bluuebunny/crossref_metadata_2025_split huggingface dataset:
Text mining to support abstract screening for knowledge syntheses: a semi-automated workflow
Authors: Pham Ba’ , Jovanovic Jelena , Bagheri Ebrahim , Antony Jesmin , Ashoor Huda , Nguyen Tam T. , Rios Patricia , Robson Reid , Thomas Sonia M. , Watt Jennifer , Straus Sharon E. , Tricco Andrea C. 
Published: May 2021

Abstract
Background
Current text mining tools supporting abstract screening in systematic reviews are not widely used, in part because they lack sensitivity and precision. We set out to develop an accessible, semi-automated “workflow” to conduct abstract screening for systematic reviews and other knowledge synthesis methods.

Methods
We adopt widely recommended text-mining and machine-learning methods to (1) process title-abstracts into numerical training data; and (2) train a classification model to predict eligible abstracts. The predicted abstracts are screened by human reviewers for (“true”) eligibility, and the newly eligible abstracts are used to identify similar abstracts, using near-neighbor methods, which are also screened. These abstracts, as well as their eligibility results, are used to update the classification model, and the above steps are iterated until no new eligible abstracts are identified. The workflow was implemented in R and evaluated using a systematic review of insulin formulations for type-1 diabetes (14,314 abstracts) and a scoping review of knowledge-synthesis methods (17,200 abstracts). Workflow performance was evaluated against the recommended practice of screening abstracts by 2 reviewers, independently. Standard measures were examined: sensitivity (inclusion of all truly eligible abstracts), specificity (exclusion of all truly ineligible abstracts), precision (inclusion of all truly eligible abstracts among all abstracts screened as eligible), F1-score (harmonic average of sensitivity and precision), and accuracy (correctly predicted eligible or ineligible abstracts). Workload reduction was measured as the hours the workflow saved, given only a subset of abstracts needed human screening.

Results
With respect to the systematic and scoping reviews respectively, the workflow attained 88%/89% sensitivity, 99%/99% specificity, 71%/72% precision, an F1-score of 79%/79%, 98%/97% accuracy, 63%/55% workload reduction, with 12%/11% fewer abstracts for full-text retrieval and screening, and 0%/1.5% missed studies in the completed reviews.

Conclusion
The workflow was a sensitive, precise, and efficient alternative to the recommended practice of screening abstracts with 2 reviewers. All eligible studies were identified in the first case, while 6 studies (1.5%) were missed in the second that would likely not impact the review’s conclusions. We have described the workflow in language accessible to reviewers with limited exposure to natural language processing and machine learning, and have made the code available to reviewers.
Characterization of the public transit air microbiome and resistome reveals geographical specificity
Authors: Leung M. H. Y. , Tong X. , Bøifot K. O. , Bezdan D. , Butler D. J. , Danko D. C. , Gohli J. , Green D. C. , Hernandez M. T. , Kelly F. J. , Levy S. , Mason-Buck G. , Nieto-Caballero M. , Syndercombe-Court D. , Udekwu K. , Young B. G. , Mason C. E. , Dybwad M. , Lee P. K. H. 
Published: May 2021

Abstract
Background
The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.

Results
City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.

Conclusions
Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.
A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota
Authors: Chung Yusook , Ryu Yongku , An Byung Chull , Yoon Yeo-Sang , Choi Oksik , Kim Tai Yeub , Yoon Jaekyung , Ahn Jun Young , Park Ho Jin , Kwon Soon-Kyeong , Kim Jihyun F. , Chung Myung Jun 
Published: May 2021

Abstract
Background
Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used as anticancer agents, but efforts to utilize attenuated pathogenic bacteria suffer from the risk of toxicity or infection. Lactic acid bacteria are safe to eat and often confer health benefits, making them ideal candidates for live vehicles engineered to deliver anticancer drugs.

