bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the Progression of Pulmonary Edema Severity: Can Pairwise Comparisons in Radiology Reports Help?
Authors: Hu Stephanie M. , Horng Steven , Berkowitz Seth J. , Liao Ruizhi , Krishnan Rahul G. , Lehman Li-wei H. , Mark Roger G. 
Published: January 2022

AbstractAccurately assessing the severity of pulmonary edema is critical for making treatment decisions in congestive heart failure patients. However, the current scale for quantifying pulmonary edema based on chest radiographs does not have well-characterized severity levels, with substantial inter-radiologist disagreement. In this study, we investigate whether comparisons documented in radiology reports can provide accurate characterizations of pulmonary edema progression. We propose a rules-based natural language processing approach to assess the change in a patient’s pulmonary edema status (e.g. better, worse, no change) by performing pairwise comparisons of consecutive radiology reports, using regular expressions and heuristics derived from clinical knowledge. Evaluated against ground-truth labels from expert radiologists, our labeler extracts comparisons describing the progression of pulmonary edema with 0.875 precision and 0.891 recall. We also demonstrate the potential utility of comparison labels in providing additional fine-grained information over noisier labels produced by models that directly estimate severity level.
Distinct Vaccine Efficacy Rates Among Health Care Workers During a COVID-19 Outbreak in Jordan
Authors: Sultan Iyad , Tbakhi Abdelghani , Abuatta Osama , Mubarak Sawsan , Alsmadi Osama , Edilbi Adib , Al-Ani Ruba , Makhlouf Manar , Hajir Rawan , Khreisat Omar , Al-Ruzzieh Majeda A. , Abdelrazeq Hikmat , Mansour Asem 
Published: January 2022

AbstractBACKGROUNDWe aimed to assess the efficacy of 3 COVID-19 vaccines in a population of health care workers at a tertiary cancer center in Amman, Jordan.METHODSWe evaluated the records of 2855 employees who were fully vaccinated with 1 of 3 different vaccines and those of 140 employees who were not vaccinated. We measured the number of SARS-CoV-2 infections that occurred at least 14 days after the second vaccine dose.RESULTSThe 100-day cumulative incidence of PCR-confirmed SARS-CoV-2 infections was 19.3% ± 3.3% for unvaccinated employees and 1.7% ± 0.27% for fully vaccinated employees. The 100-day cumulative infection rates were 0.7% ± 0.22% in BNT162b2 vaccine recipients (n = 1714), 3.6% ± 0.77% in BBIBP-CorV recipients (n = 680), and 2.3% ± 0.73% in ChAdOx1 recipients (n = 456). We used Cox regression analyses to compare the risks of SARS-CoV-2 infection among the different vaccine recipient groups and found a significantly higher infection risk in BBIBP-CorV (hazard ratio [HR] = 2.9 ± 0.31) and ChAdOx1 recipients (HR = 3.0 ± 0.41) compared to BNT162b2 recipients (P = .00039 and .0074, respectively). Vaccinated employees who had no previously confirmed SARS-CoV-2 infections were at a markedly higher risk for breakthrough infections than those who experienced prior infections (HR = 5.7 ± 0.73, P = .0178).CONCLUSIONSOur study offers a real-world example of differential vaccine efficacy among a high-risk population during a national outbreak. We also show the important synergism between a previous SARS-CoV-2 infection and vaccination.FundingNone
Waning Effectiveness of SARS-CoV-2 mRNA Vaccines in Older Adults: A Rapid Review
Authors: Nanishi Etsuro , Levy Ofer , Ozonoff Al 
Published: January 2022

AbstractThe U.S. Centers for Disease Control and Prevention (CDC) and other health agencies have recently recommended a booster dose of COVID-19 vaccines for specific vulnerable groups including adults 65 years and older. There is limited evidence whether vaccine effectiveness in older adults decreases over time, especially against severe COVID-19. We performed a rapid review of published studies available through 04 November 2021 that provide effectiveness data on mRNA vaccines approved/licensed in the United States and identified eight eligible studies which evaluated vaccine effectiveness in older adults. There is evidence of a decline in vaccine effectiveness against both SARS-CoV-2 infection and severe COVID-19 in older adults among studies which analyzed data up to July-October 2021. Our findings suggest that vaccine effectiveness diminishes in older adults, which supports the current recommendation for a booster dose in this population.
Using FIB-4 score as a screening tool in the assessment of significant liver fibrosis (F2) in patients with transfusion dependent beta thalassaemia: a cross sectional study
Authors: Padeniya Padmapani , Ediriweera Dileepa , De Silva Arjuna , Niriella Madunil , Premawardhena Anuja 
Published: January 2022

