bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distance education during COVID 19: an Italian survey on the university teachers’ perspectives and their emotional conditions
Authors: Casacchia Massimo , Cifone Maria Grazia , Giusti Laura , Fabiani Leila , Gatto Roberto , Lancia Loreto , Cinque Benedetta , Petrucci Cristina , Giannoni Mario , Ippoliti Rodolfo , Frattaroli Anna Rita , Macchiarelli Guido , Roncone Rita 
Published: June 2021

Abstract
Background
Following the COVID-19 pandemic, distance education (DE) replaced traditional “face-to-face” teaching and has become the main method of teaching. The aim of this study was to 1) evaluate the impact of DE by teachers in our department during the second semester of the 2019–20 academic year following the March–May 2020 Italian national lockdown and 2) evaluate the relationship between DE and the emotional well-being of teachers during the period of home confinement.

Methods
Ninety-seven university teachers (51.5% women; most represented age group 60–69 years range, 40.2%) responded to an anonymous online cross-sectional survey between July 15 – September 30, 2020, on the advantages and disadvantages of DE, developed by one online teacher focus group. The emotional conditions were assessed by a short version of the Beck Depression Inventory-II (BDI-II). The internal consistency reliability survey and the 10-item BDI-II were measured by Cronbach’s alpha. A correlation analysis (r-Pearson) was conducted between the overall evaluation of the experience of DE and the variables included in the study.

Results
Teachers reported difficulties in technical aspects, and in psychological factors, as the discomfort of “speaking in the void” (64.7%). The absence of “face-to-face” eye contact with the students was complained by 81% of teachers.
Significant impairments in sleep patterns and loss of energy were reported, with female teachers having greater difficulty concentrating than their male colleagues. A quarter of teachers showed depressive symptoms of varying severity.
The most satisfied teachers were those most stimulated by DE (r = 0.752, p < 0.000), who showed a lower impact of depressive symptoms (r = − 0.289, p = 0.005). The teaching load in hours influenced the perception of disadvantages (r = 0.214, p = 0.035) and contributed to a lower appreciation of the challenges of DE.
The more significant the manifestation of depressive symptoms during the lockdown was, the greater the subjective recovery of a good emotional condition once the domestic confinement was over (r = 0.344, p = 0.001), despite maintaining DE.

Conclusions
Our study highlights the impact of technical, didactic, and psychological difficulties of DE, reported by our teachers. The appreciation of their new learning promoted by DE seemed related to better emotional well-being of university teachers accepting this “challenge” in their important role in the high-education system, influencing good learning and promoting students’ professional success.
Constrained transformer network for ECG signal processing and arrhythmia classification
Authors: Che Chao , Zhang Peiliang , Zhu Min , Qu Yue , Jin Bo 
Published: June 2021

Abstract
Background
Heart disease diagnosis is a challenging task and it is important to explore useful information from the massive amount of electrocardiogram (ECG) records of patients. The high-precision diagnostic identification of ECG can save clinicians and cardiologists considerable time while helping reduce the possibility of misdiagnosis at the same time.Currently, some deep learning-based methods can effectively perform feature selection and classification prediction, reducing the consumption of manpower.

Methods
In this work, an end-to-end deep learning framework based on convolutional neural network (CNN) is proposed for ECG signal processing and arrhythmia classification. In the framework, a transformer network is embedded in CNN to capture the temporal information of ECG signals and a new link constraint is introduced to the loss function to enhance the classification ability of the embedding vector.

Results
To evaluate the proposed method, extensive experiments based on real-world data were conducted. Experimental results show that the proposed model achieve better performance than most baselines. The experiment results also proved that the transformer network pays more attention to the temporal continuity of the data and captures the hidden deep features of the data well. The link constraint strengthens the constraint on the embedded features and effectively suppresses the effect of data imbalance on the results.

Conclusions
In this paper, an end-to-end model is used to process ECG signal and classify arrhythmia. The model combine CNN and Transformer network to extract temporal information in ECG signal and is capable of performing arrhythmia classification with acceptable accuracy. The model can help cardiologists perform assisted diagnosis of heart disease and improve the efficiency of healthcare delivery.
A mixed methods evaluation of the Paediatric Musculoskeletal Matters (PMM) online portfolio
Authors: Smith Nicola , Foster Helen E. , Jandial Sharmila 
Published: June 2021

Abstract
Background
The PMM Portfolio is comprised of the Paediatric Musculoskeletal Matters (PMM) website, the paediatric Gait, Arms, Legs and Spine (pGALS) app and e-learning modules (ELM). The target audiences are non-specialists in paediatric musculoskeletal medicine. Our study aimed to evaluate impact on learning and clinical practice.

