bluuebunny/crossref_metadata_2025 huggingface dataset:
The practice of integrated healthcare and the experiences of people in Ghana’s Ashanti region
Authors: Ampomah Irene G. , Malau-Aduli Bunmi S. , Seidu Abdul-Aziz , Malau-Aduli Aduli E. O. , Emeto Theophilus I.
Published: January 2022

Background

The Ghanaian government has implemented interventions that integrate traditional medicine (TM) into its national health system in response to the high prevalence of TM use. However, empirical evidence of the experiences of service users and the practice of integrated health in Ghana is scanty. Therefore, this study explored the experiences of people with TM integration into the formal health system in Ashanti region using an adapted TM integration framework.

Methods

A sequential explanatory mixed methods study design comprising survey administration and in-depth interviews for data collection was utilised to address the research objective. Framework analysis was used in analysing the qualitative data and for triangulation of results.

Results

Participants were aware of licensing and training of TM practitioners in a science-based university in Ghana. However, knowledge of the existence of TM units in selected hospitals in the region was minimal. Integration knowledge was largely influenced by sex, marital status, household size and residential status, where males and urban dwellers were more familiar with the process than females and rural dwellers. Low patronage of integrated health services in the region was attributable to weak cross referrals. However, service users who had engaged with the integrated system recounted a satisfactory outcome.

Conclusion

Service users’ unfamiliarity with the presence of integrated facilities in Ghana could be an impediment to the practice of integrated healthcare. Sensitisation of the public about the practice of an integrated system could refine the Ghanaian integrated system. Regular evaluation of patient satisfaction and outcome measures might also serve as an effective strategy for improving health services delivery since evaluation is becoming an important component of health service design and implementation. There is the need for future studies to focus on exploring the perceptions and experiences of health practitioners and hospital administrators regarding the practice of integrated health in Ghana.
Integrated analysis of 1804 samples of six centers to construct and validate a robust immune-related prognostic signature associated with stromal cell abundance in tumor microenvironment for gastric cancer
Authors: Huo Junyu , Guan Ge , Cai Jinzhen , Wu Liqun
Published: January 2022

Background

Stromal cells in tumor microenvironment could promote immune escape through a variety of mechanisms, but there are lacking research in the field of gastric cancer (GC).

Methods

We identified differential expressed immune-related genes (DEIRGs) between the high- and low-stromal cell abundance GC samples in The Cancer Genome Atlas and GSE84437 datasets. A risk score was constructed basing on univariate cox regression analysis, LASSO regression analysis, and multivariate cox regression analysis in the training cohort (n=772). The median value of the risk score was used to classify patients into groups with high and low risk. We conducted external validation of the prognostic signature in four independent cohorts (GSE26253, n=432; GSE62254, n=300; GSE15459, n=191; GSE26901, n=109) from the Gene Expression Omnibus (GEO) database. The immune cell infiltration was quantified by the CIBERSORT method.

Results

The risk score contained 6 genes (AKT3, APOD, FAM19A5, LTBP3, NOV, and NOX4) showed good performance in predicting 5-year overall survival (OS) rate and 5-year recurrence-free survival (RFS) rate of GC patients. The risk death and recurrence of GC patients growing with the increasing risk score. The patients were clustered into three subtypes according to the infiltration of 22 kinds of immune cells quantified by the CIBERSORT method. The proportion of cluster A with the worst prognosis in the high-risk group was significantly higher than that in the low-risk group; the risk score of cluster C subtype with the best prognosis was significantly lower than that of the other two subtypes.

Conclusion

This study established and validated a robust prognostic model for gastric cancer by integrated analysis 1804 samples of six centers, and its mechanism was explored in combination with immune cell infiltration characterization.
Integrated weighted gene coexpression network analysis identifies Frizzled 2 (FZD2) as a key gene in invasive malignant pleomorphic adenoma
Authors: Han Zhenyuan , Ren Huiping , Sun Jingjing , Jin Lihui , Wang Qin , Guo Chuanbin , Tian Zhen
Published: January 2022

Background

Invasive malignant pleomorphic adenoma (IMPA) is a highly malignant neoplasm of the oral salivary glands with a poor prognosis and a considerable risk of recurrence. Many disease-causing genes of IMPA have been identified in recent decades (e.g., P53, PCNA and HMGA2), but many of these genes remain to be explored. Weighted gene coexpression network analysis (WGCNA) is a newly emerged algorithm that can cluster genes and form modules based on similar gene expression patterns. This study constructed a gene coexpression network of IMPA via WGCNA and then carried out multifaceted analysis to identify novel disease-causing genes.

Methods

RNA sequencing (RNA-seq) was performed for 10 pairs of IMPA and normal tissues to acquire the gene expression profiles. Differentially expressed genes (DEGs) were screened out with the cutoff criteria of |log2 Fold change (FC)|> 1 and adjusted p value  < 0.05. Then, WGCNA was applied to systematically identify the hidden diagnostic hub genes of IMPA.

