bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic host response and therapeutic approaches to influenza infection
Authors: Keshavarz Mohsen , Solaymani-Mohammadi Farid , Namdari Haideh , Arjeini Yaser , Mousavi Mohammad Javad , Rezaei Farhad 
Published: March 2020

AbstractBased on available metabolomic studies, influenza infection affects a variety of cellular metabolic pathways to ensure an optimal environment for its replication and production of viral particles. Following infection, glucose uptake and aerobic glycolysis increase in infected cells continually, which results in higher glucose consumption. The pentose phosphate shunt, as another glucose-consuming pathway, is enhanced by influenza infection to help produce more nucleotides, especially ATP. Regarding lipid species, following infection, levels of triglycerides, phospholipids, and several lipid derivatives undergo perturbations, some of which are associated with inflammatory responses. Also, mitochondrial fatty acid β-oxidation decreases significantly simultaneously with an increase in biosynthesis of fatty acids and membrane lipids. Moreover, essential amino acids are demonstrated to decline in infected tissues due to the production of large amounts of viral and cellular proteins. Immune responses against influenza infection, on the other hand, could significantly affect metabolic pathways. Mainly, interferon (IFN) production following viral infection affects cell function via alteration in amino acid synthesis, membrane composition, and lipid metabolism. Understanding metabolic alterations required for influenza virus replication has revealed novel therapeutic methods based on targeted inhibition of these cellular metabolic pathways.
Comparative study of whole exome sequencing-based copy number variation detection tools
Authors: Zhao Lanling , Liu Han , Yuan Xiguo , Gao Kun , Duan Junbo 
Published: March 2020

Abstract
Background
With the rapid development of whole exome sequencing (WES), an increasing number of tools are being proposed for copy number variation (CNV) detection based on this technique. However, no comprehensive guide is available for the use of these tools in clinical settings, which renders them inapplicable in practice. To resolve this problem, in this study, we evaluated the performances of four WES-based CNV tools, and established a guideline for the recommendation of a suitable tool according to the application requirements.

Results
In this study, first, we selected four WES-based CNV detection tools: CoNIFER, cn.MOPS, CNVkit and exomeCopy. Then, we evaluated their performances in terms of three aspects: sensitivity and specificity, overlapping consistency and computational costs. From this evaluation, we obtained four main results: (1) The sensitivity increases and subsequently stabilizes as the coverage or CNV size increases, while the specificity decreases. (2) CoNIFER performs better for CNV insertions than for CNV deletions, while the remaining tools exhibit the opposite trend. (3) CoNIFER, cn.MOPS and CNVkit realize satisfactory overlapping consistency, which indicates their results are trustworthy. (4) CoNIFER has the best space complexity and cn.MOPS has the best time complexity among these four tools. Finally, we established a guideline for tools’ usage according to these results.

Conclusion
No available tool performs excellently under all conditions; however, some tools perform excellently in some scenarios. Users can obtain a CNV tool recommendation from our paper according to the targeted CNV size, the CNV type or computational costs of their projects, as presented in Table 1, which is helpful even for users with limited knowledge of computer science.
Clinical significance of regional lymph node enlargement in patients with EGC within the expanded criteria for ESD
Authors: Lee Dong Seok , Park Jong Kyu , Lee Sang Jin , Cheon Gab Jin 
Published: March 2020

Abstracts
Background
Lymph node (LN) metastasis is negligible in early gastric cancer (EGC) within expanded criteria for endoscopic submucosal dissection (ESD). However, regional lymph nodes in abdominal CT scans are sometimes enlarged in patients with EGC within the expanded criteria for endoscopic submucosal dissection (ESD). In this study, we investigated the clinical significance of regional lymph node enlargement on abdominal CT scan in patients with EGC within the expanded criteria for ESD.

Methods
From December 2010 to April 2015, among 301 patients with EGC within the ESD expanded criteria, 47 patients with regional lymph node enlargement shown by abdominal CT scan were prospectively enrolled. We performed surgical resection or periodic follow-up with abdominal CT scans and upper endoscopy every 6 months to evaluate whether the enlarged lymph nodes are due to metastasis or a reactive change.

