bluuebunny/crossref_metadata_2025 huggingface dataset:
The Infectious Disease Ontology in the age of COVID-19
Authors: Babcock Shane , Beverley John , Cowell Lindsay G. , Smith Barry
Published: July 2021

Background

Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules.

Results

To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term acellular structure to cover viruses and other acellular entities studied by virologists. We now distinguish between infectious agents – organisms with an infectious disposition – and infectious structures – acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core’s content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices.

Conclusions

IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises.
Hypoxia and glucose metabolism assessed by FMISO and FDG PET for predicting IDH1 mutation and 1p/19q codeletion status in newly diagnosed malignant gliomas
Authors: Suzuki Kenta , Kawai Nobuyuki , Ogawa Tomoya , Miyake Keisuke , Shinomiya Aya , Yamamoto Yuka , Nishiyama Yoshihiro , Tamiya Takashi
Published: July 2021

Background

Tumor hypoxia and glycolysis have been recognized as determinant factors characterizing tumor aggressiveness in malignant gliomas. To clarify in vivo hypoxia and glucose metabolism in relation to isocitrate dehydrogenase (IDH) mutation and chromosome 1p and 19q (1p/19q) codeletion status, we retrospectively analyzed hypoxia as assessed by positron emission tomography (PET) with [18F]-fluoromisonidazole (FMISO) and glucose metabolism as assessed by PET with [18F]-fluoro-2-deoxy-d-glucose (FDG) in newly diagnosed malignant gliomas.

Methods

In total, 87 patients with newly diagnosed supratentorial malignant (WHO grade III and IV) gliomas were enrolled in this study. They underwent PET studies with FMISO and FDG before surgery. The molecular features and histopathological diagnoses based on the 2016 WHO classification were determined using surgical specimens. Maximal tumor-to-normal ratio (TNR) was calculated for FDG PET, and maximal tumor-to-blood SUV ratio (TBR) was calculated for FMISO PET. The PET uptake values in relation to IDH mutation and 1p/19q codeletion status were statistically analyzed.

Results

In all tumors and malignant astrocytomas, the median FMISO TBR in IDH-wildtype tumors was significantly higher than that in IDH-mutant tumors (P < 0.001 and P < 0.01, respectively). In receiver operating characteristic (ROC) analysis, the area under the curve showed that the sensitivity for the discrimination was moderate (0.7–0.8) and the specificity was low (0.65–0.68). In the same population, the median FDG TNR in IDH-wildtype tumors tended to be higher than that in IDH-mutant tumors, but the difference was not statistically significant. In WHO grade III anaplastic astrocytomas, there were no significant differences in median FMISO TBR or FDG TNR between IDH-mutant and IDH-wildtype tumors. In IDH-mutant WHO grade III anaplastic gliomas, there were no significant differences in median FMISO TBR or FDG TNR between anaplastic astrocytomas and anaplastic oligodendrogliomas.

Conclusions

Tumor hypoxia as assessed by FMISO PET was informative for prediction of the IDH mutation status in newly diagnosed malignant gliomas. However, the accuracy of the discrimination was not satisfactory for clinical application. On the other hand, glucose metabolism as assessed by FDG PET could not differentiate the IDH-mutant status. Moreover, PET studies using FMISO and FDG could not predict IDH mutation and 1p/19q codeletion status in WHO grade III tumors.
Prevalence and demographic, substance use, and mental health correlates of fasting among U.S. college students
Authors: Ganson Kyle T. , Rodgers Rachel F. , Murray Stuart B. , Nagata Jason M.
Published: July 2021

Background

Fasting is an unhealthy behavior that has been frequently used as part of weight loss attempts. To date, little research has been conducted to determine the prevalence and substance use and mental health correlates of fasting among college students. Therefore, the aim of this study was to estimate the prevalence and associations between any (≥ 1 time) and regular (≥ 13 times) occurrences of fasting in the past 4 weeks and substance use and mental health correlates among a large sample of college students from 2016 to 2020.

Methods

Data from four academic survey years (2016–2020; N = 8255) of the national (USA) Healthy Minds Study were analyzed. Unadjusted prevalence of any and regular fasting by survey year and gender was estimated. Multiple logistic regression analyses were conducted to estimate the associations between any and regular fasting and the demographic (age, body mass index, race/ethnicity, sexual orientation, highest parental education), substance use (cigarette use, marijuana use, other illicit drug use, alcohol use), and mental health (depression, anxiety, eating disorder symptoms, suicidal ideation, non-suicidal self-injury) correlates.