Results

In this research, a total of 1970 DEGs were screened out in IMPA tissues, including 1056 upregulated DEGs and 914 downregulated DEGs. Functional enrichment analysis was performed for identified DEGs and revealed an enrichment of tumor-associated GO terms and KEGG pathways. We used WGCNA to identify gene module most relevant with the histological grade of IMPA. The gene FZD2 was then recognized as the hub gene of the selected module with the highest module membership (MM) value and intramodule connectivity in protein–protein interaction (PPI) network. According to immunohistochemistry (IHC) staining, the expression level of FZD2 was higher in low-grade IMPA than in high-grade IMPA.

Conclusion

FZD2 shows an expression dynamic that is negatively correlated with the clinical malignancy of IMPA and it plays a central role in the transcription network of IMPA. Thus, FZD2 serves as a promising histological indicator for the precise prediction of IMPA histological stages.
Examining the association between opium use, cigarette smoking and alcohol consumption with the liver enzyme levels in a population-based study: Fasa Persian cohort data
Authors: Bijani Mostafa , Dehghan Azizallah , Razavi Saeed , Karimi Shahnaz
Published: January 2022

Objectives

Opium use, cigarette smoking, and alcohol consumption are serious health problems in many countries including Iran. The present study aimed to examine the association between the opium use, cigarette smoking and alcohol consumption with liver enzyme levels in Southern Iran. This analytical cross-sectional study was conducted in 2020. The entire population of the Fasa Persian cohort study in the southern region of Iran was selected as the sample. Accordingly, 10,145 people participated in the study.

Results

Results indicated that there was a significant relationship between cigarette smoking and alcohol consumption with liver enzymes (AST, ALT, and ALP). There was also a significant relationship between inhaled opium and liver enzymes, but oral opium revealed no significant relationship with the activity of liver enzymes. Accordingly, policymakers of the health care system are recommended to hold educational programs to improve the health literacy level of the society and take effective preventative strategies in reducing the use of these substances.
The role of the microbiota in the management of intensive care patients
Authors: Szychowiak Piotr , Villageois-Tran Khanh , Patrier Juliette , Timsit Jean-François , Ruppé Étienne
Published: January 2022

The composition of the gut microbiota is highly dynamic and changes according to various conditions. The gut microbiota mainly includes difficult-to-cultivate anaerobic bacteria, hence knowledge about its composition has significantly arisen from culture-independent methods based on next-generation sequencing (NGS) such as 16S profiling and shotgun metagenomics. The gut microbiota of patients hospitalized in intensive care units (ICU) undergoes many alterations because of critical illness, antibiotics, and other ICU-specific medications. It is then characterized by lower richness and diversity, and dominated by opportunistic pathogens such as Clostridioides difficile and multidrug-resistant bacteria. These alterations are associated with an increased risk of infectious complications or death. Specifically, at the time of writing, it appears possible to identify distinct microbiota patterns associated with severity or infectivity in COVID-19 patients, paving the way for the potential use of dysbiosis markers to predict patient outcomes. Correcting the microbiota disturbances to avoid their consequences is now possible. Fecal microbiota transplantation is recommended in recurrent C. difficile infections and microbiota-protecting treatments such as antibiotic inactivators are currently being developed. The growing interest in the microbiota and microbiota-associated therapies suggests that the control of the dysbiosis could be a key factor in the management of critically ill patients. The present narrative review aims to provide a synthetic overview of microbiota, from healthy individuals to critically ill patients. After an introduction to the different techniques used for studying the microbiota, we review the determinants involved in the alteration of the microbiota in ICU patients and the latter’s consequences. Last, we assess the means to prevent or correct microbiota alteration.
Health data collection methods and procedures across EU member states: findings from the InfAct Joint Action on health information
Authors: Unim Brigid , Mattei Eugenio , Carle Flavia , Tolonen Hanna , Bernal-Delgado Enrique , Achterberg Peter , Zaletel Metka , Seeling Stefanie , Haneef Romana , Lorcy Anne-Charlotte , Van Oyen Herman , Palmieri Luigi
Published: January 2022

Background

Health-related data are collected from a variety of sources for different purposes, including secondary use for population health monitoring (HM) and health system performance assessment (HSPA). Most of these data sources are not included in databases of international organizations (e.g., WHO, OECD, Eurostat), limiting their use for research activities and policy making. This study aims at identifying and describing collection methods, quality assessment procedures, availability and accessibility of health data across EU Member States (MS) for HM and HSPA.

Methods

A structured questionnaire was developed and administered through an online platform to partners of the InfAct consortium form EU MS to investigate data collections applied in HM and HSPA projects, as well as their methods and procedures. A descriptive analysis of the questionnaire results was performed.

Results

Information on 91 projects from 18 EU MS was collected. In these projects, data were mainly collected through administrative sources, population health interview or health examination surveys and from electronic medical records. Tools and methods used for data collection were mostly mandatory reports, self-administered questionnaires, or record linkage of various data sources. One-third of the projects shared data with EU research networks and less than one-third performed quality assessment of their data collection procedures using international standardized criteria. Macrodata were accessible via open access and reusable in 22 projects. Microdata were accessible upon specific request and reusable in 15 projects based on data usage licenses. Metadata was available for the majority of the projects, but followed reporting standards only in 29 projects. Overall, compliance to FAIR Data principles (Findable, Accessible, Interoperable, and Reusable) was not optimal across the EU projects.

