bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simcryocluster: a semantic similarity clustering method of cryo-EM images by adopting contrastive learning
Authors: Tang Huanrong , Wang Yaowu , Ouyang Jianquan , Wang Jinlin 
Published: February 2024

Abstract
Background
Cryo-electron microscopy (Cryo-EM) plays an increasingly important role in the determination of the three-dimensional (3D) structure of macromolecules. In order to achieve 3D reconstruction results close to atomic resolution, 2D single-particle image classification is not only conducive to single-particle selection, but also a key step that affects 3D reconstruction. The main task is to cluster and align 2D single-grain images into non-heterogeneous groups to obtain sharper single-grain images by averaging calculations. The main difficulties are that the cryo-EM single-particle image has a low signal-to-noise ratio (SNR), cannot manually label the data, and the projection direction is random and the distribution is unknown. Therefore, in the low SNR scenario, how to obtain the characteristic information of the effective particles, improve the clustering accuracy, and thus improve the reconstruction accuracy, is a key problem in the 2D image analysis of single particles of cryo-EM.

Results
Aiming at the above problems, we propose a learnable deep clustering method and a fast alignment weighted averaging method based on frequency domain space to effectively improve the class averaging results and improve the reconstruction accuracy. In particular, it is very prominent in the feature extraction and dimensionality reduction module. Compared with the classification method based on Bayesian and great likelihood, a large amount of single particle data is required to estimate the relative angle orientation of macromolecular single particles in the 3D structure, and we propose that the clustering method shows good results.

Conclusions
SimcryoCluster can use the contrastive learning method to perform well in the unlabeled high-noise cryo-EM single particle image classification task, making it an important tool for cryo-EM protein structure determination
CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data
Authors: Hauchamps Philippe , Bayat Babak , Delandre Simon , Hamrouni Mehdi , Toussaint Marie , Temmerman Stephane , Lin Dan , Gatto Laurent 
Published: February 2024

Abstract
Background
With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps: signal compensation or unmixing, scale transformation, debris, doublets and dead cells removal, batch effect correction, etc. However, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, non standardized diagnostic and visualizations, making objective comparison difficult for the end user.

Results
Here, we present CytoPipeline and CytoPipelineGUI, two R packages to build, compare and assess pre-processing pipelines for flow cytometry data. To exemplify these new tools, we present the steps involved in designing a pre-processing pipeline on a real life dataset and demonstrate different visual assessment use cases. We also set up a benchmarking comparing two pre-processing pipelines differing by their quality control methods, and show how the package visualization utilities can provide crucial user insight into the obtained benchmark metrics.

Conclusion
CytoPipeline and CytoPipelineGUI are two Bioconductor R packages that help building, visualizing and assessing pre-processing pipelines for flow cytometry data. They increase productivity during pipeline development and testing, and complement benchmarking tools, by providing user intuitive insight into benchmarking results.
Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina
Authors: Kaur Harleen , Manchanda Pooja , Sidhu Gurupkar S. , Chhuneja Parveen 
Published: February 2024

Abstract
Background
Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results.

Results
A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development.

Conclusions
The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.
Forced eruption in impacted teeth: analysis of failed cases and outcome of re-operation
Authors: Kim Jaeyeon , Jung Seoyeon , Lee Kee-Joon , Yu Hyung-Seog , Park Wonse 
Published: February 2024

Abstract
Background
Forced eruption of an impacted tooth usually requires surgical and orthodontic interventions to successfully bring the tooth into the dental arch. The clinical time required for a forced eruption is difficult to predict before treatment begins and success rates are affected by several factors before and after an eruption. This study was conducted to identify factors that affect the success of forced eruption, the duration of orthodontic treatment of impacted teeth, and the reasons for re-operation and forced eruption failure in a various teeth and cases.

Methods
In this retrospective study, the records regarding the forced eruption of 468 teeth in 371 patients from June 2006 to May 2020 at the Advanced General Dentistry Department of Yonsei University Dental Hospital were initially examined. The records of 214 teeth in 178 patients who completed orthodontic treatment were included in the analysis. Data on patient demographics, tooth characteristics, orthodontic treatment duration, re-operations, and failures were collected from electronic medical records.

