung-Jae 
Published: August 2021

AbstractFor the sensitive diagnosis of colorectal cancer lesions, advanced molecular imaging techniques using cancer-specific targets have emerged. However, issues regarding the clearance of unbound probes and immunogenicity remain unresolved. To overcome these limitations, we developed a small-sized scFv antibody fragment conjugated with FITC for the real-time detection of colorectal cancer by in vivo molecular endoscopy imaging. A small-sized scFv fragment can target colon cancer secreted protein-2 (CCSP-2), highly expressed in colorectal adenocarcinoma tissues; moreover, its full-length IgG probe has been used for molecular imaging previously. To assess the efficacy of anti-CCSP-2 scFv-FITC, surgical specimens were obtained from 21 patients with colorectal cancer for ex vivo molecular fluorescence analysis, histology, and immunohistochemistry. Orthotopic mice were administered with anti-CCSP-2 scFv-FITC topically and intravenously, and distinct tumor lesions were observed by real-time fluorescence colonoscopy. The fluorescence imaging of human colon cancer specimens allowed the differentiation of malignant tissues from non-malignant tissues (p < 0.05), and the CCSP-2 expression level was found to be correlated with the fluorescence intensity. Here, we demonstrated the feasibility and safety of anti-CCSP-2 scFv-FITC for molecular imaging as well as its potential in real-time fluorescence colonoscopy for the differential diagnosis of tumor lesions.
Enhanced CD4+ and CD8+ T cell infiltrate within convex hull defined pancreatic islet borders as autoimmune diabetes progresses
Authors: Dwyer Alexander J. , Ritz Jacob M. , Mitchell Jason S. , Martinov Tijana , Alkhatib Mohannad , Silva Nubia , Tucker Christopher G. , Fife Brian T. 
Published: August 2021

AbstractThe notion that T cell insulitis increases as type 1 diabetes (T1D) develops is unsurprising, however, the quantitative analysis of CD4+ and CD8+ T cells within the islet mass is complex and limited with standard approaches. Optical microscopy is an important and widely used method to evaluate immune cell infiltration into pancreatic islets of Langerhans for the study of disease progression or therapeutic efficacy in murine T1D. However, the accuracy of this approach is often limited by subjective and potentially biased qualitative assessment of immune cell subsets. In addition, attempts at quantitative measurements require significant time for manual analysis and often involve sophisticated and expensive imaging software. In this study, we developed and illustrate here a streamlined analytical strategy for the rapid, automated and unbiased investigation of islet area and immune cell infiltration within (insulitis) and around (peri-insulitis) pancreatic islets. To this end, we demonstrate swift and accurate detection of islet borders by modeling cross-sectional islet areas with convex polygons (convex hulls) surrounding islet-associated insulin-producing β cell and glucagon-producing α cell fluorescent signals. To accomplish this, we used a macro produced with the freeware software ImageJ equipped with the Fiji Is Just ImageJ (FIJI) image processing package. Our image analysis procedure allows for direct quantification and statistical determination of islet area and infiltration in a reproducible manner, with location-specific data that more accurately reflect islet areas as insulitis proceeds throughout T1D. Using this approach, we quantified the islet area infiltrated with CD4+ and CD8+ T cells allowing statistical comparison between different age groups of non-obese diabetic (NOD) mice progressing towards T1D. We found significantly more CD4+ and CD8+ T cells infiltrating the convex hull-defined islet mass of 13-week-old non-diabetic and 17-week-old diabetic NOD mice compared to 4-week-old NOD mice. We also determined a significant and measurable loss of islet mass in mice that developed T1D. This approach will be helpful for the location-dependent quantitative calculation of islet mass and cellular infiltration during T1D pathogenesis and can be combined with other markers of inflammation or activation in future studies.
Effects of chronic cholinergic stimulation associated with aerobic physical training on cardiac morphofunctional and autonomic parameters in spontaneously hypertensive rats
Authors: Gardim Camila B. , Veiga Ana Catarine , Aguilar Bruno A. , Philbois Stella V. , Souza Hugo C. D. 
Published: August 2021