Conclusions

Data collection and exchange procedures differ across EU MS and research data are not always available, accessible, comparable or reusable for further research and evidence-based policy making. There is a need for an EU-level health information infrastructure and governance to promote and facilitate sharing and dissemination of standardized and comparable health data, following FAIR Data principles, across the EU.
Mapping emergent public engagement in societal transitions: a scoping review
Authors: Revez Alexandra , Dunphy Niall , Harris Clodagh , Rogan Fionn , Byrne Edmond , McGookin Connor , Bolger Paul , Ó Gallachóir Brian , Barry John , Ellis Geraint , O’Dwyer Barry , Boyle Evan , Flood Stephen , Glynn James , Mullally Gerard
Published: January 2022

Background

Transition discourses are gaining prominence in efforts to imagine a future that adequately addresses the urgent need to establish low carbon and climate resilient pathways. Within these discourses the ‘public’ is seen as central to the creation and implementation of appropriate interventions. The role of public engagement in societal transformation while essential, is also complex and often poorly understood. The purpose of this paper is to enhance our understanding regarding public engagement and to address the often superficial and shallow policy discourse on this topic.

Main text

The paper offers a review of evolving literature to map emergent public engagement in processes of transition and change. We adopt a pragmatic approach towards literature retrieval and analysis which enables a cross-disciplinary and cross-sectoral review. We use a scoping review process and the three spheres of transformation framework (designated as the practical, political and personal spheres) to explore trends within this complex research field. The review draws from literature from the last two decades in the Irish context and looks at emergence and evolving spaces of public engagement within various systems of change including energy, food, coastal management and flood adaptation, among others.

Conclusions

The results highlight the siloed and fragmented way in which public engagement in transitions is carried and we propose a more cross-sectoral and cross-disciplinary approach which depends on bringing into dialogue often contrasting theories and perspectives. The paper also illustrates some shifting engagement approaches. For instance, nexus articles between the practical and political spheres suggest deeper forms of public engagement beyond aggregated consumer behaviour to align technological delivery with institutional and societal contexts. While most articles in the practical sphere draw largely on techno-economic insights this influence and cross-disciplinarity is likely to draw in further innovations. Nexus articles between the political and personal sphere are also drawing on shifting ideas of public engagement and largely stress the need to disrupt reductive notions of engagement and agency within our institutions. Many of these articles call attention to problems with top-down public engagement structures and in various ways show how they often undermine and marginalise different groups.
Toxic metal concentrations and Cu–Zn–Pb isotopic compositions in tires
Authors: Jeong Hyeryeong
Published: January 2022

Background

Particles from non-exhaust emissions derived from traffic activities are a dominant cause of toxic metal pollution in urban environments. Recently, studies applying multiple isotope values using the Iso-source and positive matrix factorization (PMF) models have begun to be used as useful tools to evaluate the contribution of each pollution source in urban environments. However, data on the metal concentrations and isotopic compositions of each potential source are lacking. Therefore, this study presents data on toxic metals and Cu, Zn, and Pb isotopic compositions in tires, which are one of the important non-exhaust emission sources.

Findings

Among the toxic metals, Zn had the highest concentration in all tire samples, and the mean concentrations were in the order of Zn > Cu > Pb > Sn > Sb > Ni > Cr > As > Cd. Ni, Zn, Sn, and Sb had higher concentrations in domestic tires (South Korea), and the Cu, Cd, and Pb concentrations were relatively higher in imported tires. The mean values of δ65CuAE647, δ66ZnIRMM3702, and 206Pb/207Pb ranged from − 1.04 to − 0.22‰, − 0.09 to − 0.03‰, and 1.1242 to 1.1747, respectively. The concentrations and isotopic compositions of Cu and Pb in the tires showed large differences depending on the product and manufacturer. However, the differences in Zn concentration and δ66ZnIRMM3702 values were very small compared with those of Cu and Pb. The relationships of the Zn concentration and isotopic composition showed that domestic tires are clearly distinguishable from imported tires. Bi-plots of Cu, Zn, and Pb isotopic compositions indicated that tires can be clearly discriminated from natural-origin and other non-exhaust traffic emission sources.

Conclusions

The multi-isotope signatures of Cu, Zn, and Pb exhibited different isotopic values for other non-exhaust traffic emission sources than for tires, and application of the multi-isotope technique may be a powerful method for distinguishing and managing non-exhaust sources of metal contamination in urban environments.
An exploratory assessment of the legislative framework for combating counterfeit medicines in South Africa
Authors: Moshoeshoe R. J. , Enslin G. M. , Katerere D. R.
Published: January 2022

Background

Substandard and Falsified (SF) medical products are a growing global concern. They harm the individual patient, the healthcare system and the economy. The World Health Organisation (WHO) has highlighted contributing factors globally: insufficient national medicine regulation, poor enforcement of existing legislation, weak stakeholder collaboration and the rise of novel viruses, such as the COVID-19. The study aimed to assess the legislative and policy framework and institutional relationships governing pharmaceuticals and anti-counterfeiting strategies.