Results
There was a significant difference in age between the success and failure forced eruption. Factors significantly affecting treatment duration were apex formation, position, rotation, and re-operation. Re-operation had a 96% success rate. The average orthodontic treatment duration was 29.99 ± 16.93 months, but the average orthodontic treatment duration for teeth that undergone re-operation was 20.36 ± 11.05 months, which was approximately 9 months shorter. Additionally, there was an interaction effect between rotation and re-operation on the duration of orthodontic treatment. The causes for failure of forced eruption in 6 cases were ankyloses (3 cases), incomplete alignment with the normal dental arch (2 cases), and a significant deviation in the impacted tooth’s location (1 case).

Conclusions
To increase the success rate of forced eruption, age should be considered as a priority, and in order to predict the treatment period, the apex formation status, position in the arch, and rotation should be considered in addition to age. When determining re-operation, considering factors such as ankylosis, root curvature, and apex formation can help in the success of orthodontic treatment.
Evaluation of whether there is residual polyp tissue after hysteroscopic morcellation at Cam and Sakura City Hospital: a retrospective cohort study
Authors: Sivas Mustafa Can , Ohanoglu Cetinel Karolin , Arslan Hilal Serap 
Published: February 2024

AbstractBackgroundIn polypectomy with mechanical hysteroscopic morcellators, the tissue removal procedure continues until no polyp tissue remains. The decision that the polypoid tissues were removed completely is made based on visual evaluation. In a situation where the polyp tissue was visually completely removed and no doubt that the polyp has been completely removed, short spindle-like tissue fragments on the polyp floor continue in most patients. There are no studies in the literature on whether visual evaluation provides adequate information at the cellular level in many patients in whom polypoid tissues have been determined to be completely removed. The aim of the present study was to analyze the pathological results of the curettage procedure, which was applied following the completion of polyp removal with operative hysteroscopy, and to evaluate whether there was residual polyp tissue in the short spindle-like tissue fragments that the mechanical hysteroscopic morcellator could not remove. The secondary aims of this study were to compare conventional loop resection hysteroscopy with hysteroscopic morcellation for the removal of endometrial polyps in terms of hemoglobin/hematocrit changes, polypectomy time and the amount of medium deficit.MethodsA total of 70 patients with a single pedunculate polypoid image of 1.5-2 cm, which was primarily visualized by office hysteroscopy, were included in the study. Patients who had undergone hysteroscopic polypectomy were divided into two groups according to the surgical device used: the morcellator group (n = 35, Group M) and the resectoscope group (n = 35, Group R). The histopathological results of hysteroscopic specimens and curettage materials of patients who had undergone curettage at the end of operative hysteroscopy were evaluated. In addition, the postoperative 24th hour Hb/HCT decrease amounts in percentage, the polypectomy time which was measured from the start of morcellation, and deficit differences were compared between groups.ResultsIn total, 7 patients in the morcellator group had residual polyp tissue detected in the full curettage material. The blood loss was lower in the morcellator group than in the resectoscope group (M, R; (-0.07 ± 0.08), (-0,11 ± 0.06), (p < 0.05), respectively). The deficit value of the morcellator group were higher (M, R; (500 ml), (300 ml), (p < 0.05), respectively). The polypectomy time was shorter in the morcellator group (M, R; mean (2.30 min), (4.6 min), (p < 0.05)).ConclusionsEven if the lesion is completely visibly removed during hysteroscopic morcellation, extra caution should be taken regarding the possibility of residual tissue. There is a need for new studies investigating the presence of residual polyp tissue.
Cross-sectional analysis of financial relationships between board certified allergists and the pharmaceutical industry in Japan
Authors: Murayama Anju , Senoo Yuki 
Published: February 2024

Abstract
Background
Financial interactions between pharmaceutical companies and physicians lead to conflicts of interest. This study examines the extent and trends of non-research payments made by pharmaceutical companies to board-certified allergists in Japan between 2016 and 2020.

Methods
A retrospective analysis of disclosed payment data from pharmaceutical companies affiliated with the Japanese Pharmaceutical Manufacturers Association was conducted. The study focused on non-research payments for lecturing, consulting, and manuscript drafting made to board-certified allergists from 2016 to 2020. We performed descriptive analyses on payment data. Trends were analyzed using generalized estimating equation models.