Results
In this study, we developed an effective bacterial drug delivery system for colorectal cancer (CRC) therapy using the lactic acid bacterium Pediococcus pentosaceus. It is equipped with dual gene cassettes driven by a strong inducible promoter that encode the therapeutic protein P8 fused to a secretion signal peptide and a complementation system. In an inducible CRC cell-derived xenograft mouse model, our synthetic probiotic significantly reduced tumor volume and inhibited tumor growth relative to the control. Mice with colitis-associated CRC induced by azoxymethane and dextran sodium sulfate exhibited polyp regression and recovered taxonomic diversity when the engineered bacterium was orally administered. Further, the synthetic probiotic modulated gut microbiota and alleviated the chemically induced dysbiosis. Correlation analysis demonstrated that specific bacterial taxa potentially associated with eubiosis or dysbiosis, such as Akkermansia or Turicibacter, have positive or negative relationships with other microbial members.

Conclusions
Taken together, our work illustrates that an effective and stable synthetic probiotic composed of P. pentosaceus and the P8 therapeutic protein can reduce CRC and contribute to rebiosis, and the validity and feasibility of cell-based designer biopharmaceuticals for both treating CRC and ameliorating impaired microbiota.
Ultrasensitive tau biosensor cells detect no seeding in Alzheimer’s disease CSF
Authors: Hitt Brian D. , Vaquer-Alicea Jaime , Manon Victor A. , Beaver Joshua D. , Kashmer Omar M. , Garcia Jan N. , Diamond Marc I. 
Published: May 2021

AbstractTau protein forms self-replicating assemblies (seeds) that may underlie progression of pathology in Alzheimer’s disease (AD) and related tauopathies. Seeding in recombinant protein preparations and brain homogenates has been quantified with “biosensor” cell lines that express tau with a disease-associated mutation (P301S) fused to complementary fluorescent proteins. Quantification of induced aggregation in cells that score positive by fluorescence resonance energy transfer (FRET) is accomplished by cell imaging or flow cytometry. Several groups have reported seeding activity in antemortem cerebrospinal fluid (CSF) using various methods, but these findings are not yet widely replicated. To address this question, we created two improved FRET-based biosensor cell lines based on tau expression, termed version 2 low (v2L) and version 2 high (v2H). We determined that v2H cells are ~ 100-fold more sensitive to AD-derived tau seeds than our original lines, and coupled with immunoprecipitation reliably detect seeding from samples containing as little as 100 attomoles of recombinant tau fibrils or ~ 32 pg of total protein from AD brain homogenate. We tested antemortem CSF from 11 subjects with a clinical diagnosis of AD, 9 confirmed by validated CSF biomarkers. We used immunoprecipitation coupled with seed detection in v2H cells and detected no tau seeding in any sample. Thus we cannot confirm prior reports of tau seeding activity in the CSF of AD patients. This next generation of ultra-sensitive tau biosensors may nonetheless be useful to the research community to quantify tau pathology as sensitively and specifically as possible.
The history of rescuing reinforcement and the preliminary study of preventive protection system for the cliff of Mogao Grottoes in Dunhuang, China
Authors: Wang Xudong , Wang Yanwu , Guo Qinglin , Pei Qiangqiang , Zhao Guojing 
Published: May 2021

Abstract
Based on the research results and practical engineering experience pertaining to the protection and reinforcement of the cliff of the Mogao Grottoes in Dunhuang, China, this paper presents a method that is mainly based on the analytic hierarchy process (AHP) to evaluate the preservation state and risk of the Mogao cliff, a means that numerical simulation was conducted to quantitatively evaluate the stability and effectiveness of protective measures for the Mogao cliff, a set of reinforcement methods which integrate the key protection techniques based on propping, anchoring, grouting, and anti-weathering and the quality control measures based on assessing their effectiveness for surrounding rocks of the grottoes, and a set of methods for monitoring and warning based on risk theory throughout the entire reinforcement process. The four above-mentioned techniques complement and support with each other, and every stage is based on research. Additionally, the protection and reinforcement concepts implemented at the Mogao cliff are summarized in this paper. Finally, preventive protection and reinforcement techniques for sandy conglomerate grottoes were established based on the research, evaluation, calculation, and monitoring. The techniques presented in this paper can be used as a theoretical foundation and provide technical guidance for the protection and reinforcement of similar cultural heritage sites all over the world.
Geometric correction for thermographic images of asteroid 162173 Ryugu by TIR (thermal infrared imager) onboard Hayabusa2
Authors: Arai Takehiko , Okada Tatsuaki , Tanaka Satoshi , Fukuhara Tetsuya , Demura Hirohide , Kouyama Toru , Sakatani Naoya , Shimaki Yuri , Senshu Hiroki , Sekiguchi Tomohiko , Takita Jun , Hirata Naru , Yamamoto Yukio 
Published: May 2021