Methods

The study was explorative and consisted of two phases. The first phase was between 2016 and 2017. It looked at document analysis (annual reports and press releases from 2011 to 2016) from government institutions involved in medicines regulation and law enforcement for SF seizure reports between 2004 and 2017. The second phase was between 2016 and 2018 through in-depth semi-structured interviews (seven in total) with selected stakeholders.

Results

First Phase—the data collected and reported by various departments was sporadic and did not always correlate for the same periods indicating, a lack of a central reporting system and stakeholder collaboration. In South Africa, counterfeiting of medicines mainly involves the smuggling of non-registered goods. The most common counterfeit items were painkillers, herbal teas, herbal ointments, while some were medical devices. Furthermore, Customs identified South Africa as a transhipment point for SF infiltration to neighbouring countries with less robust regulatory systems. Second phase—interview transcripts were analysed by thematic coding. These were identified as the adequacy of legislation, institutional capacity, enforcement and post-market surveillance, stakeholder collaboration and information sharing, and public education and awareness.

Conclusion

Document analysis and interviews indicate that South Africa already has a national drug policy and legislative framework consistent with international law. However, there is no specific pharmaceutical legislation addressing the counterfeiting of medicines. Law enforcement has also been complicated by poor stakeholder engagement and information sharing.
Hesitancy in COVID-19 vaccine uptake and its associated factors among the general adult population: a cross-sectional study in six Southeast Asian countries
Authors: Marzo Roy Rillera , Sami Waqas , Alam Md. Zakiul , Acharya Swosti , Jermsittiparsert Kittisak , Songwathana Karnjana , Pham Nhat Tan , Respati Titik , Faller Erwin Martinez , Baldonado Aries Moralidad , Aung Yadanar , Borkar Sharmila Mukund , Essar Mohammad Yasir , Shrestha Sunil , Yi Siyan
Published: January 2022

Background

Vaccines are effective and reliable public health interventions against viral outbreaks and pandemics. However, hesitancy regarding the Coronavirus disease (COVID-19) vaccine is evident worldwide. Therefore, understanding vaccination-related behavior is critical in expanding the vaccine coverage to flatten the infection curve. This study explores the public perception regarding COVID-19 vaccination and identifies factors associated with vaccine hesitancy among the general adult populations in six Southeast Asian countries.

Methods

Using a snowball sampling approach, we conducted a descriptive cross-sectional study among 5260 participants in Indonesia, Malaysia, Myanmar, Philippines, Thailand, and Vietnam between February and May 2021. Binary logistic regression analysis with a backward conditional approach was applied to identify factors associated with COVID-19 vaccine hesitancy.

Results

Of the total, 50.6% were female, and the median age was 30 years (range: 15–83 years). The majority of the participants believed that vaccination effectively prevents and controls COVID-19 (81.2%), and 84.0% would accept COVID-19 vaccines when they become available. They agreed that health providers’ advice (83.0%), vaccination convenience (75.6%), and vaccine costs (62.8%) are essential for people to decide whether to accept COVID-19 vaccines. About half (49.3%) expressed their hesitancy to receive the COVID-19 vaccines. After adjustment for other covariates, COVID-19 vaccine hesitancy was significantly associated with age, residential area, education levels, employment status, and family economic status. Participants from Indonesia, Myanmar, Thailand, and Vietnam were significantly more likely to express hesitancy in receiving COVID-19 vaccines than those from Philippines.

Conclusions

In general, participants in this multi-country study showed their optimistic perception of COVID-19 vaccines’ effectiveness and willingness to receive them. However, about half of them still expressed their hesitancy in getting vaccinated. The hesitation was associated with several socioeconomic factors and varied by country. Therefore, COVID-19 vaccination programs should consider these factors essential for increasing vaccine uptake in the populations.
The accuracy of Pleth Variability Index for directed fluid optimization in donors in living donor liver transplantation
Authors: Hilal Abdou Amr M. , Abdou Khaled M. , Kamal Mohammed M.
Published: January 2022

Background

Fluid management strongly affects hepatic resection and aims to reduce intraoperative bleeding during living donation. The Pleth Variability Index (PVI) is a tool to assess the fluid responsiveness from the pulse oximeter waveform; we evaluated the efficacy and accuracy of finger PVI compared to pulse pressure variation (PPV) from arterial waveform in predicting the fluid response in donor hepatectomy patients with the guide of non-invasive cardiac output (CO) measurements. We recruited forty patients who were candidates for right lobe hepatectomy for liver transplantation under conventional general anesthesia methods. During periods of intraoperative hypovolemia not affected by surgical manipulation, PVI, PPV, and CO were recorded then compared with definitive values after fluid bolus administration of 3–5 ml/kg aiming to give a 10% increase in CO which classified the patients into responders and non-responders.

Results

Both PPV and PVI showed a significant drop after fluid bolus dose (P < 0.001) leading to an increase of the CO (P < 0.0001), and the area under the curve was 0.934, 0.842 (95% confidence interval, 0.809 to 0.988, 0.692 to 0.938) and the standard error was 0.0336, 0.124, respectively. Pairwise comparison of PPV and PVI showed non-significant predictive value between the two variables (P = 0.4605); the difference between the two areas was 0.0921 (SE 0125 and 95% CI − 0.152 to 0.337).

