bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Authors: He Yuqi , Zhang Kaixuan , Shi Yaliang , Lin Hao , Huang Xu , Lu Xiang , Wang Zhirong , Li Wei , Feng Xibo , Shi Taoxiong , Chen Qingfu , Wang Junzhen , Tang Yu , Chapman Mark A. , Germ Mateja , Luthar Zlata , Kreft Ivan , Janovská Dagmar , Meglič Vladimir , Woo Sun-Hee , Quinet Muriel , Fernie Alisdair R. , Liu Xu , Zhou Meiliang 
Published: February 2024

AbstractBackgroundTartary buckwheat,Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated.ResultsHere, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency.ConclusionsThis study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
Rotator cuff tear patterns: MRI appearance and its surgical relevance
Authors: Yubran Alexeys Perez , Pesquera Luis Cerezal , Juan Eva Llopis San , Saralegui Fernando Idoate , Canga Alvaro Cerezal , Camara Antonio Cruz , Valdivieso Gustavo Matheus , Pisanti Lopez Carolina 
Published: February 2024

AbstractA new perspective on rotator cuff anatomy has allowed a better understanding of the patterns of the different rotator cuff tears. It is essential for radiologists to be aware of these different patterns of tears and to understand how they might influence treatment and surgical approach. Our objective is to review the arthroscopy correlated magnetic resonance imaging appearance of the different types of rotator cuff tears based on current anatomical concepts.Critical relevance statement Knowledge of the characteristics of rotator cuff tears improves our communication with the surgeon and can also make it easier for the radiologist to prepare a report that guides therapeutic conduct and serves as a prognosis for the patient.Key points• There is no universally accepted classification for RC tears.• New patterns such as delamination or myotendinous junction tears have been defined.• The most difficult feature to assess in full thickness tears on MRI is the pattern.• Fatty infiltration of the RC tendons is crucial in the prognosis and outcome.• The radiological report is an effective way of communication with the surgeon.
Graphical Abstract
Prediction of lymph node metastasis in operable cervical cancer using clinical parameters and deep learning with MRI data: a multicentre study
Authors: Qin Fengying , Sun Xinyan , Tian Mingke , Jin Shan , Yu Jian , Song Jing , Wen Feng , Xu Hongming , Yu Tao , Dong Yue 
Published: February 2024

Abstract
Objectives
To develop and validate a magnetic resonance imaging-based (MRI) deep multiple instance learning (D-MIL) model and combine it with clinical parameters for preoperative prediction of lymph node metastasis (LNM) in operable cervical cancer.

Methods
A total of 392 patients with cervical cancer were retrospectively enrolled. Clinical parameters were analysed by logistical regression to construct a clinical model (M1). A ResNet50 structure is applied to extract features at the instance level without using manual annotations about the tumour region and then construct a D-MIL model (M2). A hybrid model (M3) was constructed by M1 and M2 scores. The diagnostic performance of each model was evaluated by the area under the receiver operating characteristic curve (AUC) and compared using the Delong method. Disease-free survival (DFS) was evaluated by the Kaplan‒Meier method.

Results
SCC-Ag, maximum lymph node short diameter (LNmax), and tumour volume were found to be independent predictors of M1 model. For the diagnosis of LNM, the AUC of the training/internal/external cohort of M1 was 0.736/0.690/0.732, the AUC of the training/internal/external cohort of M2 was 0.757/0.714/0.765, and the AUC of the training/internal/external cohort of M3 was 0.838/0.764/0.835. M3 showed better performance than M1 and M2. Through the survival analysis, patients with higher hybrid model scores had a shorter time to reach DFS.

Conclusion
The proposed hybrid model could be used as a personalised non-invasive tool, which is helpful for predicting LNM in operable cervical cancer. The score of the hybrid model could also reflect the DFS of operable cervical cancer.

Critical relevance statement
Lymph node metastasis is an important factor affecting the prognosis of cervical cancer. Preoperative prediction of lymph node status is helpful to make treatment decisions, improve prognosis, and prolong survival time.

Key points
• The MRI-based deep-learning model can predict the LNM in operable cervical cancer.
• The hybrid model has the highest diagnostic efficiency for the LNM prediction.
• The score of the hybrid model can reflect the DFS of operable cervical cancer.

