bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehension of Cochlear Duct Length for Incomplete Partition Types
Authors: Aksoy Direnç Özlem , Meltem Emine , Karagöz Yeşim , Yildirim Gülşah , Mahmutoğlu Özdeş , Mahmutoğlu Abdullah Soydan 
Published: June 2023

Objective
Preoperative assessment of the cochlear duct length (CDL) and cochlear dimensions allows the selection of optimized implants. We aimed to evaluate the CDL measurements in incomplete partition (IP) defect patients and to create a reference to the literature.

Methods
Forty-one patients with IP (13 IP I, 23 IP II, and 5 IP III) and 30 controls were included in the study. The standardized cochlear image showing the basal turn in the most expansive plane was reconstructed from temporal high-resolution computed tomography images. Cochlear duct length measured manually (CDL-M) was measured by points placed consecutively on the lateral wall of the cochlea. The defined equations for estimating CDL (CDL measured according to Schurzig et al formula [CDL-Ɵ], CDL measured according to Escudé et al formula [CDL-E], CDL measured according to Alexiades et al formula [CDL-A]) were calculated from the same images. Cochlear duct length mean values obtained by each method were compared for each IP type.

Results
The longest CDL value was found in the control group, irrespective of the calculation method. Incomplete partition II cases had the most extended mean CDL among IP types. Incomplete partition III had the shortest CDL among all groups' CDL-M values. However, the mean CDL-M values of IP types I and III showed close results. There was no significant difference between the CDL-E and CDL-M values of the control group. Similarly, no significant difference was found between CDL-Ɵ and CDL-M values in IP type III cases. However, the results of other estimating formulations of all groups differed significantly from CDL-M values.

Conclusion
Cochlear duct length differences were detected between the control group and IP subtypes. These differences should be considered when choosing the appropriate electrode length. Because the results of formulas estimating CDL may differ from CDL-M in both control and IP cases, it would be more appropriate to use manual measurements in clinical practice.
Respiratory Invariant Textures From Static Computed Tomography Scans for Explainable Lung Function Characterization
Authors: Huang Yu-Hua , Teng Xinzhi , Zhang Jiang , Chen Zhi , Ma Zongrui , Ren Ge , Kong Feng-Ming (Spring) , Ge Hong , Cai Jing 
Published: June 2023

Purpose:
The inherent characteristics of lung tissue independent of breathing maneuvers may provide fundamental information for function assessment. This paper attempted to correlate textural signatures from computed tomography (CT) with pulmonary function measurements.

Materials and Methods:
Twenty-one lung cancer patients with thoracic 4-dimensional CT, DTPA-single-photon emission CT ventilation (V
NM) scans, and available spirometry measurements (forced expiratory volume in 1 s, FEV1; forced vital capacity, FVC; and FEV1/FVC) were collected. In subregional feature discovery, function-correlated candidates were identified from 79 radiomic features based on the statistical strength to differentiate defected/nondefected lung regions. Feature maps (FMs) of selected candidates were generated on 4-dimensional CT phases for a voxel-wise feature distribution study. Quantitative metrics were applied for validations, including the Spearman correlation coefficient (SCC) and the Dice similarity coefficient for FM-V
NM spatial agreement assessments, intraclass correlation coefficient for FM interphase robustness evaluations, and FM-spirometry comparisons.

Results:
At the subregion level, 8 function-correlated features were identified (effect size>0.330). The FMs of candidates yielded moderate-to-strong voxel-wise correlations with the reference V
NM. The FMs of gray level dependence matrix dependence nonuniformity showed the highest robust (intraclass correlation coefficient=0.96 and P<0.0001) spatial correlation, with median SCCs ranging from 0.54 to 0.59 throughout the 10 breathing phases. Its phase-averaged FM achieved a median SCC of 0.60, a median Dice similarity coefficient of 0.60 (0.65) for high (low) functional lung volumes, and a correlation of 0.565 (0.646) between the spatially averaged feature values and FEV1 (FEV1/FVC).

Conclusions:
The results provide further insight into the underlying association of specific pulmonary textures with both local (V
NM) and global (FEV1/FVC, FEV1) functions. Further validations of the FM generalizability and the standardization of implementation protocols are warranted before clinically relevant investigations.
Transfrontal External Ventricular Drainage Combined with OMMAYA Sac Implantation under Laser Navigation were Performed: A Technical Note
Authors: yuan Zhengbo , Cao Zhijie , Li Zefu , Sun Qikai 
Published: June 2023

Background:
Hydrocephalus caused by spontaneous intracerebral hemorrhage (ICH) is an independent risk factor with adverse effects on the progression of the disease. Until now, the choice of intraventricular catheter placement and intraventricular fibrinolysis (IVF) has been mainly based on the personal experience of the neurosurgeon.

