bluuebunny/crossref_metadata_2025_split huggingface dataset:
Femtosecond conformational changes in a photolyase guide
long-range electron transfer as resolved by serial crystallography
Authors: Cellini Andrea , Shankar Madan Kumar , Nimmrich Amke , Mutisya Jennifer , Furrer Antonia , Beale Emma , Carrillo Melissa , Malla Tek Narsingh , Maj Piotr , Vrhovac Lidija , Dworkowskic Florian , Cirelli Claudio , Johnson Philip , Ozerov Dmitry , Bacellar Camila , Standfuss Jörg , Schmidt Marius , Weinert Tobias , Ihalainen Janne , Wahlgren Weixiao , Westenhoff Sebastian 
Published: February 2023

Abstract
Charge transfer reactions in proteins are fundamentally important for life, but it is currently not clear how protein structural dynamics control these electron transfer reactions. Photolyases/cryptochromes, which repair DNA and signal in all kingdoms of life, have a paradigm electron transfer cascade. Here, photoreduction of the flavin cofactor initiates charge transfer along a chain of four conserved tryptophans. We report femtosecond X-ray crystallographic snap-shots for the Drosophila melanogaster (6-4) photolyase, revealing protein structural changes while electron transfer occurs. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at key residue asparagine 403, at a conserved salt bridge, and by rearrangements of nearby water molecules. Along the tryptophan cascade, we detect charge-induced protein structural changes close to the second tryptophan from 1 ps to 20 ps, thereby identifying methionine 408 as an active participant in the redox chain, and from 300 ps around the fourth tryptophan. The data reveal that the protein undergoes highly directed and carefully timed adaptations of its structure to facilitate electron transfer. This suggests that evolution has optimized fast protein fluctuations for optimal function.
A case of primary osteosarcoma of the penis arising from Paget’s disease: a rare diagnosis
Authors: Lang A.J. 
Published: February 2023

Abstract
A 35-year-old male with primary penile osteosarcoma which was extraaxial is presented in
this case report and literature review. This very rare diagnosis is infrequently seen in the
literature and our case highlights a case which was deemed to have arisen from a Paget’s
disease lesion with histological and immunohistochemical findings and a scoping search of
the literature provided.
STAT3-CD163 crosstalk exhibits promising biomarkers for a progressive Ischemic cardiomyopathy; integrative computational and gene expression profiling based on GEO datasets
Authors: Mohareb Mina Wageh , Kariem Mohammed Abdelghaney , Tohamy Aly , Gamal Noha M. , Mosaad Rehab M. , Esmaiel Nora N. , Fayez Alaaeldin 
Published: February 2023

Abstract
Background:Ischemic heart diseaseis one of the heaviest health-related burdens worldwide.We aimed to identify the common hub mRNA and pathways that are involved in pathological progression of ischemic cardiomyopathy(ICM). Methods:To explore potential differentially expressed genes (DEGs) of all ischemic heart disease stages, we used chipster and GEO2R tools to analyze of retrieved eight high throughput RNA datasets obtained from GEO database. Gene Ontology functional annotation and Pathways enrichment analyses were used to obtain the common functional enriched DEGs which were visualized in protein–protein interactions (PPI) network to explore the hub mRNA according to the interaction scores. Validation qRT-PCR was carried out for blood and cardiac biopsies compared with controls to validate the determined four hub mRNAs and subsequently reviewed inside comprehensive published meta-analysis database. The validated mRNAs were visualized in two interaction modules. Finally screening of approved drugs was applied.
Results: 15 common DEGs with p value ≤ 0.01 were identified and carbohydrate &amino acids metabolism and inflammatory responses were significantly enriched. STAT3, CEBPD, GLUL and CD163 were hub enriched mRNAs with interaction score ≥ 0.50. Our qRT-PCR analysis showed increased expression of STAT3 over all patients groups and CD163 mainly in cardiac samples with remarked ascending manner. Interaction modules showed co-regulators supporting high STAT3-CD163 connectivity providing potential role of STAT3-CD163 crosstalk mediated inflammatory responses in ICM progression. We determined two reported drugs targeting STAT3.
Conclusion:Post analysis of the used GEO datasets and qRT-PCR data pointed that STAT3-CD163 crosstalk was potential biomarkers for ICM progression.
Clinical trial registration: www.clinicaltrials.gov, Identifier: NCT05508269
Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila
Authors: Singh Badri Nath , Tran Hiep , Kramer Joseph , Kirishenko Elmira , Changela Neha , Wang Fei , Feng Yaping , Kumar Dibyendu , Tu Min , Lan Jie , Bizet Martin , Fuks François , Steward Ruth 
Published: February 2023