Conclusions

PVI is an unreliable indicator for fluid response in low-risk donors undergoing right lobe hepatectomy compared to PPV. We need further studies with unbiased PVI monitors in order to implement a non-invasive and safe method for fluid responsiveness.
A case of two shunts in the endovascular treatment of type II Abernethy syndrome
Authors: Bombardier Brenden , Alli Adam , Rohr Aaron , Collins Zachary , Raval Kavi
Published: January 2022

Background

Abernethy malformation is a rare condition defined by a congenital extrahepatic portosystemic shunt, often leading to absence or hypoplasia of the intrahepatic portal venous system. Although there are no consensus treatment guidelines, interventional techniques now offer minimally invasive treatment options for Abernethy malformations. This case report describes a case of Abernethy Syndrome Type II where the patient had two separate extrahepatic portosystemic shunts treated with endovascular occlusion with two Amplatzer plugs and demonstrates the feasibility of this treatment for this rare condition. This case was in a young adult, adding to the scarce literature of treatment for Abernethy syndrome in the adult population.

Case presentation

We report a case of a 20-year-old female patient with neurocognitive behavioral difficulty, voracious appetite, and chronic encephalopathy secondary to type II Abernethy malformation with not one, but two extrahepatic portosystemic shunts. The patient had failed medical management and was not a liver transplant candidate. Therefore, she presented to us for an endovascular treatment option. The two shunts were treated with endovascular occlusion using Amplatzer vascular plugs. Following embolization, flow into the hypoplastic portal vein improved with near complete occlusion of flow into the portosystemic shunts, thus restoring blood flow into the native portal system. At 3 month follow up, a CT demonstrated complete occlusion of the two portosystemic shunts, and a portal vein diminutive in caliber. The portal vein measured 7 mm in diameter on both pre and post-procedure CT scans. The total volume of the liver was found to be 843 cm3 on pre-procedure CT & 1191 cm3 on post-procedure CT.

Conclusions

This report demonstrates the feasibility of using endovascular embolization to treat Abernethy II malformations. The management strategy of Type II Abernethy Syndrome should be to redirect blood flow into the hypoplastic native portal system, allowing for physiologic hepatic metabolism of splanchnic blood, hypertrophy of the portal system, and growth of the liver from the increased trophic flow.
A decade of research on patterns and architectures for IoT security
Authors: Rajmohan Tanusan , Nguyen Phu H. , Ferry Nicolas
Published: January 2022

Security of the Internet of Things (IoT)-based Smart Systems involving sensors, actuators and distributed control loop is of paramount importance but very difficult to address. Security patterns consist of domain-independent time-proven security knowledge and expertise. How are they useful for developing secure IoT-based smart systems? Are there architectures that support IoT security? We aim to systematically review the research work published on patterns and architectures for IoT security (and privacy). Then, we want to provide an analysis on that research landscape to answer our research questions. We follow the well-known guidelines for conducting systematic literature reviews. From thousands of candidate papers initially found in our search process, we have systematically distinguished and analyzed thirty-six (36) papers that have been peer-reviewed and published around patterns and architectures for IoT security and privacy in the last decade (January 2010–December 2020). Our analysis shows that there is a rise in the number of publications tending to patterns and architectures for IoT security in the last three years. We have not seen any approach of applying systematically architectures and patterns together that can address security (and privacy) concerns not only at the architectural level, but also at the network or IoT devices level. We also explored how the research contributions in the primary studies handle the different issues from the OWASP Internet of Things (IoT) top ten vulnerabilities list. Finally, we discuss the current gaps in this research area and how to fill in the gaps for promoting the utilization of patterns for IoT security and privacy by design.
The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula
Authors: Park Tansol , Cersosimo Laura M. , Radloff Wendy , Zanton Geoffrey I. , Li Wenli
Published: January 2022

Background

Targeted modification of the dairy calf ruminal microbiome has been attempted through rumen fluid inoculation to alter productive phenotypes later in life. However, sustainable effects of the early life interventions have not been well studied, particularly on the metabolically active rumen microbiota and its functions. This study investigated the sustained effects of adult-derived rumen fluid inoculations in pre-weaning dairy calves on the active ruminal microbiome of post-weaned dairy calves analyzed via RNA-sequencing.

Results

Two different adult-derived microbial inocula (bacterial- or protozoal-enriched rumen fluid; BE or PE, respectively) were administered in pre-weaned calves (3–6 weeks) followed by analyzing active rumen microbiome of post-weaned calves (9 weeks). The shared bacterial community at the genus level of 16S amplicon-seq and RNA-seq datasets was significantly different (P = 0.024), 21 out of 31 shared major bacterial genera differed in their relative abundance between the two analytic pipelines. No significant differences were found in any of the prokaryotic alpha- and beta-diversity measurements (P > 0.05), except the archaeota that differed for BE based on the Bray–Curtis dissimilarity matrix (P = 0.009). Even though the relative abundances of potentially transferred microbial and functional features from the inocula were minor, differentially abundant prokaryotic genera significantly correlated to various fermentation and animal measurements including butyrate proportion, body weight, and papillae length and counts. The overall microbial functions were affected quantitatively by BE and qualitatively by PE (P < 0.05), and this might be supported by the individual KEGG module and CAZymes profile differences. Exclusive networks between major active microbial (bacterial and archaeal genera) and functional features (KEGG modules) were determined which were differed by microbial inoculations.