Objective:
We will introduce the clinical effect of the new external ventricular drainage (EVD), an independent innovation of our medical center, on ICH patients, hoping to inspire more neurosurgeons to apply our method.

Methods:
In this open retrospective study, We analyzed the clinical data, radiological manifestations, and prognostic scores of 10 patients with the spontaneous intracerebral hemorrhage who received transfrontal lateral ventricle puncture and drainage under laser navigation in our hospital.

Results:
A total of 10 patients with an average age of 58.10±9.97 years were enrolled for emergency surgery. All operations were completed according to the consensus specifications. It took 11.25±3.81 days for the intracranial pressure to return to normal. On admission, patients had a median GCS of 10. The median preoperative GCS was 8. The median GCS at discharge score was 15. At discharge, the median NIHSS score was 4. After 6 months of follow-up, patients had a median NIHSS score of 4. At discharge, the median ADL score of patients was 85. After 6 months of follow-up, the median ADL score of the patients was 95.

Conclusion:
In treating patients with ICH, the emergency treatment of transfrontal external ventricular drainage combined with OMMAYA sac implantation under laser navigation is a surgical method worthy of further study.
PREDICTIVE VALUE OF SOLUBLE PROGRAMMED CELL DEATH LIGAND-1 IN THE PROGRESSION OF SEPTIC PATIENTS TO CHRONIC CRITICAL ILLNESS IN THE INTENSIVE CARE UNIT: A PROSPECTIVE OBSERVATIONAL CLINICAL STUDY
Authors: Zeng Chenyu , Li Xing , Lu Zhongqian , Mu Genhua , Deng Yijun 
Published: June 2023

ABSTRACT

Background: As an immune marker, serum soluble programmed cell death ligand-1 (sPD-L1) is significantly increased in sepsis and is predictive of mortality. We investigated the prognostic value of sPD-L1 in postseptic immunosuppression and progression to chronic critical illness (CCI). Methods: Adults with sepsis in intensive care units (ICUs) for the first time were screened and assigned to either a CCI group (ICU stay ≥14 days with persistent organ dysfunction) or a rapid recovery (RAP) group based on clinical outcome. Data regarding basic admission information and clinical parameters were collected and compared across the two groups. Serum sPD-L1 levels were detected by enzyme-linked immunosorbent assay at admission and on the seventh day (D7). Logistic regression analysis was used to determine the factors affecting septic patients' lymphocytopenia diagnosis on day 7 and CCI progression during hospitalization. The receiver operating characteristic curve and DeLong test were used to assess variable predictive power. Results: During the study period, a total of 166 septic patients were admitted to the ICU, and 91 septic patients were enrolled after screening. Compared with those in healthy individuals, the sPD-L1 levels in septic patients were significantly higher and positively correlated with traditional inflammatory markers and disease severity scores (P < 0.05). In a multivariate regression analysis, sPD-L1 alone predicted lymphocytopenia on day 7 (P < 0.05). In the sepsis cohort, 59 patients (64.8%) experienced RAP, and 32 patients (35.2%) developed CCI. Compared with the RAP group, the patients in the CCI group had a higher mean age, greater severity of disease, and higher mortality (P < 0.05). D7-sPD-L1 remained higher in the CCI group, and the area under the curve that predicted the occurrence of CCI was equivalent to the APACHE II score, with areas under the curve of 0.782 and 0.708, respectively. Conclusions: The severity of infection and immunosuppression in sepsis may be linked to serum sPD-L1. D7-sPD-L1 is valuable in predicting the progression of CCI in patients.
Indocyanine Green Imaging in Laparoscopic Cholecystectomy Plus Laparoscopic Common Bile Duct Exploration: A Suitable Option for Patients With Difficult Exploration (With Videos)
Authors: Ma Chenhui , Zhang Lei , Wen Junye , Zhang Wanxing , Chen Hao 
Published: June 2023

Background:
The clinical application of indocyanine green (ICG) fluorescence imaging technology in biliary surgery has gradually highlighted its role, and its role in laparoscopic cholecystectomy plus laparoscopic common bile duct exploration (LC+LCBDE) still needs to be further explored. Therefore, we evaluated the clinical value of ICG fluorescence imaging in LC+LCBDE.