AbstractWe investigated hemodynamic, cardiac morphofunctional, and cardiovascular autonomic adaptations in spontaneously hypertensive rats (SHRs) after aerobic physical training associated with chronic cholinergic stimulation. Fifty-four SHRs were divided into two groups: trained and untrained. Each group was further subdivided into three smaller groups: vehicle, treated with pyridostigmine bromide at 5 mg/kg/day, and treated with pyridostigmine bromide at 15 mg/kg/day. The following protocols were assessed: echocardiography, autonomic double pharmacological blockade, heart rate variability (HRV), blood pressure variability (BPV), and baroreflex sensitivity (BRS). Physical training and pyridostigmine bromide reduced BP and HR and increased vagal participation in cardiac autonomic tonic balance. The associated responses were then potentialized. Treatment with pyridostigmine bromide increased HRV oscillation of both low frequency (LF: 0.2–0.75 Hz) and high frequency (HF: 0.75–3 Hz). However, the association with physical training attenuated HF oscillations. Additionally, treatment with pyridostigmine bromide also increased LF oscillations of BPV. Both treatment groups promoted morphofunctional adaptations, and associated increased ejection volume, ejection fraction, cardiac output, and cardiac index. In conclusion, the association of pyridostigmine bromide and physical training promoted greater benefits in hemodynamic parameters and increased vagal influence on cardiac autonomic tonic balance. Nonetheless, treatment with pyridostigmine bromide alone seems to negatively affect BPV and the association of treatment negatively influences HRV.
Machine learning assisted prediction of the Young’s modulus of compositionally complex alloys
Authors: Khakurel Hrishabh , Taufique M. F. N. , Roy Ankit , Balasubramanian Ganesh , Ouyang Gaoyuan , Cui Jun , Johnson Duane D. , Devanathan Ram 
Published: August 2021

AbstractWe identify compositionally complex alloys (CCAs) that offer exceptional mechanical properties for elevated temperature applications by employing machine learning (ML) in conjunction with rapid synthesis and testing of alloys for validation to accelerate alloy design. The advantages of this approach are scalability, rapidity, and reasonably accurate predictions. ML tools were implemented to predict Young’s modulus of refractory-based CCAs by employing different ML models. Our results, in conjunction with experimental validation, suggest that average valence electron concentration, the difference in atomic radius, a geometrical parameter λ and melting temperature of the alloys are the key features that determine the Young’s modulus of CCAs and refractory-based CCAs. The Gradient Boosting model provided the best predictive capabilities (mean absolute error of 6.15 GPa) among the models studied. Our approach integrates high-quality validation data from experiments, literature data for training machine-learning models, and feature selection based on physical insights. It opens a new avenue to optimize the desired materials property for different engineering applications.
Theory of mind affects the interpretation of another person's focus of attention
Authors: Dawson Jessica , Kingstone Alan , Foulsham Tom 
Published: August 2021

AbstractPeople are drawn to social, animate things more than inanimate objects. Previous research has also shown gaze following in humans, a process that has been linked to theory of mind (ToM). In three experiments, we investigated whether animacy and ToM are involved when making judgements about the location of a cursor in a scene. In Experiment 1, participants were told that this cursor represented the gaze of an observer and were asked to decide whether the observer was looking at a target object. This task is similar to that carried out by researchers manually coding eye-tracking data. The results showed that participants were biased to perceive the gaze cursor as directed towards animate objects (faces) compared to inanimate objects. In Experiments 2 and 3 we tested the role of ToM, by presenting the same scenes to new participants but now with the statement that the cursor was generated by a ‘random’ computer system or by a computer system designed to seek targets. The bias to report that the cursor was directed toward faces was abolished in Experiment 2, and minimised in Experiment 3. Together, the results indicate that people attach minds to the mere representation of an individual's gaze, and this attribution of mind influences what people believe an individual is looking at.
Benchmarking laboratory processes to characterise low-biomass respiratory microbiota
Authors: Hasrat Raiza , Kool Jolanda , de Steenhuijsen Piters Wouter A. A. , Chu Mei Ling J. N. , Kuiling Sjoerd , Groot James A. , van Logchem Elske M. , Fuentes Susana , Franz Eelco , Bogaert Debby , Bosch Thijs 
Published: August 2021

