bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of abdominal compression on target movement and extension of the external boundary of peripheral lung tumours treated with stereotactic radiotherapy based on four-dimensional computed tomography
Authors: Qi Yuanjun , Li Jianbin , Zhang Yingjie , Shao Qian , Liu Xijun , Li Fengxiang , Wang Jinzhi , Li Zhenxiang , Wang Wei 
Published: September 2021

Abstract
Background
This study aimed to investigate the effect of abdominal compression on tumour motion and target volume and to determine suitable planning target volume (PTV) margins for patients treated with lung stereotactic body radiotherapy (SBRT) based on four-dimensional computed tomography (4DCT).

Methods
Twenty-three patients diagnosed to have a peripheral pulmonary tumour were selected and divided into an all lesions group (group A), an upper middle lobe lesions group (group B), and a lower lobe lesions group (group C). Two 4DCT scans were performed in each patient, one with and one without abdominal compression. Cone beam computed tomography (CBCT) was performed before starting treatment. The gross target volumes (GTVs) were delineated and internal gross target volumes (IGTVs) were defined. IGTVs were generated using two methods: (1) the maximum intensity projections (MIPs) based on the 4DCT were reconstructed to form a single volume and defined as the IGTVMIP and (2) GTVs from all 10 phases were combined to form a single volume and defined as the IGTV10. A 5-mm, 4-mm, and 3-mm margin was added in all directions on the IGTVMIP and the volume was constructed as PTVMIP5mm, PTVMIP4mm, and PTVMIP3mm.

Results
There was no significant difference in the amplitude of tumour motion in the left–right, anterior–posterior, or superior-inferior direction according to whether or not abdominal compression was applied (group A, p = 0.43, 0.27, and 0.29, respectively; group B, p = 0.46, 0.15, and 0.45; group C, p = 0.79, 0.86, and 0.37; Wilcoxon test). However, the median IGTVMIP without abdominal compression was 33.67% higher than that with compression (p = 0.00), and the median IGTV10 without compression was 16.08% higher than that with compression (p = 0.00). The median proportion of the degree of inclusion of the IGTVCBCT in PTVMIP5mm, PTVMIP4mm, and PTVMIP3mm ≥ 95% was 100%, 100%, and 83.33%, respectively.

Conclusions
Abdominal compression was useful for reducing the size of the IGTVMIP and IGTV10 and for decreasing the PTV margins based on 4DCT. In IGTVMIP with abdominal compression, adding a 4-mm margin to account for respiration is feasible in SBRT based on 4DCT.
Similarities of developmental gene expression changes in the brain between human and experimental animals: rhesus monkey, mouse, Zebrafish, and Drosophila
Authors: Nakajima Ryuichi , Hagihara Hideo , Miyakawa Tsuyoshi 
Published: September 2021

Abstract
Aim
Experimental animals, such as non-human primates (NHPs), mice, Zebrafish, and Drosophila, are frequently employed as models to gain insights into human physiology and pathology. In developmental neuroscience and related research fields, information about the similarities of developmental gene expression patterns between animal models and humans is vital to choose what animal models to employ. Here, we aimed to statistically compare the similarities of developmental changes of gene expression patterns in the brains of humans with those of animal models frequently used in the neuroscience field.

Methods
The developmental gene expression datasets that we analyzed consist of the fold-changes and P values of gene expression in the brains of animals of various ages compared with those of the youngest postnatal animals available in the dataset. By employing the running Fisher algorithm in a bioinformatics platform, BaseSpace, we assessed similarities between the developmental changes of gene expression patterns in the human (Homo sapiens) hippocampus with those in the dentate gyrus (DG) of the rhesus monkey (Macaca mulatta), the DG of the mouse (Mus musculus), the whole brain of Zebrafish (Danio rerio), and the whole brain of Drosophila (D. melanogaster).