Abstract
Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.
Endometrial cancer PDX-derived organoids (PDXOs) and PDXs with FGFR2c isoform expression are sensitive to FGFR inhibition.
Authors: Sengal Asmerom , Bonazzi Vanessa , Smith Deborah , Moiola Cristian , Lourie Rohan , Rogers Rebecca , Colas Eva , Gil-Moreno Antonio , Frentzas Sophia , Chetty Naven , Perrin Lewis , Pollock Pamela 
Published: February 2023

Abstract
Endometrial cancer (EC) patients with metastatic/recurrent disease have limited treatment options and poor survival outcomes. Recently, we discovered the FGFR2c isoform is associated with poor prognosis in EC patients. Here we report the establishment of 14 EC patient-derived xenografts (PDX)-derived organoids (PDXOs) with or without FGFR2c expression. Treatment of 5 EC PDXOs with BGJ398 showed significant cell death in 3 models with FGFR2c expression. PDXs with FGFR2c+ showed significant tumour growth inhibition (TGI) following 21-day treatment with FGFR inhibitors (BGJ398 or pemigatinib) and significantly prolonged survival in 4/5 models. Pemigatinib + cisplatin combination therapy (n=5) resulted in significant TGI and prolonged survival in one of two p53abn PDXs. All five models treated with cisplatin alone showed de novo resistance and no survival benefit. Seven-day treatment with BGJ398 revealed a significant reduction in angiogenesis and CD206+ M2 macrophages. This data collectively supports the evaluation of FGFR inhibitors in a clinical trial.
A method for morphological feature extraction based on variational auto-encoder : an application to mandible shape
Authors: Furusawa Chikara , Tsustumi Masato , Koyabu Daisuke , Saito Nen 
Published: February 2023

Abstract
Shape measurements are crucial for evolutionary and developmental biology; however, they present difficulties in the objective and automatic quantification of arbitral shapes. Conventional approaches are based on anatomically prominent landmarks, which require manual annotations by experts. Here, we present morphological regulated variational AutoEncoder (Morpho-VAE), an image-based deep-learning framework, to conduct landmark-free shape analysis. The proposed architecture combines the unsupervised and supervised learning models to reduce dimensionality by focusing on morphological features that distinguish data with different labels. We applied the method to primate mandible image data. The extracted morphological features reflected the characteristics of the families to which the organisms belong, and then those features were visualized. Additionally, the reconstruction of the missing segments from incomplete images was demonstrated. The proposed method provides a flexible and promising tool for analyzing a wide variety of image data of biological shapes even those with missing segments.
baymobil: A Python package for detection of graft-mobile mRNA using exact Bayesian inference on RNA-Seq data
Authors: Hoerbst Franziska , Morris Richard J. , Tomkins Melissa 
Published: February 2023

