bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel cholesterol metabolism-related biomarkers for thyroid cancer to predict the prognosis, immune infiltration, and drug sensitivity
Authors: Li Xixi , Shi Pei , Wu Fei-Fei , Li Dai 
Published: May 2024

Abstract

Cholesterol metabolism plays a vital role in tumor proliferation, regulation of tumor immune escape, and drug resistance. This study aimed to investigate the predictive value of cholesterol metabolism-related genes in thyroid cancer (THCA) and the relationship between immune invasion and drug sensitivity. Methods: Cholesterol metabolism-related genes were obtained from the molecular signatures database, and univariate Cox regression and least absolute shrinkage and selection operator(LASSO) were used to construct a predictive model of cholesterol metabolism-related genes based on the TCGA-THCA dataset. The TCGA dataset was randomly divided into a training group and a validation group to verify the model's predictive value and independent prognostic effect. We then constructed a nomogram and performed enrichment analysis, immune cell infiltration, and drug sensitivity analysis. Finally, TCGA-THCA and GSE33630 datasets were used to detect the expression of signature genes, which was further verified by the HPA database. Result: Six CMRGs (FADS1, NPC2, HSD17B7, ACSL4, APOE, HMGCS2) were obtained by univariate Cox and LASSO regression to construct a prognostic model for 155 genes related to cholesterol metabolism. Their prognostic value was confirmed in the validation set, and a perfect stable nomogram was constructed combined with clinical features. We found a significant reduction in immune cell infiltration in the high-risk group and obtained sensitive drugs for different risk groups through drug sensitivity analysis. The GSE33630 dataset verified the expression of six CMRGs, and the HPA database verified the protein expression of the NPC2 gene. Conclusion: Cholesterol metabolism-related features are a promising biomarker for predicting THCA prognosis and can potentially guide immunization and targeted therapy.
The Impact of Diagnostic Errors and Malpractice Claims on Anxiety and Diagnostic Accuracy in Clinical Reasoning Education of General Practitioners
Authors: Sassen Charlotte van , Mamede Silvia , Hooftman Jacky , Broek Walter van den , Bindels Patrick , Zwaan Laura 
Published: May 2024

Abstract

Purpose
Erroneous and malpractice claim cases reflect knowledge gaps and complex contextual factors. Incorporating such cases into clinical reasoning education (CRE) can enhance learning and diagnostic skills. However, they may also elicit anxiety among learners, potentially hindering learning. As a result, the optimal utilization of such cases in CRE remains uncertain. This study aims to investigate the effect of erroneous and malpractice claim case vignettes on diagnostic accuracy and anxiety in CRE, compared to neutral cases.
Methods
In this three-phase experiment, GP residents and supervisors were randomly assigned to one of three experimental conditions: neutral (without reference to an error), erroneous (involving a diagnostic error), or malpractice claim (involving a diagnostic error along with a malpractice claim description). During the first session, participants solved six cases exclusively in the version of their assigned condition, with anxiety levels measured before and after. In the second session, they solved six different cases with identical diagnoses, along with four fillers, allowing to compare diagnostic accuracy and confidence between case versions. The third session measured the longer-term impact on the participants.
Results
There were no significant differences in anxiety levels and diagnostic accuracy scores between the conditions. Additionally, the long-term impact scores did not differ significantly between conditions.
Conclusion
Case vignettes with an error or malpractice claim were as effective as neutral case vignettes, yielding similar diagnostic accuracy and without inducing more anxiety. This suggests these cases can be integrated into CRE programs, offering a valuable source of diverse, context-rich examples without causing anxiety in learners.
Genome Evolution and Diversity of Wild and Cultivated Rice Species
Authors: Long Weixiong , He Qiang , Wang Yitao , Wang Yu , Wang Jie , Yuan Zhengqing , Wang Meijia , Chen Wei , hua Lihua , Luo Laiyang , Xu Weibiao , Li Yonghui , Li Wei , Yan Longan , Cai Yaohui , Du Huilong , Xie Hongwei 
Published: May 2024