Results
Among all possible comparisons of different ages and animals in developmental changes in gene expression patterns within the datasets, those between rhesus monkeys and mice were highly similar to those of humans with significant overlap P-value as assessed by the running Fisher algorithm. There was the highest degree of gene expression similarity between 40–59-year-old humans and 6–12-year-old rhesus monkeys (overlap P-value = 2.1 × 10− 72). The gene expression similarity between 20–39-year-old humans and 29-day-old mice was also significant (overlap P = 1.1 × 10− 44). Moreover, there was a similarity in developmental changes of gene expression patterns between 1–2-year-old Zebrafish and 40–59-year-old humans (Overlap P-value = 1.4 × 10− 6). The overlap P-value of developmental gene expression patterns between Drosophila and humans failed to reach significance (30 days Drosophila and 6–11-year-old humans; overlap P-value = 0.0614).

Conclusions
These results indicate that the developmental gene expression changes in the brains of the rhesus monkey, mouse, and Zebrafish recapitulate, to a certain degree, those in humans. Our findings support the idea that these animal models are a valid tool for investigating the development of the brain in neurophysiological and neuropsychiatric studies.
The future is now: our experience starting a remote clinical trial during the beginning of the COVID-19 pandemic
Authors: Liu Hans H. , Ezekowitz Michael D. , Columbo Michele , Khan Oneib , Martin Jack , Spahr Judith , Yaron David , Cushinotto Lisa , Kapelusznik Luciano 
Published: September 2021

Abstract
Background
The World Health Organization declared the outbreak of SARS-CoV-2 a pandemic on February 11, 2020. This organism causes COVID-19 disease and the rapid rise in cases and geographic spread strained healthcare systems. Clinical research trials were hindered by infection control measures discouraging physical contact and diversion of resources to meet emergent requirements. The need for effective treatment and prevention of COVID-19 prompted an untested investigational response. Trial groups adapted approaches using remote enrolment and consenting, newly developed diagnostic tests, delivery of study medications and devices to participants’ homes, and remote monitoring to ensure investigator/enrollee safety while preserving ethical integrity, confidentiality, and data accuracy.

Methods
Clinical researchers at our community health system in the USA undertook an outpatient randomized open-label study of hydroxychloroquine (HCQ) prophylaxis versus observation of SARS-CoV-2 infection in household COVID-19 contacts. Designed in March 2020, challenges included COVID-19 infection in the research group, HCQ shortage, and lack of well-established home SARS-CoV-2 tests and remote ECG monitoring protocols in populations naive to these procedures. The study was written, funded, and received ethical committee approval in 4 months and was completed by September 2020 during a period of fluctuating infection rates and conflicting political opinions on HCQ use; results have been published. Singular methodology included the use of a new RNA PCR saliva SARS-CoV-2 home diagnostic test and a remote smartphone-based 6-lead ECG recording system.

Results
Of 483 households contacted regarding trial participation, 209 (43.3%) did not respond to telephone calls/e-mails and 90 (18.6%) declined; others were not eligible by inclusion or exclusion criteria. Ultimately, 54 individuals were enrolled and 42 completed the study. Numbers were too small to determine the efficacy of HCQ prophylaxis. No serious treatment-related adverse events were encountered.

Conclusions
Flexibility in design, a multidisciplinary research team, prompt cooperation among research, funding, ethics review groups, and finding innovative study approaches enabled this work. Concerns were balancing study recruitment against unduly influencing individuals anxious for protection from the pandemic and exclusion of groups based on lack of Internet access and technology. An issue to address going forward is establishing research cooperation across community health systems before emergencies develop.

Trial registration
ClinicalTrials.govNCT04652648. Registered on December 3, 2020.
Field evaluation of transgenic hybrid poplars with desirable wood properties and enhanced growth for biofuel production by bicistronic expression of PdGA20ox1 and PtrMYB3 in wood-forming tissue
Authors: Cho Jin-Seong , Kim Min-Ha , Bae Eun-Kyung , Choi Young-Im , Jeon Hyung-Woo , Han Kyung-Hwan , Ko Jae-Heung 
Published: September 2021

Abstract
Background
To create an ideotype woody bioenergy crop with desirable growth and biomass properties, we utilized the viral 2A-meidated bicistronic expression strategy to express both PtrMYB3 (MYB46 ortholog of Populus trichocarpa, a master regulator of secondary wall biosynthesis) and PdGA20ox1 (a GA20-oxidase from Pinus densiflora that produces gibberellins) in wood-forming tissue (i.e., developing xylem).