AbstractObjectiveTo evaluated the performance of FIB-4 score as a screening tool to detect significant liver fibrosis (F2) compared to transient elastography (TE), among chronic transfusion-dependent beta-thalassemia (TDT) patients, in a resource-poor setting.DesignA cross-sectional studySettingAdolescent and Adult Thalassaemia Care Center (University Medical Unit), Kiribathgoda, Sri Lanka.Participants45 TDT patients who have undergone more than 100 blood transfusions with elevated serum ferritin >2000ng/mL, were selected for the study. Patients who were serologically positive for hepatitis C antibody were excluded.Outcome measuresTE and FIB-4 score were estimated at the time of recruitment in all participants. Pre-defined cut-off values for F2, extracted from previous studies for TE and FIB-4 score, were compared. A new cut-off value for FIB-4 score was estimated using ROC curve analysis to improve the sensitivity for F2 prediction.ResultsOf the selected 45 TDT patients, 22(49%) were males. FIB-4 score showed a significant linear correlation with TE (r= 0.52;p< 0.0003). The FIB-4 score was improbable to lead to a false classification of TDT patients to have F2 when the FIB-4 cut-off value was 1.3. On the other hand, it had a very low diagnostic yield in missing almost all (except one) of those who had F2. Using a much-lowered cut-off point of 0.32 for FIB-4, we improved the pick-up rate of F2 to 72%.ConclusionsRegardless of the cut-off point, FIB-4 score cannot be used as a good screening tool to pick-up F2 in patients with TDT, irrespective of their splenectomy status. On the contrary, at 1.3 cut off value though FIB-4 is a very poor detector for F2 fibrosis it will not erroneously diagnose F2 fibrosis in those who don’t have it.Article summaryStrengths and limitations of this studyThere is limited information available on the applicability of FIB-4 score to assess significant liver fibrosis in patients with transfusion-dependent beta-thalassemia (TDT).The present study among a Sri Lankan TDT population had their liver fibrosis assessed by FIB-4 score biomarker compared with Transient elastography (TE).Small sample size of the study is one of the major limitations.Even though the liver biopsy is the gold standard method of assessing liver fibrosis, non-invasive TE was used as the reference standard in our study
Structural Basis for the Calmodulin-Mediated Activation of eEF-2K
Authors: Piserchio Andrea , Isiorho Eta A. , Long Kimberly , Bohanon Amanda L. , Kumar Eric A. , Will Nathan , Jeruzalmi David , Dalby Kevin N. , Ghose Ranajeet 
Published: January 2022

AbstractTranslation is a highly energy consumptive process1tightly regulated for optimal protein quality2and adaptation to energy and nutrient availability. A key facilitator of this process is the α-kinase eEF-2K that specifically phosphorylates the GTP-dependent translocase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis3,4. eEF-2K activation requires calmodulin binding and auto-phosphorylation at the primary stimulatory site, T348. Biochemical studies have predicted that calmodulin activates eEF-2K through a unique allosteric process5mechanistically distinct from other calmodulin-dependent kinases6. Here we resolve the atomic details of this mechanism through a 2.3 Å crystal structure of the heterodimeric complex of calmodulin with the functional core of eEF-2K (eEF-2KTR). This structure, which represents the activated T348-phosphorylated state of eEF-2KTR, highlights how through an intimate association with the calmodulin C-lobe, the kinase creates a “spine” that extends from its N-terminal calmodulin-targeting motif through a conserved regulatory element to its active site. Modification of key spine residues has deleterious functional consequences.
The high mutational sensitivity of ccdA antitoxin is linked to codon optimality
Authors: Chandra Soumyanetra , Gupta Kritika , Khare Shruti , Kohli Pehu , Asok Aparna , Mohan Sonali Vishwa , Gowda Harsha , Varadarajan Raghavan 
Published: January 2022

AbstractDeep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, non active-site residues are tolerant to mutations. Here we show that the ccdA antitoxin component of the E.coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and non-synonymous point mutations than inferred previously.
Broad-spectrum mono- and combinational drug therapies for global viral pandemic preparedness
Authors: Ianevski Aleksandr , Yao Rouan , Simonsen Ronja M. , Myhre Vegard , Ravlo Erlend , Kaynova Gerda D. , Zusinaite Eva , White Judith M. , Polyak Stephen J. , Oksenych Valentyn , Windisch Marc P. , Pan Qiuwei , Lastauskienė Eglė , Vitkauskienė Astra , Matukevičius Algimantas , Tenson Tanel , Bjørås Magnar , Kainov Denis E. 
Published: January 2022