Results

Any fasting in the past 4 weeks was common among both men (14.77%) and women (18.12%) and significantly increased from 2016 (10.30%) to 2020 (19.81%) only among men. Regular fasting significantly increased among both men and women from 2016 (men: 1.46%; women: 1.79%) to 2020 (men: 3.53%; women: 6.19%). Among men and women, both any and regular fasting in the past 4 weeks were associated with higher odds of all mental health symptoms, including a positive depression, anxiety, and eating disorder screen, suicidal ideation, and non-suicidal self-injury. Among women, but not men, any and regular fasting in the past 4 weeks were associated with higher odds of marijuana use and other illicit drug use (e.g., cocaine, ecstasy).

Conclusions

The results from this study underscore both the high and increasing prevalence of fasting among a national sample of college students, as well as the substance use and mental health symptoms associated with this behavior. Healthcare professionals both on and off campus should consider screening for fasting behaviors among college students and provide appropriate intervention when needed.
Tolerance intervals in statistical software and robustness under model misspecification
Authors: Cho Kyung Serk , Tony Ng Hon Keung
Published: July 2021

A tolerance interval is a statistical interval that covers at least 100ρ%of the population of interest with a 100(1−α)%confidence, whereρandαare pre-specified values in (0, 1). In many scientific fields, such as pharmaceutical sciences, manufacturing processes, clinical sciences, and environmental sciences, tolerance intervals are used for statistical inference and quality control. Despite the usefulness of tolerance intervals, the procedures to compute tolerance intervals are not commonly implemented in statistical software packages. This paper aims to provide a comparative study of the computational procedures for tolerance intervals in some commonly used statistical software packages including JMP, Minitab, NCSS, Python, R, and SAS. On the other hand, we also investigate the effect of misspecifying the underlying probability model on the performance of tolerance intervals. We study the performance of tolerance intervals when the assumed distribution is the same as the true underlying distribution and when the assumed distribution is different from the true distribution via a Monte Carlo simulation study. We also propose a robust model selection approach to obtain tolerance intervals that are relatively insensitive to the model misspecification. We show that the proposed robust model selection approach performs well when the underlying distribution is unknown but candidate distributions are available.
Analysis of pretreatment factors associated with stability in early class III treatment
Authors: Inoue Yasuko , Deguchi Toru , Hartsfield James K. , Tome Wakako , Kitai Noriyuki
Published: July 2021

Background

The purpose of this study was to identify pretreatment factors associated with the stability of early class III treatment, since most orthodontists start the treatment with their uncertain hypotheses and/or predictions. Subjects consisted of 75 patients with a class III skeletal relationship (ANB < 2° and overjet < 0 mm) who had been consecutively treated with rapid maxillary expansion and facemask and followed until their second phase treatment. The patients were divided into two groups according to whether they showed relapse in follow-up. The stable group maintained their positive overjet (n = 55), and the unstable group experienced relapse with a zero or negative overjet (n = 20). Two general, three dental, and 13 cephalometric pretreatment factors were investigated to determine which factors were associated with stability.

Results

Sex, pretreatment age, and anteroposterior functional shift, which were hypothesized as associated factors, were not related to the stability of early class III treatment. Significant differences were detected between the two groups in the horizontal distance between the maxillary and mandibular molars in centric relation. Cephalometric variables, such as the mandibular length (Ar-Me), Wits appraisal, SN to ramus plane angle (SN-Rm), gonial angle, incisor mandibular plane angle (IMPA), and Frankfort plane to mandibular incisor angle (FMIA) showed significant differences between the groups. The horizontal distance was the most influential factor by logistic regression analysis.

Conclusions

Hypothesis (related to sex, age, functional shift) were rejected. Several cephalometric factors related to the mandible were associated with stability. The horizontal distance between the maxillary and mandibular molars in centric relation was the best predictor of early class III treatment relapse.
Defensible inferences from a nested sequence of logistic regressions: a guide for the perplexed
Authors: Gurkan Gulsah , Benjamini Yoav , Braun Henry
Published: July 2021