Methods
Mixed methods (analytics, online survey, interviews) were used with PMM and ELM registered users and purposive sampling of users using international contacts within paediatrics and paediatric rheumatology. Data was analysed using descriptive statistics and qualitative techniques. A Paired T-Test compared self-rated confidence before and after use of the PMM Portfolio.

Results
There has been wide reach for all the e-resources; PMM website (662,827 hits, 262,476 users, 214 countries, data 31st July 2020); pGALS app (12,670 downloads, 70 countries, data 31st July 2020); ELM (150 users, 30 countries, data 30th May 2019). There were 164 responses (students, trainees and health care professionals) to the survey from 25 countries. Most responders deemed the PMM Portfolio useful / very useful for their learning with significantly increased self-rated confidence in their clinical examination and reasoning skills following access to the PMM website, p = < 0.01, pGALS app, p = < 0.01 and ELM, p = < 0.01. The most popular PMM website pages related to clinical assessment techniques (especially pGALS). There was high uptake of the pGALS app and pGALS ELM especially from trainees and allied health professionals. Many clinicians reported the PMM Portfolio to be useful when used to teach others. User feedback reported that easy navigation, open access, clinical images and cases were the most valued features. User feedback highlighted need to increase awareness of the e-resources through training programmes.

Conclusions
The PMM Portfolio was developed to aid learning for clinicians who are not specialists in paediatric MSK medicine. Our evaluation demonstrates wide international reach and positive feedback on learning. The PMM Portfolio is a highly useful e-resource for paediatric rheumatologists in their teaching of others to raise awareness, facilitate early diagnosis and referral of children with suspected disease. The wide user engagement informed future PMM Portfolio development and the mixed method of evaluation is transferable to other e-resources.
Genetic transformation technologies for the common dandelion, Taraxacum officinale
Authors: Dinkeloo Kasia , Cantero Araceli Maria , Paik Inyup , Vulgamott Alexa , Ellington Andrew D , Lloyd Alan 
Published: June 2021

Abstract
Background
Taraxacum officinale, or the common dandelion, is a widespread perennial species recognized worldwide as a common lawn and garden weed. Common dandelion is also cultivated for use in teas, as edible greens, and for use in traditional medicine. It produces latex and is closely related to the Russian dandelion, T. kok-saghyz, which is being developed as a rubber crop. Additionally, the vast majority of extant common dandelions reproduce asexually through apomictically derived seeds- an important goal for many major crops in modern agriculture. As such, there is increasing interest in the molecular control of important pathways as well as basic molecular biology and reproduction of common dandelion.

Results
Here we present an improved Agrobacterium-based genetic transformation and regeneration protocol, a protocol for generation and transformation of protoplasts using free DNA, and a protocol for leaf Agrobacterium infiltration for transient gene expression. These protocols use easily obtainable leaf explants from soil-grown plants and reagents common to most molecular plant laboratories. We show that common markers used in many plant transformation systems function as expected in common dandelion including fluorescent proteins, GUS, and anthocyanin regulation, as well as resistance to kanamycin, Basta, and hygromycin.

Conclusion
Reproducible, stable and transient transformation methods are presented that will allow for needed molecular structure and function studies of genes and proteins in T. officinale.
Interobserver variability in target volume delineation in definitive radiotherapy for thoracic esophageal cancer: a multi-center study from China
Authors: Chang Xiao , Deng Wei , Wang Xin , Zhou Zongmei , Yang Jun , Guo Wenling , Liu Miaoling , Qi Xiaolu , Li Ling , Zhang Kaixian , Zhang Min , Shi Yonggang , Liu Ke , Zhao Yidian , Wang Huitao , Yu Zhilong , Zhang Jihong , Wang Lihua , Qiao Xueying , Han Chun , Zhu Shuchai , Zhang Ruohui , Chen Junqiang , Hu Cairong , Zhang Fuquan , Hou Xiaorong , Pang Qingsong , Zhang Wencheng , Li Gaofeng , Lin Hailei , Sun Xinchen , Ge Xiaolin , Li Caihong , Ge Hong , Li Dingjie , Wang Yadi , Lu Na , Gao Xianshu , Qin Shangbin , Tian Yuan , Xiao Zefen 
Published: June 2021

Abstract
Purpose
To investigate the interobserver variability (IOV) in target volume delineation of definitive radiotherapy for thoracic esophageal cancer (TEC) among cancer centers in China, and ultimately improve contouring consistency as much as possible to lay the foundation for multi-center prospective studies.