Results
Transgenic Arabidopsis plants expressing the gene construct DX15::PdGA20ox1-2A-PtrMYB3 showed a significant increase in both stem fresh weight (threefold) and secondary wall thickening (1.27-fold) relative to wild-type (WT) plants. Transgenic poplars harboring the same gene construct grown in a greenhouse for 60 days had a stem fresh weight up to 2.6-fold greater than that of WT plants. In a living modified organism (LMO) field test conducted for 3 months of active growing season, the stem height and diameter growth of the transgenic poplars were 1.7- and 1.6-fold higher than those of WT plants, respectively, with minimal adverse growth defects. Although no significant changes in secondary wall thickening of the stem tissue of the transgenic poplars were observed, cellulose content was increased up to 14.4 wt% compared to WT, resulting in improved saccharification efficiency of the transgenic poplars. Moreover, enhanced woody biomass production by the transgenic poplars was further validated by re-planting in the same LMO field for additional two growing seasons.

Conclusions
Taken together, these results show considerably enhanced wood formation of our transgenic poplars, with improved wood quality for biofuel production.
Placenta increta presenting with threatened miscarriage during the first trimester in rhesus-negative mother: a case report
Authors: Nik-Ahmad-Zuky Nik Lah , Seoparjoo Azmel , Husna Engku Ismail Engku 
Published: September 2021

Abstract
Background
Placenta accreta is known to be associated with significant maternal morbidity and mortality—primarily due to intractable bleeding during abortion or delivery at any level of gestation. The complications could be reduced if placenta accreta is suspected in a patient with a history of previous cesarean delivery and the gestational sac/placenta is located at the lower part of the uterus. Then, a proper management plan can be instituted, and complications can be reduced. The diagnosis of placenta accreta in the first trimester of pregnancy is considered uncommon.

Case presentation
A 34-year-old Malay, gravida 4, para 3, rhesus-negative woman was referred from a private hospital at 13 weeks owing to accreta suspicion for further management. She has a history of three previous lower-segment cesarean sections. She also had per vaginal bleeding in the early first trimester, which is considered to indicate threatened miscarriage. Transabdominal ultrasound revealed features consistent with placenta accreta spectrum. She was counseled for open laparotomy and hysterectomy because of potential major complication if she continued with the pregnancy. Histopathological examination revealed placenta increta.

Conclusion
A high index of suspicion of placenta previa accreta must be in practice in a patient with a history of previous cesarean deliveries and low-lying placenta upon ultrasound examination during early gestation.
Nonlinear residual echo suppression based on dual-stream DPRNN
Authors: Chen Hongsheng , Chen Guoliang , Chen Kai , Lu Jing 
Published: September 2021

AbstractThe acoustic echo cannot be entirely removed by linear adaptive filters due to the nonlinear relationship between the echo and the far-end signal. Usually, a post-processing module is required to further suppress the echo. In this paper, we propose a residual echo suppression method based on the modification of dual-path recurrent neural network (DPRNN) to improve the quality of speech communication. Both the residual signal and the auxiliary signal, the far-end signal or the output of the adaptive filter, obtained from the linear acoustic echo cancelation are adopted to form a dual-stream for the DPRNN. We validate the efficacy of the proposed method in the notoriously difficult double-talk situations and discuss the impact of different auxiliary signals on performance. We also compare the performance of the time domain and the time-frequency domain processing. Furthermore, we propose an efficient and applicable way to deploy our method to off-the-shelf loudspeakers by fine-tuning the pre-trained model with little recorded-echo data.
Diffuse leptomeningeal glioneuronal tumour (DLGNT) in children: the emerging role of genomic analysis
Authors: Manoharan Neevika , Ajuyah Pamela , Senapati Akanksha , Wong Marie , Mullins Anna , Rodriguez Michael , Doyle Helen , McCowage Geoff , Lau Loretta M. S. , Ekert Paul G. , Ziegler David S. 
Published: September 2021