Employing nested sequences of models is a common practice when exploring the extent to which one set of variables mediates the impact of another set. Such an analysis in the context of logistic regression models confronts two challenges: (i) direct comparisons of coefficients across models are generally biased due to the changes in scale that accompany the changes in the set of explanatory variables, (ii) conducting a large number of tests induces a problem of multiplicity that can lead to spurious findings of significance if not heeded. This article aims to illustrate a practical strategy for conducting analyses in the face of these challenges. The challenges—and how to address them—are illustrated using a subset of the findings reported by Braun (Large-scale Assess Educ 6(4):1–52, 2018. 10.1186/s40536-018-0058-x), drawn from the Programme for the International Assessment of Adult Competencies (PIAAC), an international, large-scale assessment of adults. For each country in the dataset, a nested pair of logistic regression models was fit in order to investigate the role of Educational Attainment and Cognitive Skills in mediating the impact of family background and demographic characteristics on the location of an individual’s annual income in the national income distribution. A modified version of the Karlson–Holm–Breen (KHB) method was employed to obtain an unbiased estimate of the true differences in the coefficients between nested logistic models. In order to address the issue of multiplicity, a recent generalization of the Benjamini–Hochberg (BH) False Discovery Rate (FDR)-controlling procedure to hierarchically structured hypotheses was employed and compared to two conventional methods. The differences between the changes in coefficients calculated conventionally and with the KHB adjustment varied from negligible to very substantial. When combined with the actual magnitudes of the coefficients, we concluded that the more proximal factors indeed act as strong mediators for the background factors, but less so for Age, and hardly at all for Gender. With respect to multiplicity, applying the FDR-controlling procedure yielded results very similar to those obtained by applying a standard per-comparison procedure, but quite a few more discoveries in comparison to the Bonferroni procedure. The KHB methodology illustrated here can be applied wherever there is interest in comparing nested logistic regressions. Modifications to account for probability sampling are practicable. The categorization of variables and the order of entry should be determined by substantive considerations. On the other hand, the BH procedure is perfectly general and can be implemented to address multiplicity issues in a broad range of settings.
Analysis and prediction of polar motion using MSSA method
Authors: Jin Xin , Liu Xin , Guo Jinyun , Shen Yi
Published: July 2021

Polar motion is the movement of the Earth's rotational axis relative to its crust, reflecting the influence of the material exchange and mass redistribution of each layer of the Earth on the Earth's rotation axis. To better analyze the temporally varying characteristics of polar motion, multi-channel singular spectrum analysis (MSSA) was used to analyze the EOP 14 C04 series released by the International Earth Rotation and Reference System Service (IERS) from 1962 to 2020, and the amplitude of the Chandler wobbles were found to fluctuate between 20 and 200 mas and decrease significantly over the last 20 years. The amplitude of annual oscillation fluctuated between 60 and 120 mas, and the long-term trend was 3.72 mas/year, moving towards N56.79 °W. To improve prediction of polar motion, the MSSA method combining linear model and autoregressive moving average model was used to predict polar motion with ahead 1 year, repeatedly. Comparing to predictions of IERS Bulletin A, the results show that the proposed method can effectively predict polar motion, and the improvement rates of polar motion prediction for 365 days into the future were approximately 50% on average.
Anterolateral ligament reconstruction in addition to primary double-bundle anterior cruciate ligament reconstruction for grade 3 pivot shift improves residual knee instability during surgery
Authors: Kawanishi Yusuke , Kobayashi Makoto , Yasuma Sanshiro , Fukushima Hiroaki , Kato Jiro , Murase Atsunori , Takenaga Tetsuya , Yoshida Masahito , Kuroyanagi Gen , Kawaguchi Yohei , Nagaya Yuko , Murakami Hideki , Nozaki Masahiro
Published: July 2021

Purpose

High-grade pivot shift in the anterior cruciate ligament (ACL) injured knee is a risk factor for postoperative residual pivot shift. Procedures in addition to ACL reconstruction such as anterolateral ligament (ALL) reconstruction have been performed for patients with a high-risk of residual pivot shift. The aim of this study was to investigate the effect of the addition of ALL reconstruction to primary double-bundle ACL reconstruction in patients with preoperative high-grade pivot shift to improve stability as evaluated by quantitative measurement.

Methods

Patients with ACL injuries who showed preoperative grade 3 subjective pivot shift and who underwent primary double-bundle ACL reconstruction combined with ALL reconstructions were retrospectively enrolled. Anterior tibial translation (ATT) in the Lachman test, and acceleration and external rotational angular velocity (ERAV) in the pivot shift were measured as quantitative values. Quantitative values before surgical intervention for ACL-injured knees (ACLD) and uninjured contralateral knees (intact), after temporary fixation of the isolated ACL grafts (ACLR), and subsequently after temporary fixation of both ACL and ALL grafts (ACLR + ALLR) were measured with the patient under general anaesthesia.

Results

In total, 18 patients were included. The ATT was lower in ACLR and ACLR + ALLR than in intact (P = .008 and .005), while there was no significant difference between ACLR and ACLR + ALLR (P > .05). The acceleration of ACLR + ALLR was lower than that for ACLR (P = .008), while there was no significant difference between intact and ACLR or ACLR + ALLR (P > .05). The ERAV of ACLR was higher than that of intact (P < .001), while that of ACLR + ALLR was lower than that of ACLR (P < 0.001), and there was no significant difference in ERAV between intact and ACLR + ALLR (P > 0.05).

Conclusion

According to quantitative assessment of the pivot shift, the addition of ALL reconstruction to primary double-bundle ACL reconstruction improved residual knee instability and restored knee stability during surgery. Combination of ALL reconstruction with primary double-bundle ACL reconstruction was effective for patients with ACL injuries exhibiting a preoperative grade 3 subjective pivot shift.