Results
The mean age of the 47 patients (38 males, 9 female) was 64.8 years. The enlarged lymph nodes were usually single (26/47, 44.6%) and sized as follows: 11 nodes were ≤ 5 mm, 19 were 6–10 mm, and 17 were ≥ 10 mm. Four of the 47 patients initially underwent surgical resection, and 8 patients underwent surgical resection after ESD. However, there was no lymph node metastasis in surgical specimens. Thirty-five patients received ESD and periodically followed up at a median duration of 56 months (IQR: 44–59 month). The enlarged lymph node disappeared in 12 of 35 patients, decreased in 9 patients and remained the same size in 13 patients, and increased in 1 patient.

Conclusion
Regional lymph node enlargement on abdominal CT scan in patients within expanded criteria for ESD of ECG may be not due to metastasis but a reactive change.
Mediastinal paraganglioma successfully resected by robot-assisted thoracoscopic surgery with en bloc chest wall resection: a case report
Authors: Shidei Hiroaki , Maeda Hideyuki , Isaka Tamami , Matsumoto Takako , Yamamoto Tomoko , Nagashima Yoji , Kanzaki Masato 
Published: March 2020

Abstract
Background
Robot-assisted thoracoscopic surgery (RATS) is useful for surgery in the apical region of the chest cavity, as it narrows towards the head. Here, we describe a nonfunctional, rib-invasive paraganglioma arising in the posterior mediastinum that was successfully removed using RATS combined with chest wall resection.

Case presentation
A 31-year-old woman presented with a posterior mediastinal mass on chest computed tomography (CT) scan during a medical check-up 2 years prior. Positron emission tomography/computed tomography scan with F-18 fluorodeoxyglucose revealed a mass associated with standardized uptake maximum value of 2.69. With a preoperative diagnosis of neurogenic tumor by CT-guided percutaneous fine-needle aspiration biopsy, we performed robot-assisted tumor resection combined with chest wall resection. The wristed instruments of the robotic surgical system have increased range of motion and enabled the tumor resection without organ injury in the thoracic cavity. Histopathology examination revealed a non-functional paraganglioma with rib invasion.

Conclusions
RATS is a useful technique, enabling safer and easier resection of a mediastinal tumor adjacent to surrounding organs.
Introducing our series: research synthesis and meta-research in biology
Authors: Nakagawa Shinichi , Koricheva Julia , Macleod Malcolm , Viechtbauer Wolfgang 
Published: March 2020

AbstractResearch synthesis is the process of bringing together findings and attributes from different publications, for example, to give a more complete description of phenomena than is usually possible in a single work. We bring the Research Synthesis Series to BMC Biology to promote meta-analyses, other research syntheses including meta-research studies, and research synthesis methodologies in biology, facilitating their dissemination to broader communities.
Assessment of the psychometric properties and refinement of the Health and Self-Management in Diabetes Questionnaire (HASMID)
Authors: Carlton Jill , Rowen Donna , Elliott Jackie 
Published: March 2020

Abstract
Background
The Health And Self-Management In Diabetes (HASMIDv1) questionnaire consists of 8 attributes, 4 about quality of life, and 4 about self-management. The overall aim of this study was to rigorously examine the psychometric properties of the HASMIDv1 questionnaire.

Methods
The study comprised two phases. Phase 1 identified items of the HASMIDv1 questionnaire that potentially required rewording through consultation with a patient involvement panel and two focus groups of people with diabetes. Phase 2 involved a cross-sectional longitudinal survey where HASMID, EQ-5D-5L, health, treatment and sociodemographic questions were administered using both paper and online versions to people with diabetes. Participants were asked to complete the survey again approximately 3 months later. Psychometric analyses were undertaken to examine floor and ceiling effects, item distributions, known group differences and internal consistency. Rasch analysis was undertaken to assess differential item functioning and disordered thresholds.