Graphical Abstract
T2WI-based MRI radiomics for the prediction of preoperative extranodal extension and prognosis in resectable rectal cancer
Authors: Li Hang , Chai Li , Pu Hong , Yin Long-lin , Li Mou , Zhang Xin , Liu Yi-sha , Pang Ming-hui , Lu Tao 
Published: February 2024

Abstract
Objective
To investigate whether T2-weighted imaging (T2WI)-based intratumoral and peritumoral radiomics can predict extranodal extension (ENE) and prognosis in patients with resectable rectal cancer.

Methods
One hundred sixty-seven patients with resectable rectal cancer including T3T4N + cases were prospectively included. Radiomics features were extracted from intratumoral, peritumoral 3 mm, and peritumoral-mesorectal fat on T2WI images. Least absolute shrinkage and selection operator regression were used for feature selection. A radiomics signature score (Radscore) was built with logistic regression analysis. The area under the receiver operating characteristic curve (AUC) was used to evaluate the performance of each Radscore. A clinical-radiomics nomogram was constructed by the most predictive radiomics signature and clinical risk factors. A prognostic model was constructed by Cox regression analysis to identify 3-year recurrence-free survival (RFS).

Results
Age, cT stage, and lymph node-irregular border and/or adjacent fat invasion were identified as independent clinical risk factors to construct a clinical model. The nomogram incorporating intratumoral and peritumoral 3 mm Radscore and independent clinical risk factors achieved a better AUC than the clinical model in the training (0.799 vs. 0.736) and validation cohorts (0.723 vs. 0.667). Nomogram-based ENE (hazard ratio [HR] = 2.625, 95% CI = 1.233–5.586, p = 0.012) and extramural vascular invasion (EMVI) (HR = 2.523, 95% CI = 1.247–5.106, p = 0.010) were independent risk factors for predicting 3-year RFS. The prognostic model constructed by these two indicators showed good performance for predicting 3-year RFS in the training (AUC = 0.761) and validation cohorts (AUC = 0.710).

Conclusion
The nomogram incorporating intratumoral and peritumoral 3 mm Radscore and clinical risk factors could predict preoperative ENE. Combining nomogram-based ENE and MRI-reported EMVI may be useful in predicting 3-year RFS.

Critical relevance statement
A clinical-radiomics nomogram could help preoperative predict ENE, and a prognostic model constructed by the nomogram-based ENE and MRI-reported EMVI could predict 3-year RFS in patients with resectable rectal cancer.

Key points
• Intratumoral and peritumoral 3 mm Radscore showed the most capability for predicting ENE.
• Clinical-radiomics nomogram achieved the best predictive performance for predicting ENE.
• Combining clinical-radiomics based-ENE and EMVI showed good performance for 3-year RFS.

Graphical Abstract
The use of PET/MRI in radiotherapy
Authors: Yan Qi , Yan Xia , Yang Xin , Li Sijin , Song Jianbo 
Published: February 2024

AbstractPositron emission tomography/magnetic resonance imaging (PET/MRI) is a hybrid imaging technique that quantitatively combines the metabolic and functional data from positron emission tomography (PET) with anatomical and physiological information from MRI. As PET/MRI technology has advanced, its applications in cancer care have expanded. Recent studies have demonstrated that PET/MRI provides unique advantages in the field of radiotherapy and has become invaluable in guiding precision radiotherapy techniques. This review discusses the rationale and clinical evidence supporting the use of PET/MRI for radiation positioning, target delineation, efficacy evaluation, and patient surveillance.Critical relevance statement This article critically assesses the transformative role of PET/MRI in advancing precision radiotherapy, providing essential insights into improved radiation positioning, target delineation, efficacy evaluation, and patient surveillance in clinical radiology practice.Key points• The emergence of PET/MRI will be a key bridge for precise radiotherapy.• PET/MRI has unique advantages in the whole process of radiotherapy.• New tracers and nanoparticle probes will broaden the use of PET/MRI in radiation.• PET/MRI will be utilized more frequently for radiotherapy.
Graphical Abstract
A retrospective study on adverse events of intravenous administration of sulfur hexafluoride microbubbles in abdominal and superficial applications in 83,778 patients
Authors: Li Di , Zhang Rui , Lan Huixia , Chen Mianni , Huang Zhenli , Zhao Huijuan , Guo Shan , Xu Ming , Lei Yangyang 
Published: February 2024

Abstract
Objectives
To investigate the rate of adverse events (AEs) caused by intravenous administration of sulfur hexafluoride microbubbles in abdominal and superficial applications retrospectively and to explore practical measures for prevention and treatment of them.