AbstractBroadly effective antiviral therapies must be developed to be ready for clinical trials, which should begin soon after the emergence of new life-threatening viruses. Here, we pave the way towards this goal by analyzing conserved druggable virus-host interactions, mechanisms of action and immunomodulatory properties of broad-spectrum antivirals (BSAs), routes of BSA delivery, and BSA interactions with other antivirals. Based on the analysis we developed scoring systems, which allowed us to predict novel BSAs and BSA-containing drug combinations (BCCs). Thus, we have developed a new strategy to broaden the spectrum of BSA indications and predict novel mono-and combinational therapies that can help better prepare for imminent future viral outbreaks.Abstract Figure
Resilient T cell responses to B.1.1.529 (Omicron) SARS-CoV-2 variant
Authors: Jergovic Mladen , Coplen Christopher P. , Uhrlaub Jennifer L. , Beitel Shawn C. , Burgess Jefferey L. , Lutrick Karen , Ellingson Katherine D. , Watanabe Makiko , Nikolich-Žugich Janko 
Published: January 2022

AbstractEmergence of the SARS-CoV-2 variant-of-concern (VOC) B.1.1.529 (Omicron) in late 2021 has raised alarm among scientific and health care communities due to a surprisingly large number of mutations in its spike protein. Public health surveillance indicates that the Omicron variant is significantly more contagious than the previously dominant VOC, B.1.617.2 (Delta). Several early reports demonstrated that Omicron exhibits a higher degree (∼10-30-fold) of escape from antibody neutralization compared to earlier lineage variants. Therefore, it is critical to determine how well the second line of adaptive immunity, T cell memory, performs against Omicron in people following COVID-19 infection and/or vaccination. To that purpose, we analyzed a cohort (n=345 subjects) of two-or three-dose messenger RNA (mRNA) vaccine recipients and COVID-19 post infection subjects (including those receiving 2 doses of mRNA vaccine after infection), recruited to the CDC-sponsored AZ HEROES research study, alongside 32 pre-pandemic control samples. We report that T cell responses against Omicron spike peptides were largely preserved in all cohorts with established immune memory. IFN-γ producing T cell responses remained equivalent to the response against the ancestral strain (WA1/2020), with some (<20%) loss in IL-2 single-or IL-2+IFNγ+ poly-functional responses. Three-dose vaccinated participants had similar responses to Omicron relative to convalescent or convalescent plus two-dose vaccinated groups and exhibited responses significantly higher than those receiving two mRNA vaccine doses. These results provide further evidence that a three-dose vaccine regimen benefits the induction of optimal functional T cell immune memory.
COWO: towards real-time spatiotemporal action localization in videos
Authors: Yi Yang , Sun Yang , Yuan Saimei , Zhu Yiji , Zhang Mengyi , Zhu Wenjun 
Published: January 2022

Purpose
The purpose of this paper is to provide a fast and accurate network for spatiotemporal action localization in videos. It detects human actions both in time and space simultaneously in real-time, which is applicable in real-world scenarios such as safety monitoring and collaborative assembly.

Design/methodology/approach
This paper design an end-to-end deep learning network called collaborator only watch once (COWO). COWO recognizes the ongoing human activities in real-time with enhanced accuracy. COWO inherits from the architecture of you only watch once (YOWO), known to be the best performing network for online action localization to date, but with three major structural modifications: COWO enhances the intraclass compactness and enlarges the interclass separability in the feature level. A new correlation channel fusion and attention mechanism are designed based on the Pearson correlation coefficient. Accordingly, a correction loss function is designed. This function minimizes the same class distance and enhances the intraclass compactness. Use a probabilistic K-means clustering technique for selecting the initial seed points. The idea behind this is that the initial distance between cluster centers should be as considerable as possible. CIOU regression loss function is applied instead of the Smooth L1 loss function to help the model converge stably.

Findings
COWO outperforms the original YOWO with improvements of frame mAP 3% and 2.1% at a speed of 35.12 fps. Compared with the two-stream, T-CNN, C3D, the improvement is about 5% and 14.5% when applied to J-HMDB-21, UCF101-24 and AGOT data sets.

Originality/value
COWO extends more flexibility for assembly scenarios as it perceives spatiotemporal human actions in real-time. It contributes to many real-world scenarios such as safety monitoring and collaborative assembly.
India’s emerging fuel mix for 2050: actions and strategies to decarbonize the transport sector
Authors: Gupta Santanu , Kar Sanjay Kumar , Harichandan Sidhartha 
Published: January 2022

Purpose
This paper aims to review the role of government initiatives for developing clean fuels in India, decarbonize the transport sector and maximize the use of renewable sources of energy. India’s socio-economic prosperity is dependent on modern energy. The authors examine the role of biofuel in India’s emerging fuel mix.