Methods
Sixteen cancer centers throughout China participated in this study. In Phase 1, three suitable cases with upper, middle, and lower TEC were chosen, and participants were asked to contour a group of gross tumor volume (GTV-T), nodal gross tumor volume (GTV-N) and clinical target volume (CTV) for each case based on their routine experience. In Phase 2, the same clinicians were instructed to follow a contouring protocol to re-contour another group of target volume. The variation of the target volume was analyzed and quantified using dice similarity coefficient (DSC).

Results
Sixteen clinicians provided routine volumes, whereas ten provided both routine and protocol volumes for each case. The IOV of routine GTV-N was the most striking in all cases, with the smallest DSC of 0.37 (95% CI 0.32–0.42), followed by CTV, whereas GTV-T showed high consistency. After following the protocol, the smallest DSC of GTV-N was improved to 0.64 (95% CI 0.45–0.83, P = 0.005) but the DSC of GTV-T and CTV remained constant in most cases.

Conclusion
Variability in target volume delineation was observed, but it could be significantly reduced and controlled using mandatory interventions.
Clinical outcome of femoral neck system versus cannulated compression screws for fixation of femoral neck fracture in younger patients
Authors: Hu Huaijian , Cheng Jingbo , Feng Mingli , Gao Zhihua , Wu Jingwei , Lu Shibao 
Published: June 2021

Abstract
Background
The clinical outcome of a new fixation device (femoral neck system, FNS) for femoral neck fractures remains unclear. The main purpose of this study was to evaluate two different internal fixation methods for the treatment of femoral neck fractures in patients aged under 60 years.

Methods
We retrospectively studied patients who underwent internal fixation surgery in our hospital for femoral neck fractures between January 2017 and January 2020. Cannulated compression screws (CCS) and FNS groups were divided according to different internal fixation methods. General data (such as sex, age, body mass index, type of fracture) of all patienFemoral neck shorteningts were collected, and joint function was evaluated using the Harris Hip Score (HHS) before and 1 year after surgery. We recorded related surgical complications, including femoral head necrosis, nonunion, and femoral neck shortening.

Results
There were no significant differences in age, sex, or body mass index between the two groups. There was no statistical difference in HHSs between the two groups before surgery. Patients who underwent FNS treatment had longer surgery time (79.75 ± 26.35 min vs. 64.58 ± 18.56 min, p = 0.031) and more blood loss (69.45 ± 50.47 mL vs. 23.71 ± 28.13 mL, p < 0.001). The degree of femoral neck shortening in the FNS group was significantly lower than that in the CCS group (10.0% vs 37.5%, p = 0.036). Regarding postoperative complications, there was no statistical difference in the incidence of femoral head necrosis and fracture nonunion between the two groups.

Conclusion
Patients younger than 60 with femoral neck fractures can obtain satisfactory clinical results with CCS or FNS treatment. FNS has excellent biomechanical properties and shows significantly higher overall construct stability.
CAR-T therapy alters synthesis of platelet-activating factor in multiple myeloma patients
Authors: Ke Mengying , Kang Liqing , Wang Ling , Yang Shu , Wang Yajun , Liu Haiyan , Gu Chunyan , Huang Hongming , Yang Ye 
Published: June 2021

AbstractThe chimera antigen receptor (CAR) T cell therapy is a novel and potential targeted therapy and has achieved satisfactory efficacy in patients with relapsed or refractory multiple myeloma (MM) in recent years. However, cytokine release syndrome (CRS) and clinical efficacy have become the major obstacles which limit the application of CAR-T in clinics. To explore the potential biomarkers in plasma for evaluating CRS and clinical efficacy, we performed metabolomic and lipidomic profiling of plasma samples from 17 relapsed or refractory MM patients received CAR-T therapy. Our study showed that glycerophosphocholine (GPC), an intermediate of platelet-activating factor (PAF)-like molecule, was significantly decreased when the participants underwent CRS, and the remarkable elevation of lysophosphatidylcholines (lysoPCs), which were catalyzed by lysoPC acyltransferase (LPCAT) was a distinct metabolism signature of relapsed or refractory MM patients with prognostic value post-CAR-T therapy. Both GPC and lysoPC are involved in platelet-activating factor (PAF) remodeling pathway. Besides, these findings were validated by LPCAT1 expression, a key factor in the PAF pathway, associated with poor outcome in three MM GEP datasets of MM. In conclusion, CAR-T therapy alters PAF synthesis in MM patients, and targeting PAF remodeling may be a promising strategy to enhance MM CAR-T therapy.
Applications of single-cell sequencing in cancer research: progress and perspectives
Authors: Lei Yalan , Tang Rong , Xu Jin , Wang Wei , Zhang Bo , Liu Jiang , Yu Xianjun , Shi Si 
Published: June 2021