Materials and Methods:
Data from 131 patients who underwent LC+LCBDE in our department between January 2019 and June 2021 were retrospectively collected and analyzed. Overall, 59 and 72 patients underwent ICG+LC+LCBDE and LC+LCBDE, respectively, and were assigned to the ICG (ICG+LC+LCBDE) and non-ICG (LC+LCBDE) groups based on their medical records. The clinical data of all patients were obtained, and the differences between the ICG and non-ICG groups were compared.

Results:
A total of 131 patients successfully underwent surgery. There were no differences in baseline characteristics between the 2 groups. In terms of perioperative results, no significant between-group differences in biliary tract exposure before Calot’s triangle dissection were noted; however, patients in the ICG group had better biliary tract observations after Calot’s triangle dissection, shorter operative time, fewer complications, earlier postoperative exhaust, and lower hospital costs.

Conclusions:
ICG imaging can assist surgeons in determining biliary tract structures and injuries during surgery and in preventing operation-related bile leakage. ICG imaging is a technique worthy of promotion in difficult surgery.
Peripheral death by neglect and limited clonal deletion during physiologic B lymphocyte development
Authors: Willett Mikala JoAnn , McNees Christopher , Sharma Sukriti , Newen Anna Minh , Pfannenstiel Dylan , Moyer Thomas , Stephany David , Douagi Iyadh , Wang Qiao , Mayer Christian Thomas 
Published: June 2023

AbstractAutoreactive B cells generated during B cell development are inactivated by clonal deletion, receptor editing or anergy. Up to 97% of immature B cells appear to die before completing maturation, but the anatomic sites and reasons underlying this massive cell loss are not fully understood. Here, we directly quantitated apoptosis and clonal deletion during physiologic B lymphocyte development using Rosa26INDIAapoptosis indicator mice. Immature B cells displayed low levels of apoptosis in the bone marrow but started dying at high levels in the periphery upon release from bone marrow sinusoids into the blood circulation. Clonal deletion of self-reactive B cells was neither a major contributor to apoptosis in the bone marrow nor the periphery. Instead, most peripheral transitional 1 B cells did not encounter the signals required for positive selection into the mature B cell compartments. This study sheds new light on B cell development and suggests that receptor editing and/or anergy efficiently control most primary autoreactivity in mice.SummaryThe large amount of cell loss predicted during B lymphocyte development is unexplained by clonal deletion of self-reactive cells. Many transitional 1 B cells die in the periphery due to failed selection in the mature B cell compartments.
Identification of bioactive constituents for colitis from traditional Chinese medicine prescription via deep neural network
Authors: Ren Zhixiang , Ren Yiming , Liu Pengfei , Shu Qi , Ma Huijuan , Xu Huan 
Published: June 2023

AbstractColitis is a commonly encountered inflammatory disease in colon tissue, which can be triggered by various causes. Although traditional Chinese medicine (TCM) has been utilized for the treatment of colitis, it is still a great challenge to identify the major bioactive constituents and their modes of action among thousands of ingredients in TCM prescriptions. Inspired by the success of artificial intelligence and deep learning methods, we proposed a deep neural network (DNN) for TCM prescription recommendation. We constructed a graph-based DNN with 9,845 nodes and 161,950 edges, which integrated microscopic information including bioactive molecules, protein targets, and extracted features of prescriptions through feature embedding. A novel and efficient data augmentation strategy was implemented to expand the sample size based on 378 collected TCM prescriptions. Network pharmacology study revealed that the 10 most frequent ingredients in generated prescriptions were associated with multiple inflammatory signaling pathways. To verify the bioactive constituents in the generated prescriptions, 5 selected constituents were administrated to BALB/c mice with colitis. Suppressive effects of disease progression and pro-inflammatory factors comparable to sulfasalazin were observed with these compounds, revealing the effectiveness of our artificial intelligence strategy on idetification of bioactive constituents from TCM prescriptions.
Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome ofMoringa oleiferareveals unanticipated complexity in NUPTś formation
Authors: Marczuk-Rojas Juan Pablo , Álamo-Sierra Angélica María , Salmerón Antonio , Alcayde Alfredo , Isanbaev Viktor , Carretero-Paulet Lorenzo 
Published: June 2023

AbstractBeyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes are featured by a small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, research on the topic was mostly focused on a limited number of species and of plastid DNA. Here, we leveraged a chromosome-scale version of theMoringa oleiferagenome, featured by the largest fraction of plastid DNA in any plant nuclear genome, to examine the chromosomal distribution and arrangement of NUPTs, to explicitly model and test the correlation between their age and size distribution, as well as to characterize their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to study the mechanisms of origin and evolutionary fate of NUPTs.Significance statementSequencing of plant genomes has revealed the presence of a variable, but significant, content of DNA arising from their organelles,i.e., plastids and mitochondria. However, the mechanisms underlying their origin and fixation are not yet fully elucidated. Here, by thoroughly examining the spatial and temporal distribution of the large fraction of plastid DNA present in the nuclear genome of the orphan cropMoringa oleifera, we identified their episodic origin trough seemingly distinct mechanisms, highlighting the complexity of the molecular and evolutionary dynamics underlying their origin and fixation and revealing moringa as an outstanding model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.
The impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes
Authors: Dym Orly , Aggawal Nidhi , Ashani Yaacov , Albeck Shira , Unger Tamar , Rogotner Shelly Hamer , Silman Israel , Tawfik Dan S. , Sussman Joel L. 
Published: June 2023

AbstractWhile attempting to study the 3D structure of proteins with bound ligands, one often encounters considerable difficulties. We illustrate, as an example, the bacterial enzyme phosphotriesterase and specifically examine the effects of multiple factors such as the molecular constructs, ligands used during protein expression and purification, crystallization precipitance, and space group on the visualization of molecular complexes of organophosphate ligands bound to the enzyme.We analyzed twelve crystal structures of the different phosphotriesterase constructs derived by directed evolution in both apo and holo forms (in complex with organophosphate analogs), with resolutions up to 1.38 Å. Crystals obtained from three different crystallization conditions, crystallized in four space groups, with and without N-terminal tags, were utilized to investigate the impact of these factors on visualizing molecular complexes of ligands bound to the enzyme. The study revealed that residual tags used for protein expression can lodge in the active site and hinder ligand binding. Additionally, the space groups in which the proteins are crystallized can significantly impact the visualization of the organophosphate ligands bound to the phosphotriesterase. The study also reveals that the crystallization precipitants can compete with and even preclude ligand binding, leading to false positives or the incorrect identification of lead drug candidates, which is particularly crucial for ligands with pharmacological and toxicological contexts.Overall, this study provides valuable insights into the challenges and considerations involved in studying the 3D structure of proteins with bound ligands, highlighting the importance of careful experimental design and rigorous data analysis to ensure the accuracy and reliability of the resulting protein-ligand structures.
A detailed Molecular Network Map and Model of the NLRP3 Inflammasome
Authors: Krantz Marcus , Eklund Daniel , Särndahl Eva , Hedbrant Alexander 
Published: June 2023

AbstractThe NLRP3 inflammasome is a key regulator of inflammation that responds to a broad range of stimuli. The exact mechanism of activation has not been determined, but there is a consensus on cellular potassium efflux as a major common denominator. Once NLRP3 is activated, it forms high-order complexes together with NEK7 that trigger aggregation of ASC into specks. Typically, there is only one speck per cell, consistent with the proposal that specks form – or end up at – the centrosome. ASC polymerisation in turn triggers caspase-1 activation, leading to maturation and release of IL-1β and pyroptosis, i.e., highly inflammatory cell death. Several gain-of-function mutations in the NLRP3 inflammasome have been suggested to induce spontaneous activation of NLRP3 and hence contribute to development and disease severity in numerous autoinflammatory and autoimmune diseases. Consequently, the NLRP3 inflammasome is of significant clinical interest, and recent attention has drastically improved our insight in the range of involved triggers and mechanisms of signal transduction. However, despite recent progress in knowledge, a clear and comprehensive overview of how these mechanisms interplay to shape the system level function is missing from the literature. Here, we provide such an overview as a resource to researchers working in or entering the field, as well as a computational model that allows for evaluating and explaining the function of the NLRP3 inflammasome system from the current molecular knowledge. We present a detailed reconstruction of the molecular network surrounding the NLRP3 inflammasome, which account for each specific reaction and the known regulatory constraints on each event as well as the mechanisms of drug action and impact of genetics when known. Furthermore, an executable model from this network reconstruction is generated with the aim to be used to explain NLRP3 activation from priming and activation to the maturation and release of IL-1β and IL-18. Finally, we test this detailed mechanistic model against data on the effect of different modes of inhibition of NLRP3 assembly. While the exact mechanisms of NLRP3 activation remains elusive, the literature indicates that the different stimuli converge on a single activation mechanism that is additionally controlled by distinct (positive or negative) priming and licensing events through covalent modifications of the NLRP3 molecule. Taken together, we present a compilation of the literature knowledge on the molecular mechanisms on NLRP3 activation, a detailed mechanistic model of NLRP3 activation, and explore the convergence of diverse NLRP3 activation stimuli into a single input mechanism.