Abstract

Rice (Oryza sativa L.) is a vital staple food globally, but its genetic diversity has decreased due to extensive breeding. However, research on genome evolution and diversity of wild rice species, particularly those with BB, CC, BBCC, CCDD, EE, FF, and GG genome types, is limited, impeding their potential in rice breeding1,2. This study presents chromosome-scale genomes of thirteen representatives wild rice species from the Oryza genus. By integrating these genomes with four previously published ones, a total of 101,723 gene families were identified across the genus, including 9,834 (9.67%) core gene families. Additionally, 63,881 new gene families absent in cultivated rice species were discovered. Comparative genomic analysis among Oryza genomes reveals potential mechanisms underlying genome size variation, centromere evolution, and gene number and expression influenced by transposable elements. Extensive structural rearrangements, large scale sub-genomes exchanges, and widespread allelic variations and regulatory sequence variations were discovered in wild rice. We noticed an inversion that are pervasive occurred in Oryza rufipogon and Oryza sativa japonica, which is tightly linked to a locus that might contributed to the expansion of geographical range. Interestingly, a notable expansion but less diversity in disease resistance genes in cultivated genomes was observed, likely due to the random loss of some R genes and extensive amplification of others for specific diseases during domestication and artificial selection. This comprehensive study not only provide previously hidden legacy accessible to genetic studies and breeding but also deepens our understanding of rice evolution and biology.
Construction and application of evaluation indicator system for homogenous medical services in multi-campus management of public hospitals
Authors: Hao-Yu Wang , Yan Yang , Manchen Lu , Yaoyao Liu , Yu Zhang , Tongbin Xue , Xuezhen Liu , Wanying Zhao , Di Tian , Yuan Zhou , Ye Wu , Dian Zhou 
Published: May 2024

Abstract

Background
To organize the concepts and research progress of multi-campus management and homogeneity in Chinese public hospitals; construct a systematic, rational, and scientific evaluation indicator system and assessment method; and conduct an empirical analysis. This study aims to provide a theoretical basis and practical guidance for the practice of multicampus development in public hospitals.
Methods
The Donabedian model was used to construct an evaluation framework and the Delphi method was used to establish a set of evaluation indicators for the homogeneous management of public hospitals with multiple campuses. The analytic hierarchy process (AHP) was applied to determine the weights of various indicators and perform consistency checks. The TOPSIS + RSR method was used for comprehensive evaluation.
Results
This study identified 3 primary indicators (resource input, operational efficiency, and quality of care), 9 secondary indicators (infrastructure, talent support, revenue and expenditure structure, cost control, medical services, service volume, technical safeguards, patient safety, and rational use of medications), and 41 tertiary indicators. During weighting as part of the analytic hierarchy process, the consistency ratio of the judgment matrices was found to be less than 0.100. Eleven clinical departments were included in the empirical study, and the results of the TOPSIS method of analysis showed that the highest level of homogeneous management was in Department B (gynecology) and the lowest in Department I (neurosurgery). The results of the RSR method showed that the management levels could be graded as high, medium, or low, with a statistically significant linear regression equation between Ci and the corresponding Probit probability (F = 402.1, P < 0.001).
Conclusions
The evaluation indicator system constructed in this study was based on XX, with comprehensive indicators and reliable results. Empirical research has demonstrated its effectiveness in assessing the homogeneous management level of the same department across different campuses. To further optimize the homogeneous management of public hospitals with multiple campuses, the following two strategies could be considered: (1) improving the precision of resource allocation and (2) enhancing the quality and efficiency of sustained coordination.
Distal esophageal spasm and gastroesophageal reflux disease: debunking myths and associations
Authors: Seltzer Emily S. , Sehmbhi Mantej , Sandhu Robinderpal , Cavaliere Kimberly , Luo Yuying , Smith Michael S. , Jodorkovsky Daniela 
Published: May 2024