Conclusions

This study demonstrated that actively transcribed microbial and functional features showed reliable connections with different fermentations and animal development responses through adult rumen fluid inoculations compared to our previous 16S amplicon sequencing results. Exclusive microbial and functional networks of the active rumen microbiome of dairy calves created by BE and PE might also be responsible for the different ruminal and animal characteristics. Further understanding of the other parts of the gastrointestinal tract (e.g., abomasum, omasum, and small intestine) using metatranscriptomics will be necessary to elucidate undetermined biological factors affected by microbial inoculations.
Agreement between low-dose and ultra-low-dose chest CT for the diagnosis of viral pneumonia imaging patterns during the COVID-19 pandemic
Authors: Bahrami-Motlagh Hooman , Moharamzad Yashar , Izadi Amoli Golnaz , Abbasi Sahar , Abrishami Alireza , Khazaei Mehdi , Davarpanah Amir H. , Sanei Taheri Morteza
Published: January 2022

Background

Chest CT scan has an important role in the diagnosis and management of COVID-19 infection. A major concern in radiologic assessment of the patients is the radiation dose. Research has been done to evaluate low-dose chest CT in the diagnosis of pulmonary lesions with promising findings. We decided to determine diagnostic performance of ultra-low-dose chest CT in comparison to low-dose CT for viral pneumonia during the COVID-19 pandemic.

Results

167 patients underwent both low-dose and ultra-low-dose chest CT scans. Two radiologists blinded to the diagnosis independently examined ultra-low-dose chest CT scans for findings consistent with COVID-19 pneumonia. In case of any disagreement, a third senior radiologist made the final diagnosis. Agreement between two CT protocols regarding ground-glass opacity, consolidation, reticulation, and nodular infiltration were recorded. On low-dose chest CT, 44 patients had findings consistent with COVID-19 infection. Ultra-low-dose chest CT had sensitivity and specificity values of 100% and 98.4%, respectively for diagnosis of viral pneumonia. Two patients were falsely categorized to have pneumonia on ultra-low-dose CT scan. Positive predictive value and negative predictive value of ultra-low-dose CT scan were respectively 95.7% and 100%. There was good agreement between low-dose and ultra-low-dose methods (kappa = 0.97; P < 0.001). Perfect agreement between low-dose and ultra-low-dose scans was found regarding diagnosis of ground-glass opacity (kappa = 0.83, P < 0.001), consolidation (kappa = 0.88, P < 0.001), reticulation (kappa = 0.82, P < 0.001), and nodular infiltration (kappa = 0.87, P < 0.001).

Conclusion

Ultra-low-dose chest CT scan is comparable to low-dose chest CT for detection of lung infiltration during the COVID-19 outbreak while maintaining less radiation dose. It can also be used instead of low-dose chest CT scan for patient triage in circumstances where rapid-abundant PCR tests are not available.
Rates of sustainment in the Universal Stages of Implementation Completion
Authors: Wong Dylan Randall , Schaper Holle , Saldana Lisa
Published: January 2022

Background

Sustainment is a desirable outcome of implementation, but its precise definition remains unclear, contributing to the difficulty of identifying a generalized rate of sustainment. Several studies and reviews on the topic differ on both definition and levels of analysis. Furthermore, methodological limitations might have influenced the results, including the unknown quality with which some interventions were delivered. The Universal Stages of Implementation Completion (UniSIC) is a standardized measurement tool that tracks the implementation process and milestone completion across a wide range of real-world implementations—this provides a unique opportunity to identify a generalized rate of sustainment.

Methods

UniSIC data was captured from the SIC website on 27 September 2020 and included data from all sites (n = 1778) that had been tracked to date. Data were restricted to sites that achieved competency in program delivery, and thus had a newly adopted program worthy of sustainment. Dates and indicator variables of implementation activities were combined to form two alternate definitions of sustainment: sustained (start-up) was achieved if sites continued to deliver services 2 years past their program start-up date; sustained (competent) was achieved if sites continued to deliver services 2 years past their competence and/or certification date. Of sites eligible for inclusion based on these definitions (N = 208), descriptive analyses were conducted to determine a rate of sustainment for all programs that successfully started a program. These definitions were also applied to a combined sample for a general rate of sustainment among all sites. Rates of competency among both a sample of sites that started up and a combined sample were also identified.

Results

The rate of competence was 58.5% and the rate of sustained (start-up) was 37.1%, while the rate of sustained (competent) was 25.1%. The rates of competence and sustainment among the combined samples were far lower: 15.6% for competence, 6.8% for sustained (start-up), and 4.4% for sustained (competent).