AbstractThe low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.
Development of diabetes mellitus following hormone therapy in prostate cancer patients is associated with early progression to castration resistance
Authors: Hayashi Tomonori , Miyamoto Tomoyoshi , Nagai Noriaki , Kawabata Atsufumi 
Published: August 2021

AbstractTo identify risk factors for the prognosis of prostate cancer (PC), we retrospectively analyzed the impact of lifestyle-related disorders as well as PC characteristics at initial diagnosis on the progression to castration-resistant PC (CRPC) in PC patients undergoing hormone therapy. Of 648 PC patients, 230 who underwent hormone therapy and met inclusion criteria were enrolled in this study. CRPC developed in 48 patients (20.9%). Univariate analysis using Cox proportional hazard model indicated that newly developed diabetes mellitus (DM) following hormone therapy (postDM), but not preexisting DM, as well as PC characteristics at initial diagnosis including prostate-specific antigen (PSA) ≥ 18 were significantly associated with the progression to CRPC. A similar tendency was also observed in the relationship between newly developed hypertension following hormone therapy and CRPC progression. On the other hand, neither dyslipidemia nor hyperuricemia, regardless the onset timing, exhibited any association with CRPC progression. In multivariate analysis, postDM and PSA ≥ 18 were extracted as independent risk factors for CRPC progression (adjusted hazard ratios, 3.38 and 2.34; p values, 0.016 and 0.019, respectively). Kaplan–Meier analysis and log-rank test clearly indicated earlier progression to CRPC in PC patients who developed postDM or had relatively advanced initial PC characteristics including PSA ≥ 18. Together, the development of lifestyle-related disorders, particularly DM, following hormone therapy, as well as advanced PC characteristics at initial diagnosis is considered to predict earlier progression to CRPC and poor prognosis in PC patients undergoing hormone therapy.
Development of a new method for assessing otolith function in mice using three-dimensional binocular analysis of the otolith-ocular reflex
Authors: Harada Shotaro , Imai Takao , Takimoto Yasumitsu , Ohta Yumi , Sato Takashi , Kamakura Takefumi , Takeda Noriaki , Kitahara Tadashi , Kondo Makoto , Ueno Yuya , Shimada Shoichi , Inohara Hidenori 
Published: August 2021

AbstractIn the interaural direction, translational linear acceleration is loaded during lateral translational movement and gravitational acceleration is loaded during lateral tilting movement. These two types of acceleration induce eye movements via two kinds of otolith-ocular reflexes to compensate for movement and maintain clear vision: horizontal eye movement during translational movement, and torsional eye movement (torsion) during tilting movement. Although the two types of acceleration cannot be discriminated, the two otolith-ocular reflexes can distinguish them effectively. In the current study, we tested whether lateral-eyed mice exhibit both of these otolith-ocular reflexes. In addition, we propose a new index for assessing the otolith-ocular reflex in mice. During lateral translational movement, mice did not show appropriate horizontal eye movement, but exhibited unnecessary vertical torsion-like eye movement that compensated for the angle between the body axis and gravito-inertial acceleration (GIA; i.e., the sum of gravity and inertial force due to movement) by interpreting GIA as gravity. Using the new index (amplitude of vertical component of eye movement)/(angle between body axis and GIA), the mouse otolith-ocular reflex can be assessed without determining whether the otolith-ocular reflex is induced during translational movement or during tilting movement.
Postoperative outcomes of elderly patients undergoing partial nephrectomy
Authors: Ingels Alexandre , Duc Sophie , Bensalah Karim , Bigot Pierre , Paparel Philippe , Beauval Jean-Baptiste , Salomon Laurent , De La Taille Alexandre , Lang Hervé , Nouhaud François-Xavier , Batista Da Costa José , Dariane Charles , Baumert Hervé , Roupret Morgan , Waeckel Thibaut , Lebacle Cédric , Long Jean-Alexandre , Henon François , Patard Jean-Jacques , Doumerc Nicolas , Mejean Arnaud , Videau Marie-Neige , Bernhard Jean-Christophe 
Published: August 2021