Results
Phase 1 derived five alternative wordings to items: Irritable, Affects Mealtimes, Daily Routine, Social Activities and Problem. Phase 2 achieved 2835 responses at time point 1 (n = 1944 online, n = 891 paper version) and 1243 at time point 2 (n = 533 online, n = 710 paper version). Overall the HASMID items performed well, though two alternative worded items (Irritable and Social Activities) provided additional information not fully captured by the original HASMID items.

Conclusion
Psychometric evaluation and Rasch analysis were used in conjunction with expert opinion to determine the final questionnaire. The application of psychometric analyses or Rasch analysis alone to inform item selection would have resulted in different items being selected for the final instrument. The benefit of a combined approach has produced an instrument which has a broader evaluation of self-management. The final validated HASMID-10 is a short self-report PRO that can be used to evaluate the impact of self-management for people living with diabetes. HASMID-10 can be scored using total summative scores, with utility and monetary values also available for use in cost-utility and cost-benefit analyses.
Factors influencing sexual and reproductive health of Muslim women: a systematic review
Authors: Alomair Noura , Alageel Samah , Davies Nathan , Bailey Julia V. 
Published: March 2020

AbstractBackgroundIn Islamic societies, issues related to sexual and reproductive health (SRH) are rarely discussed and considered sensitive subjects. This review aimed to identify any personal, religious, cultural, or structural barriers to SRH service and education among Muslim women worldwide.MethodsA search for qualitative and quantitative studies was conducted on seven electronic databases. A narrative synthesis using thematic analysis was conducted.ResultsFifty-nine studies were included from 22 countries: 19 qualitative, 38 quantitative and two mixed methods. Many Muslim women have poor SRH knowledge, and negative attitudes which influence their access to, and use of SRH services. Barriers to contraception use among Muslim women included a lack of basic reproductive knowledge, insufficient knowledge about contraception, misconceptions, and negative attitudes. Women had negative attitudes towards family planning for limiting the number of children but not for child spacing, which reflected religious views towards family planning. Religious and cultural beliefs were barriers to contraception use and access to SRH services and information. Family and the community have a significant impact on women’s contraceptive use and access to SRH services. Husband and family opposition played a significant role in contraception access and use. Fear of stigmatization and being labelled as having pre-marital sexual relations among unmarried women acted as the main barrier to accessing contraception and seeking SRH information and services.ConclusionThe findings reveal that there are multiple levels of factors that influence Muslim women’s SRH. Poor SRH knowledge and practices among Muslim women is complex matter that is affected by personal, community, cultural, religious factors and existing policies and regulations. All these factors overlap and are affected by each other. There is an urgent need for interventions addressing modifiable barriers to SRH education and services to improve knowledge, informed choice and access to services to facilitate better sexual and reproductive wellbeing for Muslim women. It is important to note that while this review aimed to report findings on Muslim women, we acknowledge that significant variations exist within every culture and religion.
This was the year that was: brain barriers and brain fluid research in 2019
Authors: Keep Richard F. , Jones Hazel C. , Drewes Lester R. 
Published: March 2020

AbstractThis editorial highlights advances in brain barrier and brain fluid research published in 2019, as well as addressing current controversies and pressing needs. Topics include recent advances related to: the cerebral endothelium and the neurovascular unit; the choroid plexus, arachnoid membrane; cerebrospinal fluid and the glymphatic hypothesis; the impact of disease states on brain barriers and brain fluids; drug delivery to the brain; and translation of preclinical data to the clinic. This editorial also mourns the loss of two important figures in the field, Malcolm B. Segal and Edward G. Stopa.
Conserved contributions of NMDA receptor subtypes to synaptic responses in lamina II spinal neurons across early postnatal development
Authors: Mahmoud Hadir , Martin Newton , Hildebrand Michael E. 
Published: March 2020