Abstract

Background
Distal esophageal spasm (DES) is a rare motility disorder presenting with dysphagia or chest pain. Although studies suggest a link between DES and gastroesophageal reflux disease (GERD), data supporting a distinct GERD-related phenotype are limited.
Aims
This study aims to investigate demographic, symptomatic, and physiologic differences between DES subjects with and without GERD.
Methods
A retrospective cohort analysis of DES patients determined by high resolution manometry (HRM) was conducted between 2/2020-1/2023. Demographics, medications, symptoms, and quantitative reflux testing data were collected. DES subjects with reflux (R-DES) were defined by presence of Los Angeles Grade B/C/D esophagitis, Barrett’s metaplasia, or abnormal pH testing. DES subjects without reflux (NR-DES) had normal parameters. Statistical analysis employed two-sided or Wilcoxon Rank-Sum, Chi-squared or Fisher’s exact tests, and multivariate logistic regression.
Results
Of 69 DES subjects, 32 (46.3%) had GERD. R-DES and NR-DES patients had similar demographic variables except for higher BMI in R-DES (30.41 vs 26.88, p = 0.01). R-DES and NR-DES shared similar symptom profiles (heartburn p = 0.67, dysphagia p = 0.448, chest pain p = 0.32). Proton pump inhibitor use was similar between groups (78.1% vs 91.9%, p = 0.202). HRM metrics were comparable except for basal LES tone (20.7 mmHg vs 32.99 mmHg, p = 0.03) and median IRP 11.82 mmHg vs 17.20 mmHg, p = 0.017).
Conclusions
This study found no distinguishing clinical or physiologic differences between DES patients with and without GERD, challenging the historical emphasis of GERD in DES pathogenesis. The impact of GERD management on the natural history of DES remains uncertain.
Provocative measures in the sonographic evaluation of varicocele in obese patients and relation of different grades of varicocele with intra-testicular hemodynamics
Authors: Hasan Zain ul , Gilani Syed Amir , Hanif Asif , Bacha Raham , Fatima Zareen 
Published: May 2024

Abstract

Background
Doppler ultrasonography is typically used to diagnose as a non-invasive imaging technique for the evaluation of varicocele. The Valsalva maneuver and standing position cause reflux of blood through incompetent venous valves, aiding in identifying the varicocele. Varicocele also compromises blood return and leads to an increase in intratesticular artery resistance and pulsatility. However, the efficacy of the standing position Valsalva maneuver and intratesticular artery resistance and pulsatility indices in obese patients for diagnosing varicocele remains uncertain. Obesity presents unique challenges during sonography due to increased adipose tissue and altered venous hemodynamics.
Objective
To evaluate the effect of standing position and Valsalva maneuver on the sonographic diagnosis of varicocele in obese patients and the relation of different grades of varicocele with intratesticular hemodynamics.
Methods
This cross-sectional study was conducted at Gilani Ultrasound Centre, Lahore, Pakistan, from March 2019 to October 2023 on 107 obese male patients, and comprised aged 20–45 years diagnosed with varicocele and infertility having varicocele. Patients with testicular surgery, anomalous genitalia, lower limb edema, abdominal ascites or pleural effusion were excluded.
Results
The mean age of 30.16 ± 3.62 (23 to 39) years. The mean of BMI was 34.51 ± 2.09 (30 to 40), the mean of right-sided varicose veins diameter in laying position was 2.16 ± 0.75 (0.8 to 5.1)mm, while the mean of right-sided varicose veins diameter in standing position was 2.5 ± 0.86 (1.1 to 6.0)mm, and the mean of left-sided varicose veins diameter in laying position was 2.63 ± 0.68 (0.9 to 5.5)mm, while the mean of left-sided varicose veins diameter in standing position was 3.11 ± 0.75 (1.3 to 6.4)mm. The mean of right-sided intratesticular artery resistive index was 0.63 ± 0.07 (0.49 to 0.88), while the mean of left-sided intratesticular artery resistive index was 0.67 ± 0.07 (0.50 to 0.92).
Conclusion
A significant impact of the provocative measures like standing position and Valsalva maneuver is observed on the sonographic diagnosis of varicocele and statically significant increases in the intratesticular artery resistive and pulsatility indices were noted.
The Validity of Content Mapping: Let’s Call a Spade a Spade
Authors: Kampen Jarl K. , Tobi Hilde , Hagenaars Jos , Breuer Marian 
Published: May 2024

Abstract

Concept Mapping (CM) is
promoted as a research method suitable for interdisciplinary and
international research, “… best suited to applications where
diverse or wide-ranging opinions need to be gathered and made sense
of." Our study does not support these claims. We created a
situation where 54 statements were sorted on just 2 different
attributes. Neither the conventional analytic approach in CM nor
alternative clustering algorithms appear able to reveal these
attributes. CM may be appropriate to use when groups can be assumed
to be homogeneous, but CM cannot test this assumption. Discovering
which attributes are used by sorters requires thematic analysis or
focus groups.
Observation on the effect of reconstruction of the forearm rotation function with an external fixator in the treatment of congenital radioulnar synostosis
Authors: Dong Yanzhao , xu Junfang , Wang Feipeng , Jia Yunheng , Feng GuoMing , Liu Yu , Xue Han 
Published: May 2024