AbstractThe thermal infrared imager (TIR) onboard the Hayabusa2 spacecraft performed thermographic observations of the asteroid 162173 Ryugu (1999 JU$$_3$$

3

) from June 2018 to November 2019. Our previous reports revealed that the surface of Ryugu was globally filled with porous materials and had high surface roughness. These results were derived from making the observed temperature maps of TIR using a projection method onto the shape model of Ryugu as geometric corrections. The pointing directions of TIR were calculated using an interpolation of data from the SPICE kernels (NASA/NAIF) during the periods when the optical navigation camera (ONC) and the light detection and ranging (LIDAR) observations were performed. However, the mapping accuracy of the observed TIR images was degraded when the ONC and LIDAR were not performed with TIR. Also, the orbital and attitudinal fluctuations of Hayabusa2 increased the error of the temperature maps. In this paper, to solve the temperature image mapping problems, we improved the correction method by fitting all of the observed TIR images with the surface coordinate addressed on the high-definition shape model of Ryugu (SFM 800k v20180804). This correction adjusted the pointing direction of TIR by rotating the TIR frame relative to the Hayabusa2 frame using a least squares fit. As a result, the temperature maps spatially spreading areas were converged within high-resolved $$0.5^\circ$$

0
.

5
∘

by $$0.5^\circ$$

0
.

5
∘

maps. The estimated thermal inertia, for instance, was approximately 300$$\sim$$
∼
350 Jm$$^{-2}$$

-
2

s$$^{-0.5}$$

-
0.5

K$$^{-1}$$

-
1

at the hot area of the Ejima Saxum. This estimation was succeeded in case that the surface topographic features were larger than the pixel scale of TIR. However, the thermal inertia estimation of smooth terrains, such as the Urashima crater, was difficult because of surface roughness effects, where roughness was probably much smaller than the pixel scale of TIR.
Professional identity and experience of undergraduate students: an analysis of semantic networks
Authors: Carvalho Luara , de Amorim-Ribeiro Elisa Maria Barbosa , do Vale Cunha Marcelo , Mourão Luciana 
Published: May 2021

AbstractWork experiences during undergraduate studies can be remarkable in the journey of undergraduate students. The objective of this study was to assess, by analyzing semantic networks, the role of work experiences in the meanings those individuals attribute to professional identity. The sample consisted of 2291 students (60% women) divided into three groups: do not work, work in a field related to their course, work in a field not related to their course. The semantic networks of these groups were composed of words uttered from the professional identity prime. We chose to work with the critical network, obtained from the analysis of the incidence-fidelity indexes of the word pairs. The results evidence that work experiences are related to how undergraduate students attribute meaning to professional identity, in such a way that three different networks were formed for these groups. The network of those who work outside their field was the only one that integrated words with negative content, while the semantic networks of those who do not work and those who work in their field, despite containing words that do not always coincide, present a similar macrostructure. We conclude that work experiences play an important role in the meanings that undergraduate students attribute to professional identity. The study innovates by revealing elements of professional-identity construction, besides allowing for reflections on the effects of work experiences during the college period.
Spatial and temporal analysis of hospitalized dengue patients in Bandung: demographics and risk
Authors: Faridah Lia , Mindra I. Gede Nyoman , Putra Ramadhani Eka , Fauziah Nisa , Agustian Dwi , Natalia Yessika Adelwin , Watanabe Kozo 
Published: May 2021

Abstract
Background
Bandung, the fourth largest city in Indonesia and capital of West Java province, has been considered a major endemic area of dengue, and studies show that the incidence in this city could increase and spread rapidly. At the same time, estimation of incidence could be inaccurate due to a lack of reliable surveillance systems. To provide strategic information for the dengue control program in the face of limited capacity, this study used spatial pattern analysis of a possible outbreak of dengue cases, through the Geographic Information System (GIS). To further enhance the information needed for effective policymaking, we also analyzed the demographic pattern of dengue cases.