Results
Of the 3,943 board-certified allergists, 2,398 (60.8%) received non-research payments totaling $43.4 million over five years. Lecturing fees comprised 85.7% ($37.2 million) of the total payment amounts. For allergists who received at least one payment, the median amount per allergist was $3,106 (interquartile range: $966 – $12,124), in contrast to a mean of $18,092 (standard deviation: $49,233) over the five-year span. The top 1% and 10% of these allergists accounted for 20.8% and 68.8% of all non-research payments, respectively. The annual payment amounts significantly increased by 7.2% annual increase (95% CI: 4.4 – 10.0%, p < 0.001) each year until 2019, but saw a significant decrease in 2020 amid the COVID-19 pandemic.

Conclusion
The majority of allergists received non-research payments, with a notable concentration among a small group. Payments increased annually until the pandemic’s onset, which coincided with a substantial decrease. Further research is needed to explore the implications of these financial interactions on clinical practice and patient care in Japan.
Levels and predictors of empathy, self-awareness, and perceived stress among nursing students: a cross sectional study
Authors: Hamaideh Shaher H. , Abuhammad Sawsan , Khait Abdallah Abu , Al-Modallal Hanan , Hamdan-Mansour Ayman M , Masa’deh Rami , Alrjoub Saleem 
Published: February 2024

Abstract
Background
High levels of empathy and self-awareness and low level of stress among nursing students are the core elements of improving patients’ care and outcomes. The purpose of this study is to assess the levels, relationships, and predictors of empathy, self-awareness, and perceived stress in a sample of undergraduate Jordanian nursing students.

Methods
A descriptive cross-sectional design was employed to collect data from 330 students using a web-based survey.

Results
The total mean scores of empathy, self-awareness, and perceived stress were 75.75, 40.17, and 55.65, respectively. Students who are studying in public universities, with higher GPA, who have no intention to leave nursing, and who are satisfied with nursing; reported higher level of empathy. Students with lower income level, who have no intention to leave nursing, and who are satisfied with nursing; reported higher level of self-awareness. Female students, those who sleeping 6 h and less, did not get a balanced diet or perform exercise, studying in public universities, lower GPA, have intention to leave nursing, and did not satisfy with nursing; reported higher level of perceived stress.

Conclusions
Nursing students reported adequate empathy level, low self-awareness level, and moderate perceived stress level. Students who are satisfied and have no intention to leave nursing reported higher level of empathy, self-awareness, and perceived stress. It is necessary to conduct interventional programs that enhance students’ well-being especially empathy and self-awareness, and reduce the level of their stress.
Changes in plasma PLAC-1 concentration and its expression during early-mid pregnancy in bovine placental tissues – a pilot study
Authors: Jamioł Monika , Sozoniuk Magdalena , Wawrzykowski Jacek , Kankofer Marta 
Published: February 2024

Abstract
Background
Placenta-specific protein 1 (PLAC1) is a small secreted protein considered to be a molecule with a significant role in the development of the placenta and the establishment of the mother-foetus interface. This study aimed to confirm the presence of bovine PLAC1 and to examine its profile in the placenta and plasma in the first six months of pregnancy. The expression pattern of PLAC1 was analysed by RT-qPCR and Western Blotting. Quantitative evaluation was carried out using ELISA.

Results
PLAC1 concentrations in the plasma of pregnant cows were significantly higher (p < 0.05) than those obtained from non-pregnant animals. PLAC1 protein concentrations in the placental tissues of the foetal part were significantly (p < 0.05) higher than in the tissues of the maternal part of the placenta. PLAC1 transcripts were detected in both placental tissue samples and epithelial cell cultures.