Materials and methods
This study enrolled 83,778 contrast-enhanced ultrasound (CEUS) examinations using sulfur hexafluoride microbubbles intravenously performed during 11 years. Age, gender, and target organs of all CEUS patients were recorded. For cases of AEs, their medical history and laboratory results were also collected. The process of AEs was assessed and categorized. Besides, the management of AEs were recorded.

Results
Twenty patients had sulfur hexafluoride microbubbles-related AEs. The AE rate was 0.024%. No significant difference was observed between patients with AEs and the whole group for age and sex distribution. All AEs happened in liver examinations. Among them, 7 (35%) were mild, 8 (40%) were moderate, and 5 (25%) were severe. They were categorized into 15 allergic-like reactions and 5 physiologic reactions. The manifestations of mild and moderate AEs mainly include urticaria, chills, and mild hypoxia, which could be eased by simple management. Severe cases had anaphylactic shock, generalized convulsions, and diffuse erythema with hypotension respectively. They need close monitoring and oxygen inhalation with anti-shock and anti-anaphylactic treatment. Most cases started within 30 min and recovered within 1 day.

Conclusions
Intravenous administration of sulfur hexafluoride microbubbles in abdominal and superficial applications was safe with rare AEs. AEs were more likely to happen in abdominal applications than superficial ones. A well-designed emergency plan should be available for clinical use of sulfur hexafluoride microbubbles to reduce AEs and to deal with AEs properly.

Critical relevance statement
Intravenous administration of sulfur hexafluoride microbubbles in abdominal and superficial applications reported few AEs and could be considered safe but severe AEs are life-threatening. We analyzed the influence factors of AEs and propose some methods for prevention and treatment of them, which can further improve the safety of sulfur hexafluoride microbubbles in clinical practice.

Key points
• The AE rate of sulfur hexafluoride microbubbles in abdominal and superficial applications was 0.024%.
• Patients were more likely to have AEs in abdominal applications than superficial ones.
• Severe AEs are life-threatening and need prompt identification and treatment.
• We summarized some detailed suggestions for clinical prevention and treatment of AEs.

Graphical Abstract
Deep learning model based on multi-lesion and time series CT images for predicting the benefits from anti-HER2 targeted therapy in stage IV gastric cancer
Authors: He Meng , Chen Zi-fan , Liu Song , Chen Yang , Zhang Huan , Zhang Li , Zhao Jie , Yang Jie , Zhang Xiao-tian , Shen Lin , Gao Jian-bo , Dong Bin , Tang Lei 
Published: February 2024

Abstract
Objective
To develop and validate a deep learning model based on multi-lesion and time series CT images in predicting overall survival (OS) in patients with stage IV gastric cancer (GC) receiving anti-HER2 targeted therapy.

Methods
A total of 207 patients were enrolled in this multicenter study, with 137 patients for retrospective training and internal validation, 33 patients for prospective validation, and 37 patients for external validation. All patients received anti-HER2 targeted therapy and underwent pre- and post-treatment CT scans (baseline and at least one follow-up). The proposed deep learning model evaluated the multiple lesions in time series CT images to predict risk probabilities. We further evaluated and validated the risk score of the nomogram combining a two-follow-up lesion-based deep learning model (LDLM-2F), tumor markers, and clinical information for predicting the benefits from treatment (Nomo-LDLM-2F).

Results
In the internal validation and prospective cohorts, the one-year AUCs for Nomo-LDLM-2F using the time series medical images and tumor markers were 0.894 (0.728–1.000) and 0.809 (0.561–1.000), respectively. In the external validation cohort, the one-year AUC of Nomo-LDLM-2F without tumor markers was 0.771 (0.510–1.000). Patients with a low Nomo-LDLM-2F score derived survival benefits from anti-HER2 targeted therapy significantly compared to those with a high Nomo-LDLM-2F score (all p < 0.05).