AbstractSingle-cell sequencing, including genomics, transcriptomics, epigenomics, proteomics and metabolomics sequencing, is a powerful tool to decipher the cellular and molecular landscape at a single-cell resolution, unlike bulk sequencing, which provides averaged data. The use of single-cell sequencing in cancer research has revolutionized our understanding of the biological characteristics and dynamics within cancer lesions. In this review, we summarize emerging single-cell sequencing technologies and recent cancer research progress obtained by single-cell sequencing, including information related to the landscapes of malignant cells and immune cells, tumor heterogeneity, circulating tumor cells and the underlying mechanisms of tumor biological behaviors. Overall, the prospects of single-cell sequencing in facilitating diagnosis, targeted therapy and prognostic prediction among a spectrum of tumors are bright. In the near future, advances in single-cell sequencing will undoubtedly improve our understanding of the biological characteristics of tumors and highlight potential precise therapeutic targets for patients.
Natural product triptolide induces GSDME-mediated pyroptosis in head and neck cancer through suppressing mitochondrial hexokinase-ΙΙ
Authors: Cai Jing , Yi Mei , Tan Yixin , Li Xiaoling , Li Guiyuan , Zeng Zhaoyang , Xiong Wei , Xiang Bo 
Published: June 2021

Abstract
Background
Pyroptosis is a lytic cell death form executed by gasdermins family proteins. Induction of tumor pyroptosis promotes anti-tumor immunity and is a potential cancer treatment strategy. Triptolide (TPL) is a natural product isolated from the traditional Chinese herb which possesses potent anti-tumor activity in human cancers. However, its role in pyroptosis remains to be elucidated.

Methods
Cell survival was measured by colony formation assay. Cell apoptosis was determined by Annexin V assay. Pyroptosis was evaluated by morphological features and release of interleukin 1β and lactate dehydrogenase A (LDHA). Immunofluorescence staining was employed to measure subcellular localization of proteins. Tumorigenicity was assessed by a xenograft tumor model. Expression levels of mRNAs or proteins were determined by qPCR or western blot assay, respectively.

Results
Triptolide eliminates head and neck cancer cells through inducing gasdermin E (GSDME) mediated pyroptosis. Silencing GSDME attenuates the cytotoxicity of TPL against cancer cells. TPL treatment suppresses expression of c-myc and mitochondrial hexokinase II (HK-II) in cancer cells, leading to activation of the BAD/BAX-caspase 3 cascade and cleavage of GSDME by active caspase 3. Silencing HK-II sensitizes cancer cells to TPL induced pyroptosis, whereas enforced expression of HK-II prevents TPL induced pyroptosis. Mechanistically, HK-II prevents mitochondrial translocation of BAD, BAX proteins and activation of caspase 3, thus attenuating cleavage of GSDME and pyroptosis upon TPL treatment. Furthermore, TPL treatment suppresses NRF2/SLC7A11 (also known as xCT) axis and induces reactive oxygen species (ROS) accumulation, regardless of the status of GSDME. Combination of TPL with erastin, an inhibitor of SLC7A11, exerts robust synergistic effect in suppression of tumor survival in vitro and in a nude mice model.