AbstractTo describe clinical outcomes of patients aged 75 years and above after partial nephrectomy (PN), and to assess independent factors of postoperative complications. We retrospectively reviewed information from our multi-institutional database. Every patient over 75 years old who underwent a PN between 2003 and 2016 was included. Peri-operative and follow up data were collected. Multivariate logistic regression was performed to determine independent predictive factors of postoperative complications. We reviewed 191 procedures including 69 (40%) open-surgery, and 122 (60%) laparoscopic procedures, of which 105 were robot-assisted. Median follow-up was 25 months. The mean age was 78 [75–88]. The American Society of Anesthesiologist’s score was 1, 2, 3 and 4 in 10.5%, 60%, 29% and 0.5% of patients respectively. The mean tumor size was 4.6 cm. Indication of PN was elective in 122 (65%) patients and imperative in 52 patients (28%). The median length of surgery was 150(± 60) minutes, and the median estimated blood loss 200 ml. The mean glomerular filtration rate was 71.5 ml/minute preoperatively, and 62 ml/min three months after surgery. The severe complications (Clavien III-V) rate was 6.2%. On multivariate analysis, the robotic-assisted procedure was an independent protective factor of medical postoperative complications (Odds Ration (OR) = 0.31 [0.12–0.80], p = 0.01). It was adjusted for age and RENAL score, robotic-assisted surgery (OR = 0.22 [0.06–0.79], p = 0.02), and tumor size (OR = 1.13 [1.02–1.26], p = 0.01), but the patients age did not forecast surgical complications. Partial nephrectomy can be performed safely in elderly patients with an acceptable morbidity, and should be considered as a viable treatment option. Robotic assistance is an independent protective factor of postoperative complications.
Reveals of candidate active ingredients in Justicia and its anti-thrombotic action of mechanism based on network pharmacology approach and experimental validation
Authors: Hong Zongchao , Zhang Ting , Zhang Ying , Xie Zhoutao , Lu Yi , Yao Yunfeng , Yang Yanfang , Wu Hezhen , Liu Bo 
Published: August 2021

AbstractThrombotic diseases seriously threaten human life. Justicia, as a common Chinese medicine, is usually used for anti-inflammatory treatment, and further studies have found that it has an inhibitory effect on platelet aggregation. Therefore, it can be inferred that Justicia can be used as a therapeutic drug for thrombosis. This work aims to reveal the pharmacological mechanism of the anti-thrombotic effect of Justicia through network pharmacology combined with wet experimental verification. During the analysis, 461 compound targets were predicted from various databases and 881 thrombus-related targets were collected. Then, herb-compound-target network and protein–protein interaction network of disease and prediction targets were constructed and cluster analysis was applied to further explore the connection between the targets. In addition, Gene Ontology (GO) and pathway (KEGG) enrichment were used to further determine the association between target proteins and diseases. Finally, the expression of hub target proteins of the core component and the anti-thrombotic effect of Justicia’s core compounds were verified by experiments. In conclusion, the core bioactive components, especially justicidin D, can reduce thrombosis by regulating F2, MMP9, CXCL12, MET, RAC1, PDE5A, and ABCB1. The combination of network pharmacology and the experimental research strategies proposed in this paper provides a comprehensive method for systematically exploring the therapeutic mechanism of multi-component medicine.