Conclusion
The Nomo-LDLM-2F score derived from multi-lesion and time series CT images holds promise for the effective readout of OS probability in patients with HER2-positive stage IV GC receiving anti-HER2 therapy.

Critical relevance statement
The deep learning model using baseline and early follow-up CT images aims to predict OS in patients with stage IV gastric cancer receiving anti-HER2 targeted therapy. This model highlights the spatiotemporal heterogeneity of stage IV GC, assisting clinicians in the early evaluation of the efficacy of anti-HER2 therapy.

Key points
• Multi-lesion and time series model revealed the spatiotemporal heterogeneity in anti-HER2 therapy.
• The Nomo-LDLM-2F score was a valuable prognostic marker for anti-HER2 therapy.
• CT-based deep learning model incorporating time-series tumor markers improved performance.

Graphical Abstract
Impact of tissue factor expression and administration routes on thrombosis development induced by mesenchymal stem/stromal cell infusions: re-evaluating the dogma
Authors: Hoang Van T. , Le Duc Son , Hoang Duc M. , Phan Trang Thi Kieu , Ngo Lan Anh Thi , Nguyen Trung Kien , Bui Viet Anh , Nguyen Thanh Liem 
Published: February 2024

Abstract
Background
Hyperactive coagulation might cause dangerous complications such as portal vein thrombosis and pulmonary embolism after mesenchymal stem/stromal cell (MSC) therapy. Tissue factor (TF), an initiator of the extrinsic coagulation pathway, has been suggested as a predictor of this process.

Methods
The expression of TF and other pro- and anticoagulant genes was analyzed in xeno- and serum-free manufactured MSCs. Furthermore, culture factors affecting its expression in MSCs were investigated. Finally, coagulation tests of fibrinogen, D-dimer, aPPTs, PTs, and TTs were measured in patient serum after umbilical cord (UC)-MSC infusions to challenge a potential connection between TF expression and MSC-induced coagulant activity.

Results
Xeno- and serum-free cultured adipose tissue and UC-derived MSCs expressed the highest level of TF, followed by those from dental pulp, and the lowest expression was observed in MSCs of bone marrow origin. Environmental factors such as cell density, hypoxia, and inflammation impact TF expression, so in vitro analysis might fail to reflect their in vivo behaviors. MSCs also expressed heterogeneous levels of the coagulant factor COL1A1 and surface phosphatidylserine and anticoagulant factors TFPI and PTGIR. MSCs of diverse origins induced fibrin clots in healthy plasma that were partially suppressed by an anti-TF inhibitory monoclonal antibody. Furthermore, human umbilical vein endothelial cells exhibited coagulant activity in vitro despite their negative expression of TF and COL1A1. Patients receiving intravenous UC-MSC infusion exhibited a transient increase in D-dimer serum concentration, while this remained stable in the group with intrathecal infusion. There was no correlation between TF expression and D-dimer or other coagulation indicators.

Conclusions
The study suggests that TF cannot be used as a solid biomarker to predict MSC-induced hypercoagulation. Local administration, prophylactic intervention with anticoagulation drugs, and monitoring of coagulation indicators are useful to prevent thrombogenic events in patients receiving MSCs.
Trial registration NCT05292625. Registered March 23, 2022, retrospectively registered, https://www.clinicaltrials.gov/ct2/show/NCT05292625?term=NCT05292625&draw=2&rank=1. NCT04919135. Registered June 9, 2021, https://www.clinicaltrials.gov/ct2/show/NCT04919135?term=NCT04919135&draw=2&rank=1.
Ensemble coding of multiple facial expressions is not affected by attentional load
Authors: Liu Yujuan , Ji Luyan 
Published: February 2024