Conclusions
In conclusion, the results of the present preliminary study suggest that PLAC1 is involved in the development of bovine placenta. The presence of this protein in the plasma of pregnant animals as early as the first month may make it a potential candidate as a pregnancy marker in cows. Further studies on exact mechanisms of action of PLAC1 in bovine placenta are necessary.
A multidisciplinary study on Clinostomum infections in Nile tilapia: micro-morphology, oxidative stress, immunology, and histopathology
Authors: Mahdy Olfat A. , Abdel-Maogood Sahar Z. , Abdelsalam Mohamed , Salem Mai A. 
Published: February 2024

AbstractYellow grub disease, caused by Clinostomum metacercaria, is an endemic zoonotic infection in freshwater fish, responsible for Halzoun syndrome transmitted through the consumption of raw infected fish. This study aimed to conduct a multidisciplinary investigation integrating detailed morphology, oxidative stress, immunology, and histopathology alteration to advance our understanding of Clinostomum infection. In this annual study, 400 Nile tilapia (Oreochromis niloticus) were collected from the Nile River at Al Bahr Al Aazam, Giza Governorate to assess Clinostomum infection prevalence. Of the examined fish, 160 individuals (40.0%) harboured larval Clinostomum infections. Clinostomum metacercariae were observed in various anatomical locations, with 135 fish (33.8%) in buccal cavities, 21 fish (5.25%) in gill chambers, and 4 fish (1.0%) on the skin. Infection intensity ranged from 2 to 12 cysts per fish, averaging 5 cysts, notably with skin infections characterized by a single cyst in each fish. Macroscopic encysted metacercariae were collected from buccal cavities, gills, and skin. Micro-morphology revealed distinct features in C. complanatum, including an elliptical oral sucker with collar-like rings and large sensory papilla-like structures, contrasting with the absence of these features in C. phalacrocoracis. Oxidative stress, assessed through malondialdehyde (MDA) and nitric oxide levels, revealed an elevation in MDA to 35.13 ± 6 nmol/g and nitric oxide to 25.80 ± 3.12 µmol/g in infected fish. In infected fish, MHC-I gene expression increased approximately 13-fold, MHC-II peaked at 19-fold, and IL-1β significantly upregulated by 17-fold, compared to control levels. Histopathology detailed associated lesions, such as cyst encapsulation and eosinophilic infiltration. Clinstomiasis and its impacts on fish hosts offer crucial insights to control this emerging fish-borne zoonotic disease, threatening wildlife, aquaculture, and human health.
Low frequency of SLC26A4 c.919-2A > G variant among patients with nonsyndromic hearing loss in Yunnan of Southwest China
Authors: Li Yan-Qiong , Ma Heng , Wang Qin-Yao , Liu De-Sheng , Wang Wei , Li Shi-Xin , Zuo Rong-Xia , Shen Tao , Zhu Bao-Sheng , Sa Ya-Lian 
Published: February 2024

Abstract
Background
Gene variants are responsible for more than half of hearing loss, particularly in nonsyndromic hearing loss (NSHL). The most common pathogenic variant in SLC26A4 gene found in East Asian populations is c.919-2A > G followed by c.2168A > G (p.H723R). This study was to evaluate their variant frequencies in patients with NSHL from special education schools in nine different areas of Southwest China’s Yunnan.

Methods
We performed molecular characterization by PCR-products directly Sanger sequencing of the SLC26A4 c.919-2AG and c.2168 A > G variants in 1167 patients with NSHL including 533 Han Chinese and 634 ethnic minorities.

Results
The SLC26A4 c.919-2A > G variant was discovered in 8 patients with a homozygous state (0.69%) and twenty-five heterozygous (2.14%) in 1167 patients with NSHL. The total carrier rate of the c.919-2A > G variant was found in Han Chinese patients with 4.50% and ethnic minority patients with 1.42%. A significant difference existed between the two groups (P < 0.05). The c.919-2A > G allele variant frequency was ranged from 3.93% in Kunming to zero in Lincang and Nvjiang areas of Yunnan. We further detected the SLC26A4 c.2168 A > G variant in this cohort with one homozygotes (0.09%) and seven heterozygotes (0.60%), which was detected in Baoshan, Honghe, Licang and Pu`er areas. Between Han Chinese group (0.94%) and ethnic minority group (0.47%), there was no statistical significance (P > 0.05). Three Han Chinese patients (0.26%) carried compound heterozygosity for c.919-2A > G and c.2168 A > G.

Conclusion
These data suggest that the variants in both SLC26A4 c.919-2A > G and c.2168 A > G were relatively less frequencies in this cohort compared to the average levels in most regions of China, as well as significantly lower than that in Han-Chinese patients. These results broadened Chinese population genetic information resources and provided more detailed information for regional genetic counselling for Yunnan.