AbstractNMDA receptors are heteromeric complexes that contribute to excitatory synaptic transmission and plasticity. The presence of specific variants of GluN2 subunits in these complexes enables diversity in NMDA receptor function and regulation. At brain synapses, there is a switch from slow GluN2B-mediated NMDA receptors to faster GluN2A-dominated NMDA receptors as well as an increase in the ratio of AMPA to NMDA receptors during early postnatal development. This glutamate receptor switch is observed across brain regions and is critical for synaptic maturation, circuit development, and associative learning. However, whether a similar receptor subunit switch occurs within pain processing neurons in the developing spinal cord remains untested. To investigate this, we performed whole-cell patch clamp recordings of excitatory synaptic responses from lamina II dorsal horn neurons of one to three week-old rats. We found that GluN2B and GluN2A both prominently contribute to NMDA receptor responses at neonatal lamina II synapses, with a small contribution from GluN2D as well. Surprisingly, we found that this molecular identity of NMDA receptor responses as well as the relative contribution of AMPA receptors versus NMDA receptors did not change at lamina II synapses across early postnatal development (P7 to P21). The lack of a developmental switch and persistence of slow-decaying GluN2B- and GluN2D-mediated synaptic responses throughout neuronal maturation in the dorsal horn has implications for understanding both the regulation of synaptic glutamatergic receptors as well as spinal mechanisms of pain processing.
Comparative analysis of abdominal fluid cytokine levels in ovarian hyperstimulation syndrome (OHSS)
Authors: Farkas Balint , Boldizsar Ferenc , Bohonyi Noemi , Farkas Nelli , Marczi Saska , Kovacs Gabor L. , Bodis Jozsef , Koppan Miklos 
Published: March 2020

Abstract
Background
Ovarian hyperstimulation syndrome (OHSS) is a rare, yet severe, iatrogenic complication of ovulation induction therapy during assisted reproductive procedures. Our group previously detected atypical cells in the ascitic fluid of OHSS patients, although no malignancy developed during follow up. Here, the aim was to perform a comparative analysis of the cytokines present in the abdominal fluid of patients affected by OHSS versus patients with advanced ovarian cancer, a benign adnexal mass, or ovarian endometriosis.

Methods
This prospective, non-randomized study was conducted at the Clinical Center of the University of Pecs Department of Obstetrics and Gynecology/Reproductive Center between October 2016 and March 2018. Abdominal fluid samples were obtained from 76 patients and subjected to Luminex analysis. The samples were collected from patients with OHSS (OHSS; n = 16), advanced ovarian cancer (OC; n = 22), a benign adnexal mass (BAM; n = 21), or ovarian endometriosis (EM; n = 17). Data were subjected to the non-parametric Kruskal-Wallis test and Spearman’s rank correlation coefficient to identify statistical differences between the four study groups.

Results
Leukocytosis and hemoconcentration were detected in the peripheral blood of OHSS patients. Abdominal fluid analysis further revealed significantly higher levels of interleukin (IL)-6, IL-8, IL-10, and transforming growth factor (TGF)-β in both the OHSS and OC groups compared to the BAM and EM groups. The highest concentration of vascular endothelial growth factor (VEGF) was detected in the OC group, while a significantly lower level was detected in the OHSS group. Moreover, VEGF levels in OC and OHSS groups were significantly elevated compared to the levels in the BAM and EM groups.

Conclusions
Vasoactive and hematogenic cytokines were present at higher levels in both the OHSS and OC abdominal fluid samples compared to the fluid samples obtained from the peritoneal cavity of the BAM patients. It is possible that these cytokines play an important role in the formation of ascites.
Trypanosome infection rate in Glossina tachinoides: infested rivers of Limmu Kosa District Jimma Zone, Western Ethiopia
Authors: Meharenet Behablom , Alemu Dereje 
Published: March 2020

Abstract
Objective
Trypanosomosis is a disease of domestic animals and humans resulting from infection with parasitaemic protozoa of the genus Trypanosoma transmitted primarily by tsetse flies. A cross-sectional study was conducted from January-March 2018, to estimate the infection rate of trypanosome in Glossina tachinoides, their distribution, magnitude and involved trypanosome species in Limmu Kosa District of Jimma zone.