Abstract
Background: A popular method for the detection of graft-mobile mRNA on a genomic scale in plants is to perform RNA-Seq on heterografts comprising different ecotypes, species, or cultivars (types). Transcripts from one plant type that are detected in the other type can be assumed to have been transported across the graft junction. A necessary step is the ability to differentiate between transcripts from each plant type, which can be achieved based on known single nucleotide polymorphisms (SNPs) between types. One current challenge is to differentiate between RNA-Seq reads associated with specific SNPs and RNA-Seq errors. Here, we present baymobil, a Python package that implements a Bayesian framework for determining between graft-mobile transcripts and sequencing errors.
Results: baymobil takes processed RNA-Seq data from homo- and heterografted plant samples as input and for each mRNA calculates a Bayes factor: the ratio of the evidence for transcripts having crossed the graft junction over the evidence for the data being a consequence of sequencing errors. These Bayes factors can be used to rank mRNAs based on the statistical support for their mobility. Furthermore, the package includes functions for the creation of simulated RNA-Seq datasets, which have been used to demonstrate that this approach outperforms existing mobility criteria and is a necessary step in the successful detection of graft-mobile mRNA.
Conclusion: The baymobil Python package improves the accuracy of pipelines for the detection of graft-mobile mRNA based on SNP differences between heterografted types. It is openly and freely available via GitHub, and is easily installed with pip and pypi. A detailed tutorial with test data and results for the statistics and simulation package baymobil can be found on github.com/mtomtom/baymobil.
The Thermal Error Modeling Approach of Feeding Axes for Horizontal CNC Lathes Based on Transfer Learning
Authors: Zhou Dan , Zeng Fuhong , Jia Shuyuan 
Published: February 2023

Abstract
Modeling the thermal error for each feeding axis of the CNC machine one by one will lead to an exponential increase in the thermal error compensation time. Th e feeding axes in the same CNC machine tool have similar thermal characteristics. The thermal error modeling approach based on transfer learning was proposed to improve the efficiency of thermal error modeling. The thermal error module was bulit for the X-axis of the horizontal lathe. Then, the thermal error module of the X-axis was transferred to the Z-axis of the same lathe by transfer learning based on domain adaptation. After verification, the prediction residual range of the Z-axis thermal error module based on transfer learning was only -3.2μm~1.4μm, which has proved that the method proposed in this paper is effective in thermal error modeling of the feeding axis. It will provide an effective means to effectively improve the efficiency of thermal error modeling for the feeding axes of CNC machine tools.
Clinical characteristics of autoimmune encephalitis with co-existence of multiple anti-neuronal antibodies
Authors: Zhou Yiyi , Chen Hao , Zhu Min , Li Menghua , Wang Lianqun , Xie Zunchun , Zhou Meihong , Wu Xiaomu , Hong Daojun 
Published: February 2023

Abstract
Background
Autoimmune encephalitis (AE) usually referred to a single anti-neuronal antibody-mediated encephalopathy syndrome. AE with co-existence of multiple anti-neuronal antibodies was reported in a few case reports or single-center retrospective studies. Further studies might be helpful to elucidate the uncertainties of clinical features, treatment and prognosis.
Methods
AE patients with two or more anti-neuronal antibodies were retrospectively recruited between August 2019 and February 2022 in our center. Clinical and laboratory data were collected. A total of 83 AE cases (9 cases in this study and 74 cases in the literatures) with multiple anti-neuronal antibodies were summarized and re-analyzed.
Results
Nine AE patients with co-existence of multiple anti-neuronal antibodies were identified from our 85 AE patients. The combination of anti-neuronal antibodies included NMDAR plus CASPR2 in 3 cases, NMDAR plus GABABR in 2 cases, AMPAR2 plus Hu in one, LGI1 plus IGLON5 in one, LGI1 plus CASPR2 in one, NMDAR plus GABABR and GAD65 in one. All 9 patients presented with encephalitis symptoms, clinically characterized by disturbance of consciousness, seizures, cognitive impairment, and psychiatric disorder. All 83 cases revealed that 73 cases had co-existence of two types of antibodies, 8 cases had three types, and 2 cases had four types. Thirty-nine cases (39/83, 46.9%) were confirmed or suspected to be accompanied with tumors, of which the most common was lung cancer (28/83, 33.7%). Partial or complete recovery was achieved in 57 cases (57/83, 68.6%), and 26 cases (26/83 31.3%) died during treatment or follow-up.
Conclusions
AE with co-existence of multiple anti-neuronal antibodies was a specific subgroup, which was increasingly recognized in the clinical practice. The co-existence of multiple anti-neuronal antibodies had complicated impacts on clinical features, disease progression, and prognosis.
The influence factors of clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy
Authors: tang binbin , xiping Zhang 
Published: February 2023