Abstract

Purpose: To observe the effect of the forearm rotation function reconstruction with an external fixator in treating congenital radioulnar synostosis.
Methods: From July 2017 to July 2023, 6 patients (9 sides) with congenital radioulnar synostosis who underwent reconstruction of the forearm rotation with the external fixator were retrospectively analyzed. The extent of flexion and rotation, the of Broberg and Morrey scores, and the grade according to the classification system proposed by Failla et al were compared before and after the operation.
Results: All patients were followed up for an average of 12.00(8.00,38.50) months. The average range of rotation, the scores of Broberg and Morrey increased from 0°, 84.89 ±2.03 points to 83.22°±25.37°, 92.67 ± 1.66 points, respectively. The differences were statistically significant (t = 9.72, P < 0.01, t = 19.42, P < 0.01). There was no significant difference in forearm flexion before and after the operation ( Z = 1.34, P = 0.18 ). According to the Failla classification system, 2 forearms were classified as poor preoperatively, 6 as fair and 1 as good. Two forearms were assessed as excellent, 6 as good and 1 as fair during the last follow-up.
Conclusion: Reconstruction of the forearm rotation function with an external fixator is safe and effective for treating congenital radioulnar synostosis. This technique can restore the partial rotational function of the forearm.
Virtual Screening of Molecules via Neural Fingerprint-based Deep Learning Technique
Authors: Monsia Rivaaj , Bhattacharyya Sudeep 
Published: May 2024

Abstract

A machine learning-based drug screening technique has been developed and optimized using convolutional neural network-derived fingerprints. The optimization of weights in the neural network-based fingerprinting technique was compared with fixed Morgan fingerprints in regard to binary classification on drug-target binding affinity. The assessment was carried out using six different target proteins using randomly chosen small molecules from the ZINC15 database for training. This new architecture proved to be more efficient in screening molecules that less favorably bind to specific targets and retaining molecules that favorably bind to it. Scientific contribution We have developed a new neural fingerprint-based screening model that has a significant ability to capture hits. Despite using a smaller dataset, this model is capable of mapping chemical space similar to other contemporary algorithms designed for molecular screening. The novelty of the present algorithm lies in the speed with which the models are trained and tuned before testing its predictive capabilities and hence is a significant step forward in the field of machine learning-embedded computational drug discovery.
Synthesis, characterization and humidity sensing applications of calcium oxide nanoparticles synthesized by facile chemical precipitation method
Authors: Khan Asif , Din Israf Ud 
Published: May 2024

Abstract

Calcium oxide nanoparticles were prepared by mixing aqueous calcium nitrate tetrahydrate solution with sodium hydroxide solution. After short time, a precipitate of white colour of calcium hydroxide was formed. This precipitate was then dried in an electric oven to form powder. The formed dried powder was then calcinated for 3 hours at about 600 oC by applying an electric furnace to form CaO nanoparticles. Characterization of the prepared nanomaterials was performed by applying various characterization methods. X-ray photoelectron spectroscopy (XPS) analysis was performed to study the surface chemical properties, UV-Visible spectroscopy was studied to examine the optical characteristics of the formed materials, thermogravimetric analysis (TGA) was done to study the thermal stability of the products and nitrogen adsorption-desorption was carried out to find out the porosity and surface area of the formed sample calcium oxide nanopartilcles. Humidity sensing performance was studied by measuring the variations in resistance of the sensor using LCR meter as a result of changes in humidity levels in a sealed chamber. From the results of XPS, it was proved that the sample mainly contains calcium and oxygen along with small amounts of impurities such as magnesium, sodium and chlorine. UV-Visible spectra showed two absorption bands at 230 nm and 267 nm. A broad absorption band was also found ranging from 300 nm to 350 nm. The band gap energy calculated from UV-Visible results was observed as 3.39 eV. TGA study confirmed that the weight loss occurred in two steps at two different temperatures. From nitrogen adsorption-desorption, BET surface area was calculated to be 129.49 m2/g and BJH surface area was observed to be 101.34. The average pore size estimated from BJH pore size distribution was 1.704 nm and the average pore volume was observed as 0.238 cc/g. The humidity sensing data showed a decrease in resistance of the sample with increase in the value of humidity, while sensitivity of the sample was increased linearly with increase in humidity levels. The response and recovery times of the sensor were 79 sec and 147 sec respectively. Humidity sensor stability evaluated for 90 days at 15 days intervals were noted and the results indicated that the formed sensor was 65 % stable for the above mentioned period. The results of the studied parameters concluded that the prepared calcium oxide nanoparticles can be effectively used for humidity sensing applications.
Exploring the potential of designed peptides containing lysine and arginine repeats against VIM-2 metallo-beta-lactamases
Authors: Anand Ananya Anurag , Sahoo Amaresh Kumar , Samanta Sintu Kumar 
Published: May 2024