Methods
Monthly reports of dengue cases from January 2014 to December 2016 from 16 hospitals in Bandung were collected as the database, which consisted of address, sex, age, and code to anonymize the patients. The address was then transformed into geocoding and used to estimate the relative risk of a particular area’s developing a cluster of dengue cases. We used the kernel density estimation method to analyze the dynamics of change of dengue cases.

Results
The model showed that the spatial cluster of the relative risk of dengue incidence was relatively unchanged for 3 years. Dengue high-risk areas predominated in the southern and southeastern parts of Bandung, while low-risk areas were found mostly in its western and northeastern regions. The kernel density estimation showed strong cluster groups of dengue cases in the city.

Conclusions
This study demonstrated a strong pattern of reported cases related to specific demographic groups (males and children). Furthermore, spatial analysis using GIS also visualized the dynamic development of the aggregation of disease incidence (hotspots) for dengue cases in Bandung. These data may provide strategic information for the planning and design of dengue control programs.
Advanced atomic force microscopy-based techniques for nanoscale characterization of switching devices for emerging neuromorphic applications
Authors: Kim Young-Min , Lee Jihye , Jeon Deok-Jin , Oh Si-Eun , Yeo Jong-Souk 
Published: May 2021

AbstractNeuromorphic systems require integrated structures with high-density memory and selector devices to avoid interference and recognition errors between neighboring memory cells. To improve the performance of a selector device, it is important to understand the characteristics of the switching process. As changes by switching cycle occur at local nanoscale areas, a high-resolution analysis method is needed to investigate this phenomenon. Atomic force microscopy (AFM) is used to analyze the local changes because it offers nanoscale detection with high-resolution capabilities. This review introduces various types of AFM such as conductive AFM (C-AFM), electrostatic force microscopy (EFM), and Kelvin probe force microscopy (KPFM) to study switching behaviors.
The effect of hepatitis C virologic clearance on cardiovascular disease biomarker lipoprotein-associated phospholipase A2 and its relation to serum lipids
Authors: Isaac Amira , Elmarashly Basant , El Saeed Kadry , Mohamed Rasha Samir , Ibrahim Shereen Abdelmonem , Safwat Eslam 
Published: May 2021

Abstract
Background
Chronic hepatitis C virus (HCV) infection has been linked to cardiovascular disease (CVD). However, CVD risk prediction in chronic HCV-infected patients is problematic as the prevalence of different cardiac biomarkers in these patients is currently unknown. Serum lipids, which are routinely used in traditional CVD risk scores, may underestimate CVD risk in these patients, while non-hepatically produced biomarkers, including lipoprotein-associated phospholipase A2 (Lp-PLA2), may better reflect CVD risk. In this study, we aimed to evaluate the effect of sustained virologic response (SVR) on CVD risk, predicted by Lp-PLA2 mass in comparison with serum lipid levels.

Results
Ninety chronic HCV-infected patients were enrolled in this study. Serum Lp-PLA2 mass was measured before and after HCV treatment via direct-acting antivirals and compared with the changes in serum lipids and Framingham risk score (FRS). The Lp-PLA2 level was categorized into high (>235 ng/ml) or low predicted CVD risk (≤235 ng/ml). Mean Lp-PLA2 mass significantly decreased from 322.37 ± 79.15 ng/ml to 263.79 ± 51.804 ng/ml with SVR, and the number of high-risk patients significantly dropped from 82.22 to 60% after treatment. Total cholesterol, low-density lipoprotein, and high-density lipoprotein levels were low/optimal at baseline (170 ± 40.34 mg/dl, 71.98 ± 24.12 mg/dl, and 48.43 ± 6.79 mg/dl) and significantly increased with SVR (195.66 ± 55.68 mg/dl, 103.24 ± 46.57 mg/dl, and 53.91 ± 8.67 mg/dl). According to FRS, only 30% of patients were moderate/high risk at baseline and insignificantly declined to 28.89% post-treatment.