Abstract
Objective
To investigate predictive indicators of clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy.
Methods
290 female patients with breast cancer who treated with neoadjuvant chemotherapy were enrolled in this study. The collected data including tumor position, tumor size, cTNM staging, LNR, pathological molecular types(including ER, PR, Her-2, Ki-67 and so on), neoadjuvant chemotherapy regimens, pathological complete response rate, postoperative treatment and survival time.
Results
Neoadjuvant chemotherapy curative effect was related to pausimenia, T staging, N staging, ER/PR and Ki-67(P < 0.05), N staging (OR = 0.041, 95% CI = 0.012 ~ 0.134) and Ki-67 (OR = 9.340, 95% CI = 1.770 ~ 49.286) were independent risk factors of pCR. Recurrence of metastases was related to T staging, LNR, Ki-67, ET regimen, postoperative chemotherapy and postoperation radiotherapy(P < 0.05), T staging (OR = 1.731, 95%CI = 1.244 ~ 2.408), LNR (OR = 2.726, 95%CI = 1.430 ~ 5.197) and Ki-67 (OR = 3.107, 95%CI = 1.395 ~ 6.920) were independent risk factors of recurrence of metastases. Patients with low Ki-67 expression, low LNR, T1 staging and T2 staging and N0/N1/N2 staging had a better prognosis.
Conclusion
Clinical efficacy and prognosis of breast cancer patients treated with neoadjuvant chemotherapy were related to cTNM staging, LNR, ER/PR and Ki-67.
Mother’s perceptions and concerns over sharing sexual and reproductive health information with their adolescent daughters- A qualitative study among mothers of adolescent girls aged 14-19 years in the developing world, Sri Lanka
Authors: Mataraarachchi D , Pathirana T.E.A , Mahesh P.K Buddhika , Vithana P.V.S.C 
Published: February 2023

Abstract

Introduction Studies across the world have shown that parent-adolescent SRH communication can prevent unhealthy SRH practices among adolescents and promote their sexual and reproductive health. Parents’ ability to provide individualized sexuality education to suit the needs of their children, their family, and societal values, and the fact that children have more opportunities in the family, makes parent-based sexuality education of children a better approach to Sri Lankan context. Objective To explore mother’s perceptions and concerns over sharing sexual and reproductive health information with their daughters among Sinhalese mothers of adolescent girls aged 14–19 years in Sri Lanka Methodology Six Focus group discussions were carried out among mothers of adolescent girls aged 14–19 years. Each focus group discussion included 10–12 participants. A Focus Group Discussion guide developed after an extensive literature search and expert opinion was used to retrieve information from mothers. Data management and analysis mainly followed an inductive approach to thematic analysis principles. The analysis results were presented in narrative form using quotes in respondents’ own words that highlighted the theory. Results The mean age of the participants was 43.5 years while 62.4% (n = 40) were educated above the Ordinary level. Analysis of data identified eight main themes from the FGDs. Many mothers thought that sexual and reproductive information is important to adolescent girls. They tried to keep their girl adolescent informed about SRH issues that she may face during this time. They preferred abstinence-only education over abstinence-plus education. Lack of skills and lack of knowledge on adolescent SRH issues was a major challenge identified by the mothers to communicate SRH matters with their children. Conclusions and recommendations Although mothers perceived their role as primary sex educators to their children, they were not confident about their knowledge and skills in discussing SRH matters with children. Implementation of interventions to improve mothers’ attitudes and skills in communicating SRH matters with children is recommended.
Thromboelastograhpy of hemostasis in hepatocellular carcinoma with underlying cirrhosis and massive intraoperative blood loss in liver resection
Authors: Di Ying , Li Jialu , Ye Chunjuan , Yu Xiaoqing , Wang Zheng , Zhu Qianqian 
Published: February 2023

Abstract
Objects

The presence of underlying cirrhosis in patients with hepatocellular carcinoma (HCC) might further complicate hemostasis. Thromboelastography (TEG) is a global coagulation test that accurately reflects hemostatic function in patients with liver cirrhosis. Therefore, we aimed to explore the association between TEG parameters and HCC with underlying cirrhosis or massive intraoperative blood loss during liver resection.