Abstract

The persistent development of bacterial resistance to β-lactam antibiotics presents a serious risk to public health worldwide. The ability of metallo-β-lactamases (MBLs) to hydrolyze a wide range of β-lactam antibiotics and render them ineffective makes them a difficult challenge. The creation of clinically useful inhibitors against MBLs like VIM-2 is still challenging. In this study, we examine the inhibitory capacity of peptides against VIM-2 of Pseudomonas aeruginosa. Deriving inspiration from earlier studies on arginine-rich peptides, we hypothesized that lysine repeats with similar nature may show comparable binding with VIM-2.We found that lysine repeats are much more stable than arginine repeats, and show comparable binding with VIM-2. Initially, we designed a library of peptides containing various combinations of lysine and arginine residues, with the sequence length of 30 amino acids. By means of computational modeling, P-P docking and molecular dynamics simulations, we evaluated the stability and binding affinity of these peptides in complex with VIM-2. Furthermore, peptides showing best binding with VIM-2 were subjected to optimization such that the length was reduced to 12 residues. This optimization of peptide length to reduce charge and potential toxicity enhances the translational prospects of the sequences. We observed that PolyKR (6) was found to be the lead candidate. We demonstrate that incorporation of KR repeats in peptide sequences can be of help in enhancing their binding affinity towards VIM-2. Further, wet-laboratory validation needs to be performed in order to study the interaction of the peptide with the VIM-2 MBL in detail.
A retrospective analysis of gastric cancer lymph node based on groups, regions, and stages
Authors: Song Si-kai , Zhu Jiang , Feng Hai-min , Ma An-she , Yang Chao-gang 
Published: May 2024

Abstract

Objective
The consistency between clinical staging and pathological staging of lymph nodes (LNs) in gastric cancer (GC) remains consistently low, and there is currently no standardized imaging criterion available for diagnosing lymph node metastasis (LNM). To clarify the differences in LNs among different groups, regions, and stages, we conducted a study on the LNs of patients with GC, utilizing imaging and histopathology as the fundamental basis.
Methods
This study retrospectively analyzed the clinical data of 100 patients diagnosed with GC who underwent surgical treatment at Zhongnan Hospital of Wuhan University between January 2022 and May 2023. We collected the basic characteristics of patients, as well as pathological and radiological data of LNs, and compared these data among different groups, regions, and stages.
Results
In terms of pathology, a total of 3566 LNs were collected, with a median of 35 (17–72). In terms of imaging, a total of 2233 LNs were collected, with a median of 22 (3–47). Differences were observed in the long-axis diameter (LAD), short-axis diameter (SAD), ratios of long to short axis RLSA), and product of long and short axis (PLSA) between negative LNs and positive LNs. However, only within group 3 did the RLSA show statistical difference after conducting grouping analysis. The areas under the curve (AUC) for the LAD, SAD, PLSA, and their combination index (CI) in diagnosing LNM were 0.817, 0.817, 0.828, and 0.827 respectively. Diverse groups, regions, and stages exerted a more pronounced influence on LN groups 1–6, while exhibiting a comparatively lesser impact on LN groups 7–16.
Conclusion
The LAD, SAD, and PLSA exhibited significant diagnostic value for LNM and could be employed as diagnostic criteria; however, the RLSA demonstrated limited diagnostic value. The formulation of diagnostic criteria should consider the impact of groups, regions, and stages in order to enhance the sensitivity and specificity.