Design/methodology/approach
A 20-year timeframe between 2000 and 2021 was set to learn about the subject and find the existing gaps. Of the 40 research papers, the authors found using keywords and delimiting criteria in the database, the authors have shortlisted 21 papers, which provided the theoretical framework for the study. Additionally, the authors used the government database to develop future projections using compound annual growth rate and trend analysis.

Findings
The study findings suggest that India should strictly implement the Biofuel Policy to promote indigenous production of biofuel to enhance affordability and accessibility. With blending options available with biofuels and biogas, the country can replace the right proportion of fossil fuel use by 2050. It will not only decrease India’s import dependence but also will create new job opportunities, specifically in tribal and remote locations and promote green energy mix. With emerging options like electric vehicle and hydrogen, the transport sector could be decarbonized to a greater extent.

Social implications
Indigenous cleaner fuel adoption and transport sector will generate additional employment and cut down fossil fuel import. Financial savings through reduced fossil fuel import will be directed toward social development.

Originality/value
The paper carries out critical analysis for the active use of modern green fuels in the present and coming days. Such unique analysis must help India to balance its energy basket.
Weaknesses of Malaysian public procurement: a review of auditor general’s reports
Authors: Mohamad Azmi Siti Maryam , Ismail Suhaiza 
Published: January 2022

Purpose
This paper aims to systematically analyze the weaknesses of public procurement in Malaysia as reported in the Auditor General’s Reports from 2011 until 2018. Specifically, the study examines the types of weaknesses, the modes of public procurement involved with the weaknesses, the procurement categories involved with the weaknesses and the key recommendations to mitigate the weaknesses in public procurement.

Design/methodology/approach
A document analysis was adopted in achieving the objective. The Auditor General’s reports and the reports of activities of federal ministries/departments published by the National Audit Department, Malaysia from the year 2011 until 2018 are the main documents used in this study. The data gathered were analyzed using frequency distribution and displayed with descriptive statistics and relevant graphs.

Findings
The findings of the study revealed that the top five reported are non-compliance to scope, specifications and terms of contracts; delayed completion/non-completion of project; poor documentation; low quality of products, service and work; and little or no prior planning. It is also found that direct negotiation mode was reported with the highest issues of public procurement, while the procurement mode with the least public procurement weaknesses is direct purchase. Moreover, it was found that work category is the highest with public procurement issues reported compared to supplies and services. The top recommendations given by the Auditor General were to improve internal control, to enhance monitoring, to establish planning in details, to improve assets management and to take appropriate actions toward contractors and procurement officers when needed.

Originality/value
This is among a few studies that attempted to systematically examine the main issues regarding the public procurement activities in Malaysia. This study highlighted pertinent aspects of the public procurement activities, which need close attention by the relevant authorities to ensure efficient and effective public procurement.
Design and evaluation of a micro resonator structure as a biosensor for droplet analysis with a standard fabrication method
Authors: Eidi Amin , Shamsi Mousa , Badri Ghavifekr Habib 
Published: January 2022

Purpose
In this work, the sensing and actuating elements are designed with interdigitated capacitors away from the sensitive element on which the droplet is placed. This pattern helps to prevent interference of electrical elements with the droplet. Choosing shear resonance mode at this proposed structure minimizes the damping effect of droplet touch by the resonator structure. The glass-based standard fabrication method of the proposed biosensor is presented exactly.

Design/methodology/approach
Mechanical resonator sensors are extremely limited because of the high damping factor and the high electrical conductivity in the aqueous environment. In this work, a molecule detector biosensor is proposed for droplet analysis, which is possible to fabricate using micro-electro-mechanical systems (MEMS) technology. By electromechanical coupling of resonators as a mechanical resonator structure, a standing mechanical wave is formed at this structure by electrostatic actuating elements.

Findings
In this paper, a mechanical resonator structure as a biosensor is proposed for micro-droplet analysis that can be fabricated by MEMS technology. It is designed at a lower cost fabrication method using electrostatic technology and interdigitated capacitors. The response of the biosensor displacement frequency at the resonance frequency of the desired mode is reasonable for measuring the capacitive changes of its output. The mass sensitivity of the proposed biosensor is in the range of 1 ng, and it has a large sensitive area for capturing target molecules.

Originality/value
To evaluate the quality of the proposed design, the stimulated analysis is conducted by COMSOL and results are presented.