Methods

Demographic, clinical, and laboratory data of adult HCC patients who underwent TEG prior to live resection or any blood transfusions were collected. The clinical severity of cirrhosis was categorized. Liver resections were classified into low, medium, and high complexity.

Results

A total of 833 patients with HCC were included. There was a longer K-times (2.43 ± 0.98 vs. 1.92 ± 0.79, p < 0.001), smaller α‑angles (60.32 ± 11.33 vs. 64.69 ± 7.77, p < 0.001), lower maximum amplitude (MA) (55.32 ± 8.06 vs. 61.38 ± 7.66, p < 0.001) in cirrhotic patients than those non-cirrhotic patients. After multivariate adjusted logistic analysis, the lower MA (OR = 0.947, 95%CI, 0.916–0.980, p = 0.002) was still associated with cirrhosis. Furthermore, the AUC of the MA for predicting cirrhosis was 0.710 (95% CI, 0.666–0.754, p < 0.001). The association between MA and clinical cirrhosis severity was also statistically significant but weak (r=-0.068, p = 0.020). There were no significantly differences between patient with and without massive intraoperative blood loss regarding TEG parameters (all p > 0.05). After multivariate adjusted analysis, the CTP class B (OR = 2.274, 95%CI, 1.424–3.630, p = 0.001), open surgery (OR = 2.668, 95%CI, 1.780–3.998, p < 0.001), and more surgery complexity (medium, OR = 2.663, 95%CI, 1.091-6.500, p = 0.031; high, OR = 4.425, 95%CI, 1.695–11.552, p = 0.002) was independently associated with massive intraoperative blood loss.

Conclusions

The results of present study implied that though the MA was associated with cirrhosis, it could not discriminate the stage of cirrhosis in patients with HCC. Preoperative TEG parameters could not predict intraoperative massive blood loss in HCC with underlying cirrhosis.
Studies on combining ability for yield related traits in Fenugreek (Trigonella foenum- graecum L.) .
Authors: Kumar Sharvan , Singh Devraj , Kumar Manjeet , Yadav Hridesh , Yadav Vikash Kumar 
Published: February 2023

Abstract
The present investigation entitled “Studies on combining ability for yield related traits in Fenugreek (Trigonella foenum- garacum L.) ..” was conducted during Rabi seasons of 2018-19 (E1) and 2019-20 (E2) at the Main Experiment Station (MES). Department of Vegetable Science, Acharya Narendra Deva University of Agriculture & Technology, Narendra Nagar, Kumarganj, Ayodhya (U.P.) India. Ten homozygous, superior and optimally divergent lines of fenugreek having Indian adaptability were used for carrying out half diallel design to study General Combining Ability (GCA) and Specific Combining Ability (SCA) estimates for Days to 50 per cent flowering, Days to maturity, Plant height (cm), Number of branches per plant, pod length (cm), Number of pods per plant, Number of seed per pods, Test weight (g), Biological yield (g), Harvest index (%) and yield per plant (g). The analysis of variances due to both GCA and SCA were significant, suggesting that both additive and non-additive genetic variance were involved for genetic control of the character Number of pods per plant, Number of seed per pods and yield per plant (g). However, the variance due to GCA was more pronounced for Days to 50 per cent flowering, Days to maturity, pod length (cm), Number of pods per plant, Number of seed per pods, Test weight (g), Biological yield (g), Harvest index (%) and yield per plant (g), as a result of additive gene action. The parents P2, P4 and P7 were best general combiner for earliness, whereas P4, P6 and P9 showed best GCA effect for yield during the both season and over the season (Pooled). The best ten crosses having high negative SCA effects for days to 50 per cent flowering during both season and four crosses during E1, five crosses E2 and pooled for days to maturity showed best specific combiner for earliness. Forty five crosses, only thirty crosses in E1, twenty four crosses in E2 and thirty one crosses in pooled exhibited positive and significant SCA effects, indicating good specific combining ability for yield per plant.