Conclusions

These identified rates of sustainment are accurate initial estimates of sustainment of community-based practices, or in general. Future research on rates of sustainment should carefully define measures of sustainment and be transparent about the real-world conditions on which analyses are centered.
The role of veterinarians in the One Health approach to antimicrobial resistance perspectives in Jordan
Authors: Bazzi Randa , Alaboudi Akram , Rácz Gábor
Published: January 2022

This study aims to evaluate the role of Jordanian veterinarians in terms of their knowledge, attitudes and common practices in combating antimicrobial resistance (AMR) and summarize the registered veterinary drugs between 2017 2020. Descriptive study data were collected using a standardized questionnaire that focused on the knowledge, attitudes, and practices of Jordanian veterinarians. The findings were analyzed descriptively; 84% of the participants agreed with the statement on the definition of AMR. The majority (95.65%) of participants agreed that AMR is a challenge for the veterinary sector in Jordan and that it should be prioritized over other zoonotic diseases. Approximately 69% of the participants believed that the misuse and overuse of antimicrobials by unqualified, fraudulent, or unauthorized practitioners is the primary reason for the rise of cases associated with AMR and the challenges that accompany these. The most common practice among the respondents in this study was to recommend clients (e.g., farmers and owners) to practice good animal husbandry (80.00%). The study also revealed that there was a significant difference (p = 0.015) between attendance at AMR training sessions and the professional sector (private, public, and academic) of the veterinarians. This study underscores the importance of implementing a continuous education program on AMR so as to enhance the all-round knowledge of veterinarians and improve their advisory skills. In addition, laws should be enacted to ensure that veterinarians prescribe the correct antimicrobials and to improve surveillance systems for monitoring the use of antimicrobials in veterinary medicine.
eSyM: An Electronic Health Record–Integrated Patient-Reported Outcomes–Based Cancer Symptom Management Program Used by Six Diverse Health Systems
Authors: Hassett Michael J. , Cronin Christine , Tsou Terrence C. , Wedge Jason , Bian Jessica , Dizon Don S. , Hazard-Jenkins Hannah , Osarogiagbon Raymond U. , Wong Sandra , Basch Ethan , Austin Toby , McCleary Nadine , Schrag Deborah
Published: January 2022

PURPOSE

Collecting patient-reported outcomes (PROs) can improve symptom control and quality of life, enhance doctor-patient communication, and reduce acute care needs for patients with cancer. Digital solutions facilitate PRO collection, but without robust electronic health record (EHR) integration, effective deployment can be hampered by low patient and clinician engagement and high development and deployment costs. The important components of digital PRO platforms have been defined, but procedures for implementing integrated solutions are not readily available.

METHODS

As part of the NCI's IMPACT consortium, six health care systems partnered with Epic to develop an EHR-integrated, PRO-based electronic symptom management program (eSyM) to optimize postoperative recovery and well-being during chemotherapy. The agile development process incorporated user-centered design principles that required engagement from patients, clinicians, and health care systems. Whenever possible, the system used validated content from the public domain and took advantage of existing EHR capabilities to automate processes.

RESULTS

eSyM includes symptom surveys on the basis of the PRO-Common Terminology Criteria for Adverse Events (PRO-CTCAE) plus two global wellness questions; reminders and symptom self-management tip sheets for patients; alerts and symptom reports for clinicians; and population management dashboards. EHR dependencies include a secure Health Insurance Portability and Accountability Act-compliant patient portal; diagnosis, procedure and chemotherapy treatment plan data; registries that identify and track target populations; and the ability to create reminders, alerts, reports, dashboards, and charting shortcuts.

CONCLUSION

eSyM incorporates validated content and leverages existing EHR capabilities. Build challenges include the innate technical limitations of the EHR, the constrained availability of site technical resources, and sites' heterogenous EHR configurations and policies. Integration of PRO-based symptom management programs into the EHR could help overcome adoption barriers, consolidate clinical workflows, and foster scalability and sustainability. We intend to make eSyM available to all Epic users.
Precision Medicine Landscape of Genomic Testing for Patients With Cancer in the National Institutes of Health All of Us Database Using Informatics Approaches
Authors: Ronquillo Jay G. , Lester William T.
Published: January 2022

PURPOSE

The rapid growth of biomedical data ecosystems has catalyzed research for oncology and precision medicine. We leverage federal cloud-based precision medicine databases and tools to better understand the current landscape of precision medicine and genomic testing for patients with cancer.

METHODS

Retrospective observational study of genomic testing for patients with cancer in the National Institutes of Health All of Us Research Program, with the cancer cohort defined as having at least two documented or reported cancer diagnoses.

RESULTS

There were 5,678 (1.8%) All of Us participants in the cancer cohort, with a significant difference between cancer status by age category, sex, race, and ethnicity ( P < .001 for all). There were 295 (5.2%) patients with cancer who received genomic testing compared with 6,734 (2.2%) of noncancer patients, with 752 genomic tests commonly focused on gene mutations (primarily pharmacogenomics), molecular pathology, or clinical cytogenetic reports.