AbstractDiffuse leptomeningeal glioneuronal tumours (DLGNT) represent rare enigmatic CNS tumours of childhood. Most patients with this disease share common radiological and histopathological features but the clinical course of this disease is variable. A radiological hallmark of this disease is widespread leptomeningeal enhancement that may involve the entire neuroaxis with predilection for the posterior fossa and spine. The classic pathologic features include low- to moderate-density cellular lesions with OLIG2 expression and evidence of ‘oligodendroglioma-like’ appearance. The MAPK/ERK signaling pathway has recently been reported as a potential driver of tumourigenesis in up to 80% of DLGNT with KIAA1549:BRAF fusions being the most common event seen. Until now, limited analysis of the biological drivers of tumourigenesis has been undertaken via targeted profiling, chromosomal analysis and immunohistochemistry. Our study represents the first examples of comprehensive genomic sequencing in DLGNT and shows that it is not only feasible but crucial to our understanding of this rare disease. Moreover, we demonstrate that DLGNT may be more genomically complex than single-event MAPK/ERK signaling pathway tumours.
The effects of vitamin D supplementation in carpal tunnel syndrome treatment outcomes: a systematic review
Authors: Anusitviwat Chirathit , Suwanno Porames , Suwannaphisit Sitthiphong 
Published: September 2021

Abstract
Purpose
Vitamin D deficiency is related to carpal tunnel syndrome symptoms. Correcting vitamin D levels by supplementation was supposed to improve carpel tunnel symptoms, though there is a lack of aggregated data about treatment outcomes. This study aimed to examine whether vitamin D supplementation could improve the treatment outcomes in carpal tunnel syndrome patients.

Methods
A comprehensive search of the PubMed, Cochrane Library, Scopus, and Web of Science databases for articles on vitamin D and carpel tunnel syndrome from January 2000 to March 2021 was performed. The article screening and data extraction were performed by two investigators independently with blinding to decisions on selected studies. All included studies had assessed the quality of evidence using the Methodological Index for Non-Randomized Studies (MINORS) scoring system.

Results
We retrieved four studies that met the eligibility criteria. The treatment outcomes were evaluated by visual analog scale (124 wrists), functional scores (176 patients), muscle strength (84 patients), and nerve conduction velocity (216 wrists). After vitamin D supplementation, two studies reported improved pain scores and nerve conduction velocity, and three studies showed enhancement of functional status.

Conclusion
Vitamin D administration could offer favorable outcomes in pain improvement, better functional status, and increased sensory conduction velocity in carpal tunnel syndrome. However, there is to date no recommendations concerning a standardized dose or duration of vitamin D administration in carpal tunnel syndrome; prescribing vitamin D at the usual appropriate dose is suggested as an additional treatment in patients with mild to moderate carpel tunnel symptoms.

Level of Evidence
Level IV, therapeutic study
CT and MRI findings of cystic renal cell carcinoma: comparison with cystic collecting duct carcinoma
Authors: Zhu Qingqiang , Ling Jun , Ye Jing , Zhu Wenrong , Wu Jingtao , Chen Wenxin 
Published: September 2021

Abstract
Background
Cystic renal cell carcinoma (CRCC) and cystic collecting duct carcinoma (CCDC) share similar oncogeni and some imaging findings. The aim of this study was to characterize the clinical and CT imagings features of CRCC and CCDC.

Methods
Thirty-three patients with CRCC and thirteen patients with CCDC with pathologically proven were retrospectively studied. Tumor characteristics were assessed.

Results
On CT imaging, 33 patients(100 %) with CRCC and 13 patients(100 %) with CCDC, tumors calcifications (8 vs. 9, P < 0.0001), had a clear boundary (capsule sign, 30 vs. 2, P < 0.0001), infiltrative appearance (1 vs. 13, P < 0.0001), exogenous appearance (29 vs. 3, P < 0.0001), invaded the renal pelvis or ureter (1 vs. 10, P < 0.0001), hemorrhage (1 vs. 10, P < 0.0001), had retroperitoneal lymph node or distant metastasis (2 vs. 10, P < 0.0001), thickened enhancing internal septations (31 vs. 2, P < 0.0001), and mural soft-tissue nodules (21 vs. 1, P < 0.0001). On MR imaging,13 patients(39 %) with CRCC and 4 patients(31 %) with CCDC, all CRCCs appeared hypointense on T1-weighted images and hyperintense on T2-weighted images, however, all CCDCs appeared hypointense on T1-weighted images and hypointense on T2-weighted images(P < 0.0001). 33 patients with CRCC, they were all alive from3 years to 10 years follow-up, however, 13 patients with CCDC, of which 11 patients were able to be followed up, and 9 patients expired within 5 years of the initial diagnosis and the others are currently still alive.