Results
Study methodology involved entomological survey using monoconical traps to study the magnitude of Fly density Flay/Trap/Day (FTD) and tsetse fly dissection to estimate infection rate of trypanosome in vector flies. The study result indicated that there was only one species of Tsetse fly Glossina tachinoides detected with FTD = 4.45. From the total of (n = 284) dissected Glossina tachinoides flies only (n = 5) positive for Trypanosome resulting in 1.76% Infection Rate. Peak trypanosome infections were observed in female tsetse 2.04%, n = 4 and 1.14%, n = 1 in males. Furthermore, 1.06% of Glossina tachinoides were infected by Trypanosome vivax and the remaining 0.70% was Trypanosome congolense. Finally, the study concluded with the recommendation of control and suppression of the vector and parasite was mandatory due to Pathogenic Animal Trypanosomosis.
ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning
Authors: Jiang Dejun , Lei Tailong , Wang Zhe , Shen Chao , Cao Dongsheng , Hou Tingjun 
Published: March 2020

AbstractBreast cancer resistance protein (BCRP/ABCG2), an ATP-binding cassette (ABC) efflux transporter, plays a critical role in multi-drug resistance (MDR) to anti-cancer drugs and drug–drug interactions. The prediction of BCRP inhibition can facilitate evaluating potential drug resistance and drug–drug interactions in early stage of drug discovery. Here we reported a structurally diverse dataset consisting of 1098 BCRP inhibitors and 1701 non-inhibitors. Analysis of various physicochemical properties illustrates that BCRP inhibitors are more hydrophobic and aromatic than non-inhibitors. We then developed a series of quantitative structure–activity relationship (QSAR) models to discriminate between BCRP inhibitors and non-inhibitors. The optimal feature subset was determined by a wrapper feature selection method named rfSA (simulated annealing algorithm coupled with random forest), and the classification models were established by using seven machine learning approaches based on the optimal feature subset, including a deep learning method, two ensemble learning methods, and four classical machine learning methods. The statistical results demonstrated that three methods, including support vector machine (SVM), deep neural networks (DNN) and extreme gradient boosting (XGBoost), outperformed the others, and the SVM classifier yielded the best predictions (MCC = 0.812 and AUC = 0.958 for the test set). Then, a perturbation-based model-agnostic method was used to interpret our models and analyze the representative features for different models. The application domain analysis demonstrated the prediction reliability of our models. Moreover, the important structural fragments related to BCRP inhibition were identified by the information gain (IG) method along with the frequency analysis. In conclusion, we believe that the classification models developed in this study can be regarded as simple and accurate tools to distinguish BCRP inhibitors from non-inhibitors in drug design and discovery pipelines.
Multiclass audio segmentation based on recurrent neural networks for broadcast domain data
Authors: Gimeno Pablo , Viñals Ignacio , Ortega Alfonso , Miguel Antonio , Lleida Eduardo 
Published: March 2020

AbstractThis paper presents a new approach based on recurrent neural networks (RNN) to the multiclass audio segmentation task whose goal is to classify an audio signal as speech, music, noise or a combination of these. The proposed system is based on the use of bidirectional long short-term Memory (BLSTM) networks to model temporal dependencies in the signal. The RNN is complemented by a resegmentation module, gaining long term stability by means of the tied state concept in hidden Markov models. We explore different neural architectures introducing temporal pooling layers to reduce the neural network output sampling rate. Our findings show that removing redundant temporal information is beneficial for the segmentation system showing a relative improvement close to 5%. Furthermore, this solution does not increase the number of parameters of the model and reduces the number of operations per second, allowing our system to achieve a real-time factor below 0.04 if running on CPU and below 0.03 if running on GPU. This new architecture combined with a data-agnostic data augmentation technique called mixup allows our system to achieve competitive results in both the Albayzín 2010 and 2012 evaluation datasets, presenting a relative improvement of 19.72% and 5.35% compared to the best results found in the literature for these databases.