Conclusions
This study not only provides a new paradigm of TPL in cancer therapy, but also highlights a crucial role of mitochondrial HK-II in linking glucose metabolism with pyroptosis.
Genetic and morphological estimates of androgen exposure predict social deficits in multiple neurodevelopmental disorder cohorts
Authors: McKenna Brooke G. , Huang Yongchao , Vervier Kévin , Hofammann Dabney , Cafferata Mary , Al-Momani Seima , Lowenthal Florencia , Zhang Angela , Koh Jin-Young , Thenuwara Savantha , Brueggeman Leo , Bahl Ethan , Koomar Tanner , Pottschmidt Natalie , Kalmus Taylor , Casten Lucas , Thomas Taylor R. , Michaelson Jacob J. 
Published: June 2021

Abstract
Background
Neurodevelopmental disorders (NDDs) such as autism spectrum disorder (ASD) display a strong male bias. Androgen exposure is profoundly increased in typical male development, but it also varies within the sexes, and previous work has sought to connect morphological proxies of androgen exposure, including digit ratio and facial morphology, to neurodevelopmental outcomes. The results of these studies have been mixed, and the relationships between androgen exposure and behavior remain unclear.

Methods
Here, we measured both digit ratio masculinity (DRM) and facial landmark masculinity (FLM) in the same neurodevelopmental cohort (N = 763) and compared these proxies of androgen exposure to clinical and parent-reported features as well as polygenic risk scores.

Results
We found that FLM was significantly associated with NDD diagnosis (ASD, ADHD, ID; all $$p<0.05$$

p
<
0.05

), while DRM was not. When testing for association with parent-reported problems, we found that both FLM and DRM were positively associated with concerns about social behavior ($$\rho =0.19$$

ρ
=
0.19

, $$p=0.004$$

p
=
0.004

; $$\rho =0.2$$

ρ
=
0.2

, $$p=0.004$$

p
=
0.004

, respectively). Furthermore, we found evidence via polygenic risk scores (PRS) that DRM indexes masculinity via testosterone levels ($$t=4.0$$

t
=
4.0

, $$p=8.8\times 10^{-5}$$

p
=
8.8
×

10

-
5

), while FLM indexes masculinity through a negative relationship with sex hormone binding globulin (SHBG) levels ($$t=-3.3$$

t
=
-
3.3

, $$p=0.001$$

p
=
0.001

). Finally, using the SPARK cohort (N = 9419) we replicated the observed relationship between polygenic estimates of testosterone, SHBG, and social functioning ($$t=-2.3$$

t
=
-
2.3

, $$p=0.02$$

p
=
0.02

, and $$t=4.2$$

t
=
4.2

, $$p={3.2\times 10^{-5}}$$

p
=

3.2
×

10

-
5

for testosterone and SHBG, respectively). Remarkably, when considered over the extremes of each variable, these quantitative sex effects on social functioning were comparable to the effect of binary sex itself (binary male: $$-0.22\pm 0.05$$

-
0.22
±
0.05

; testosterone: $$-0.35\pm 0.15$$

-
0.35
±
0.15

from 0.1%-ile to 99.9%-ile; SHBG: $$0.64\pm 0.15$$

0.64
±
0.15

from 0.1%-ile to 99.9%-ile).

Limitations
In the devGenes and SPARK cohorts, our analyses rely on indirect, rather than direct measurement of androgens and related molecules.

Conclusions
These findings and their replication in the large SPARK cohort lend support to the hypothesis that increasing net androgen exposure diminishes capacity for social functioning in both males and females.
GNINA 1.0: molecular docking with deep learning
Authors: McNutt Andrew T. , Francoeur Paul , Aggarwal Rishal , Masuda Tomohide , Meli Rocco , Ragoza Matthew , Sunseri Jocelyn , Koes David Ryan 
Published: June 2021

AbstractMolecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline as they determine the fitness of sampled poses. Here we describe and evaluate the 1.0 release of the Gnina docking software, which utilizes an ensemble of convolutional neural networks (CNNs) as a scoring function. We also explore an array of parameter values for Gnina 1.0 to optimize docking performance and computational cost. Docking performance, as evaluated by the percentage of targets where the top pose is better than 2Å root mean square deviation (Top1), is compared to AutoDock Vina scoring when utilizing explicitly defined binding pockets or whole protein docking.Gnina, utilizing a CNN scoring function to rescore the output poses, outperforms AutoDock Vina scoring on redocking and cross-docking tasks when the binding pocket is defined (Top1 increases from 58% to 73% and from 27% to 37%, respectively) and when the whole protein defines the binding pocket (Top1 increases from 31% to 38% and from 12% to 16%, respectively). The derived ensemble of CNNs generalizes to unseen proteins and ligands and produces scores that correlate well with the root mean square deviation to the known binding pose. We provide the 1.0 version ofGninaunder an open source license for use as a molecular docking tool athttps://github.com/gnina/gnina.