Conclusions
Distinguishing features of CRCC and CCDC included calcifications, capsule signs, infiltrative appearance, metastasis, internal septations, mural nodules and signal on CT or MR images. These imaging features may help in differentiating the two renal tumor types.
Variation in serum urate levels in the absence of gout and urate lowering therapy
Authors: Shaffer Andrew , Rahn Elizabeth , Saag Kenneth , Mudano Amy , Gaffo Angelo 
Published: September 2021

Abstract
Background
Previous studies have noted significant variation in serum urate (sUA) levels, and it is unknown how this influences the accuracy of hyperuricemia classification based on single data points. Despite this known variability, hyperuricemic patients are often used as a control group in gout studies. Our objective was to determine the accuracy of hyperuricemia classifications based on single data points versus multiple data points given the degree of variability observed with serial measurements of sUA.

Methods
Data was analyzed from a cross-over clinical trial of urate-lowering therapy in young adults without a gout diagnosis. In the control phase, sUA levels used for this analysis were collected at 2–4 week intervals. Mean coefficient of variation for sUA was determined, as were rates of conversion between normouricemia (sUA ≤6.8 mg/dL) and hyperuricemia (sUA > 6.8 mg/dL).

Results
Mean study participant (n = 85) age was 27.8 ± 7.0 years, with 39% female participants and 41% African-American participants. Mean sUA coefficient of variation was 8.5% ± 4.9% (1 to 23%). There was no significant difference in variation between men and women, or between participants initially normouricemic and those who were initially hyperuricemic.
Among those initially normouricemic (n = 72), 21% converted to hyperuricemia during at least one subsequent measurement. The subgroup with initial sUA < 6.0 (n = 54) was much less likely to have future values in the range of hyperuricemia compared to the group with screening sUA values between 6.0–6.8 (n = 18) (7% vs 39%, p = 0.0037).
Of the participants initially hyperuricemic (n = 13), 46% were later normouricemic during at least one measurement.

Conclusion
Single sUA measurements were unreliable in hyperuricemia classification due to spontaneous variation. Knowing this, if a single measurement must be used in classification, it is worth noting that those with an sUA of < 6.0 mg/dL were less likely to demonstrate future hyperuricemic measurements and this could be considered a safer threshold to rule out intermittent hyperuricemia based on a single measurement point.

Trial registration
Data from parent study ClinicalTrials.gov Identifier: NCT02038179.
Dynamic graph exploration by interactively linked node-link diagrams and matrix visualizations
Authors: Burch Michael , ten Brinke Kiet Bennema , Castella Adrien , Peters Ghassen Karray Sebastiaan , Shteriyanov Vasil , Vlasvinkel Rinse 
Published: September 2021

AbstractThe visualization of dynamic graphs is a challenging task owing to the various properties of the underlying relational data and the additional time-varying property. For sparse and small graphs, the most efficient approach to such visualization is node-link diagrams, whereas for dense graphs with attached data, adjacency matrices might be the better choice. Because graphs can contain both properties, being globally sparse and locally dense, a combination of several visual metaphors as well as static and dynamic visualizations is beneficial. In this paper, a visually and algorithmically scalable approach that provides views and perspectives on graphs as interactively linked node-link and adjacency matrix visualizations is described. As the novelty of this technique, insights such as clusters or anomalies from one or several combined views can be used to influence the layout or reordering of the other views. Moreover, the importance of nodes and node groups can be detected, computed, and visualized by considering several layout and reordering properties in combination as well as different edge properties for the same set of nodes. As an additional feature set, an automatic identification of groups, clusters, and outliers is provided over time, and based on the visual outcome of the node-link and matrix visualizations, the repertoire of the supported layout and matrix reordering techniques is extended, and more interaction techniques are provided when considering the dynamics of the graph data. Finally, a small user experiment was conducted to investigate the usability of the proposed approach. The usefulness of the proposed tool is illustrated by applying it to a graph dataset, such as e co-authorships, co-citations, and a Comprehensible Perl Archive Network distribution.