CONCLUSION

Although not yet ubiquitous, diverse clinical genomic analyses in oncology can set the stage to grow the practice of precision medicine by integrating research patient data repositories, cancer data ecosystems, and biomedical informatics.
New Era for Malignant Pleural Mesothelioma: Updates on Therapeutic Options
Authors: Tsao Anne S. , Pass Harvey I. , Rimner Andreas , Mansfield Aaron S.
Published: January 2022

Malignant pleural mesothelioma (MPM) is a rare malignancy with few treatment options. Recent advances have led to US Food and Drug Administration approvals and changes in the standard of care with a novel biomedical device approved for use with platinum-pemetrexed, and also for immunotherapy agents to be included as a frontline treatment option in unresectable disease. Although predictive biomarkers for systemic therapy are not currently in use in clinical practice, it is essential to correctly identify the MPM histology to determine an optimal treatment plan. Patients with nonepithelioid MPM may have a greater magnitude of benefit to dual immunotherapy checkpoint inhibitors and this regimen should be preferred in the frontline setting for these patients. However, all patients with MPM can derive benefit from immunotherapy treatments, and these agents should ultimately be used at some point during their treatment journey. There are ongoing studies in the frontline unresectable setting that may further define the frontline therapy space, but a critical area of research will need to focus on the immunotherapy refractory population. This review article will describe the new developments in the areas of biology with genomics and chromothripsis, and also focus on updates in treatment strategies in radiology, surgery, radiation, and medical oncology with cellular therapies. These recent innovations are generating momentum to find better therapies for this disease.
Surgical Issues for Operable Early-Stage Non–Small-Cell Lung Cancer
Authors: Donington Jessica , Schumacher Lana , Yanagawa Jane
Published: January 2022

Surgical care for early stage non–small-cell lung cancer continuously evolves with new procedures, techniques and care pathways. The most obvious recent change was the transition to minimally invasive procedures, but numerous other aspects of care have also been refined to improve safety and tolerability. These care advancements are essential as we move into an era with increased early detection as a result of screening and greater indications for the use of adjuvant and neoadjuvant strategies.
Managing Central Nervous System Spread of Lung Cancer: The State of the Art
Authors: Tsui David Chun Cheong , Camidge D. Ross , Rusthoven Chad G.
Published: January 2022

Brain metastases (BrM) are common in both non–small-cell lung cancer and small-cell lung cancer. Substantial progress in BrM management has occurred in the past decade related to advances in both radiation and medical oncology. Recent and ongoing radiation trials have focused on increasing the candidacy for focal therapy of BrM with stereotactic radiosurgery; reducing the toxicity and improving patient selection for whole brain radiotherapy; and, in small-cell lung cancer, evaluating brain magnetic resonance imaging surveillance without prophylactic cranial irradiation, hippocampal avoidance in prophylactic cranial irradiation and whole brain radiotherapy, and the role of upfront stereotactic radiosurgery for BrM. In medical oncology, the development of multiple tyrosine kinase inhibitors with encouraging CNS activity and emerging data on the CNS activity of immune checkpoint inhibitors in some patients have opened the door to novel systemic and multidisciplinary treatment strategies for the management of BrM. Future research will focus on more robust characterizations of the CNS activity of targeted therapy and immunotherapies, as well as optimal integration and patient selection for multidisciplinary strategies involving CNS-active drugs, radiation therapy, and CNS surveillance.
Isocitrate Dehydrogenase–Mutated Cholangiocarcinoma: Natural History and Clinical Outcomes
Authors: Wintheiser Grant , Zemla Tyler , Shi Qian , Tran Nguyen , Prasai Kritika , Tella Sri Harsha , Mody Kabir , Ahn Daniel , Borad Mitesh , Bekaii-Saab Tanios , Mahipal Amit
Published: January 2022

Purpose

Clinical-pathologic features and natural history of patients with isocitrate dehydrogenase ( IDH)-mutant intrahepatic cholangiocarcinoma (CCA) are not well characterized. Here, we sought to describe the natural history, clinical phenotype, and prognostic impact of advanced, IDH-mutated CCA.

METHODS

We conducted a multicentric, retrospective analysis of patients with IDH-mutated (IDH1 or IDH2) CCA between 2010 and 2020. Median overall survival (OS) and progression-free survival (PFS) analyses were performed using the Kaplan-Meier method. Chi-square test was used to analyze disease control rate (DCR) and overall response rate (ORR). Matched controls were used for comparing survival between patients with and without IDH mutations (mIDH).

RESULTS

Sixty-five patients with IDH-mutated CCA were included. All patients had intrahepatic CCA. On first-line chemotherapy, median OS and median PFS were 21.2 months and 8.3 months, respectively. Notably, median OS (32.4 v 19.5 months, P = .12) and PFS (18.0 v 8.0 months, P = .12) were not significantly affected by disease status at presentation (locally advanced v metastatic, respectively). Median OS was significantly longer in patients with mIDH (21.2 v 10.5 months; P < .01). First-line gemcitabine-containing regimens had a significantly higher DCR and ORR than non–gemcitabine-containing regimens (DCR: 75% v 33%, P = .01; ORR: 39% v 0%, P = .02). In patients receiving IDH inhibitor therapy, median PFS was 4.6 months with a DCR of 29%.

CONCLUSION

CCA with m IDH confers a unique subtype resulting in a better survival compared with that of counterparts. IDH inhibitors represent a promising therapeutic option in later lines of therapy in this subgroup.