AbstractHuman observers can extract the mean emotion from multiple faces rapidly and precisely. However, whether attention is required in the ensemble coding of facial expressions remains debated. In this study, we examined the effect of attentional load on mean emotion processing with the dual-task paradigm. Individual emotion processing was also investigated as the control task. In the experiment, the letter string and a set of four happy or angry faces of various emotional intensities were shown. Participants had to complete the string task first, judging either the string color (low attention load) or the presence of the target letter (high attention load). Then a cue appeared indicating whether the secondary task was to evaluate the mean emotion of the faces or the emotion of the cued single face, and participants made their judgments on the visual analog scale. The results showed that compared with the color task, the letter task had a longer response time and lower accuracy, which verified the valid manipulation of the attention loads. More importantly, there was no significant difference in averaging performance between the low and high attention loads. By contrast, the individual face processing was impaired under the high attention load relative to the low attentional load. In addition, the advantage of extracting mean emotion over individual emotion was larger under the high attentional load. These results support the power of averaging and provide new evidence that a rather small amount of attention is needed in the ensemble coding of multiple facial expressions.
Perpetrators from Treblinka: interdisciplinary investigations of seven single graves with “Trawniki Men”
Authors: Drath Joanna , Jarzęcka-Stąporek Joanna , Zacharczuk Julia , Lisman Dagmara , Cytacka Sandra , Szargut Maria , Bulut Ozgur , Spradley Kate , Jasinski Marek E. , Parafiniuk Mirosław , Ossowski Andrzej 
Published: February 2024

Abstract
At the Treblinka extermination and forced labor camp only a few SS soldiers and around a hundred watchmen kept guard over thousands of prisoners. Despite their lower rank in the Nazi hierarchy than SS soldiers, watchmen were vital to implementing “Operation Reinhard” in the field. Prisoners in Nazi camps were terrified by their brutality and ruthlessness.
The guards were intermediaries between the camp’s inmates and the commanding crew, so in cases of a prisoners’ riot, they were the first target. The historical records mention several incidents where the watchmen died at the hands of the captives. However, little is known regarding how the dead bodies of the guards were treated nor what the funeral customs looked like in the camps.
In 2019, a row of individual burials was discovered at the former Treblinka extermination and forced labor camp. Seven of those graves were explored to identify the people buried in such an unusual manner and to find out what had caused their deaths. A thorough multidisciplinary study, combining the forensic disciplines of archaeology, anthropology, medicine, and genetics provided the answer.
Considering archaeological findings, it can be deduced that the graves belong to the Treblinka guards. The analysis conducted by an anthropologist indicates that the assessed biological profile aligns with the antemortem data of the Treblinka watchmen. Moreover, a study examining perimortem trauma has unveiled that out of the seven men studied, at least two met a violent demise. These findings are crucial in narrowing down the identification process.
The results of our study contribute to a general understanding of the funerary customs prevalent in concentration camps worldwide. Prior to this work, there had never been any analysis or publication of the characteristics of watchmen graves at Nazi camps, making our results unique.
Density, abundance, and activity of the chilla or grey fox (Lycalopex griseus) in Isla Grande de Tierra del Fuego, Chile
Authors: Zurita Carlos , Oporto Javier , Valverde Ignacio , Bernales Borja , Soto Nicolás , Rau Jaime R. , Jaksic Fabián M. 
Published: February 2024

Abstract
Background
The chilla or grey fox (Lycalopex griseus) is a native species from continental Chile and neighboring areas of Argentina. It was introduced to Isla Grande de Tierra del Fuego in 1951 and began to increase its abundance, to the chagrin of local sheep ranchers. Since 1998, its hunting has been authorized. Here we update information on the density, abundance, and activity of this fox in the Chilean sector of Tierra del Fuego Island, to evaluate its population trend since the last census conducted by the Servicio Agrícola y Ganadero (SAG) in 2007.

Methods and results
We carried out two fox censuses on a 941-km transect on public roads, divided into eight routes, from October to November (spring) of 2021 and 2022, following the same design used by SAG for the fox assessments carried out from 1999 to 2007. We report a reduction of > 50% in the density and abundance of chilla foxes with respect to the 2007 estimate, which could be attributed to the interference by free-ranging dogs (Canis lupus familiaris), through restricting the use of space by the fox, while transmitting diseases and parasites, and to human hunting pressure and vehicle collisions.

Discussion
The chilla fox decline highlights the need for an in-depth study to determine the ecological and socioeconomic impact of this exotic species on the ecosystems of Tierra del Fuego Island and the desirability of its management, if needed.