Conclusion
Lp-PLA2 may be a better predictor of CVD risk in chronic HCV-infected patients. Furthermore, SVR may reduce hepatic inflammation and consequently CVD risk.
A new stability-indicating RP-HPLC method for the determination of dicyclomine hydrochloride and dimethicone combination in tablet dosage forms
Authors: Saroja J. , P.V. Anantha Lakshmi , Rammohan Y. , Divya Reddy D. 
Published: May 2021

AbstractBackgroundWe describe a “stability-indicating liquid chromatography” technique for the estimation of dimethicone (DEC) and dicyclomine hydrochloride (DEH) in the established tablet formulations. Individual quantification of DEH and DEC was reported. But simultaneous quantification of DEH and DEC was lacking. DEH and DEC were analysed on an “XTerra C18column (250 mm × 4.6 mm, 5 μm)” with the mobile phase solvent run isocratically with 0.1M K2HPO4-acetonitrile (55:45, v/v) on a flow speed of 1.0 mL/min.ResultsThe chromatographic run period for the DEC and DEH assay was 6.0 min with retention times of 2.134 and 2.865 min, respectively. The method was validated for accuracy (99.453 to 100.417% and 99.703 to 100.303% recovery values for DEH and DEC, respectively), precision (RSV value 0.135% for DEC and 0.171% for DEH), linearity (5–15 μg/mL for DEH and 20–60 μg/mL for DEC), selectivity (no hinderance from excipients) and specificity (no hinderance from degradants) recovery.ConclusionThe developed stability-indicating liquid chromatography process was well applied to established tablet formulations.
Prior Frequent Emergency Department Use as a Predictor of Emergency Department Visits After a New Cancer Diagnosis
Authors: Hong Arthur S. , Nguyen Danh Q. , Lee Simon Craddock , Courtney D. Mark , Sweetenham John W. , Sadeghi Navid , Cox John V. , Fullington Hannah , Halm Ethan A. 
Published: May 2021

PURPOSE: To determine whether emergency department (ED) visit history prior to cancer diagnosis is associated with ED visit volume after cancer diagnosis. METHODS: This was a retrospective cohort study of adults (≥ 18 years) with an incident cancer diagnosis (excluding nonmelanoma skin cancers or leukemia) at an academic medical center between 2008 and 2018 and a safety-net hospital between 2012 and 2016. Our primary outcome was the number of ED visits in the first 6 months after cancer diagnosis, modeled using a multivariable negative binomial regression accounting for ED visit history in the 6-12 months preceding cancer diagnosis, electronic health record proxy social determinants of health, and clinical cancer-related characteristics. RESULTS: Among 35,090 patients with cancer (49% female and 50% non-White), 57% had ≥ 1 ED visit in the 6 months immediately following cancer diagnosis and 20% had ≥ 1 ED visit in the 6-12 months prior to cancer diagnosis. The strongest predictor of postdiagnosis ED visits was frequent (≥ 4) prediagnosis ED visits (adjusted incidence rate ratio [aIRR]: 3.68; 95% CI, 3.36 to 4.02). Other covariates associated with greater postdiagnosis ED use included having 1-3 prediagnosis ED visits (aIRR: 1.32; 95% CI, 1.28 to 1.36), Hispanic (aIRR: 1.12; 95% CI, 1.07 to 1.17) and Black (aIRR: 1.21; 95% CI, 1.17 to 1.25) race, homelessness (aIRR: 1.95; 95% CI, 1.73 to 2.20), advanced-stage cancer (aIRR: 1.30; 95% CI, 1.26 to 1.35), and treatment regimens including chemotherapy (aIRR: 1.44; 95% CI, 1.40 to 1.48). CONCLUSION: The strongest independent predictor for ED use after a new cancer diagnosis was frequent ED visits before cancer diagnosis. Efforts to reduce potentially avoidable ED visits among patients with cancer should consider educational initiatives that target heavy prior ED users and offer them alternative ways to seek urgent medical care.