Level of evidence

IV
Plasma proenkephalin A 119–159 on intensive care unit admission is a predictor of organ failure and 30-day mortality
Authors: Frigyesi Attila , Boström Lisa , Lengquist Maria , Johnsson Patrik , Lundberg Oscar H. M. , Spångfors Martin , Annborn Martin , Cronberg Tobias , Nielsen Niklas , Levin Helena , Friberg Hans
Published: July 2021

Background

Proenkephalin A 119-159 (penKid) has been suggested as a marker of renal failure and poor outcome. We aimed to investigate the association of penKid on ICU admission with organ dysfunction and mortality in a mixed ICU population. In this retrospective, observational study, admission penKid levels from prospectively collected blood samples of consecutive patients admitted to four Swedish ICUs were analysed. The association of penKid with day-two sequential organ failure assessment (SOFA) scores and 30-day mortality was investigated using (ordinal) logistic regression. The predictive power of penKid for 30-day mortality and dialysis was assessed using the area under the receiver operating characteristic curve (AUC).

Results

Of 1978 included patients, 632 fulfilled the sepsis 3-criteria, 190 had a cardiac arrest, and 157 had experienced trauma. Admission penKid was positively associated with 30-day mortality with an odds ratio of 1.95 (95% confidence interval 1.75–2.18, p < 0.001), and predicted 30-day mortality in the entire ICU population with an AUC of 0.71 (95% confidence interval 0.68–0.73) as well as in the sepsis, cardiac arrest and trauma subgroups (AUCs of 0.61–0.84). Correction for admission plasma creatinine revealed that penKid correlated with neurological dysfunction.

Conclusion

Plasma penKid on ICU admission is associated with day-two organ dysfunction and predictive of 30-day mortality in a mixed ICU-population, as well as in sepsis, cardiac arrest and trauma subgroups. In addition to being a marker of renal dysfunction, plasma penKid is associated with neurologic dysfunction in the entire ICU population, and cardiovascular dysfunction in sepsis.
Saltmarsh vegetation and social environment influence flexible seasonal vigilance strategies for two sympatric migratory curlew species in adjacent coastal habitats
Authors: Zhang Jing , Zhang Hang , Liu Yu , Lloyd Huw , Li Jianqiang , Zhang Zhengwang , Li Donglai
Published: July 2021

Background

Animals need to adjust their vigilance strategies when foraging between physically contrasting vegetated and non-vegetated habitats. Vegetated habitats may pose a greater risk for some if vegetation characteristics function as a visual obstruction but benefit others if they serve as protective shelter. Variation in group size, presence of similar species, along with variation in environmental conditions and anthropogenic disturbance can also influence vigilance investment.

Methods

In this study, we quantified the vigilance behaviour of two large-bodied, sympatric migratory curlew species—Far Eastern Curlew (Numenius madagascariensis) and Eurasian Curlew (N. arquata)—in vegetated Suaeda salsa saltmarsh and non-vegetated mudflat habitat in Liaohekou National Nature Reserve, China. We used linear mixed models to examine the effects of habitat type, season, tide time, flock size (conspecific and heterospecific), and human disturbance on curlew vigilance investment.

Results

Both species spent a higher percentage of time under visual obstruction in S. salsa habitat compared to mudflat habitat but in response, only Far Eastern Curlew increased their percentage of vigilance time, indicating that visual obstruction in this habitat is only a concern for this species. There was no evidence that S. salsa vegetation served as a form of cryptic background colouration since neither species decreased their vigilance effect in S. salsa habitat in spring compared to the autumn migration season. The effect of curlew social environment (i.e. flock size) was habitat dependent since percentage of vigilance time by curlews in saltmarsh increased with both the number of individual curlews and number of other birds present, but not in mudflat habitat.

Conclusions

We conclude that both migratory curlew species exhibit a flexible vigilance adjustment strategy to cope with the different environmental and social conditions of adjacent and sharply contrasting coastal habitats, and that the trade-off between the risks of foraging and the abundance of prey may be a relatively common phenomenon in these and other shorebird populations.
Positive change in asthma control using therapeutic patient education in severe uncontrolled asthma: a one-year prospective study
Authors: Zhang Xiaoxian , Lai Zhengdao , Qiu Rihuang , Guo E , Li Jing , Zhang Qingling , Li Naijian
Published: July 2021

Background

Severe asthma is difficult to control. Therapeutic patient education enables patients to better understand their disease and cope with treatment, but the effect of therapeutic patient education in severe uncontrolled asthma is unclear. We evaluated whether therapeutic patient education is effective in improving asthma control and decreasing the frequency of exacerbations in severe uncontrolled asthma.

Methods

This was a prospective, observational, and self-controlled study that enrolled 40 subjects with severe uncontrolled asthma. Patients were seen at a clinic four times (on day 1 and after 3, 6, and 12 months). After baseline data collection, the subjects completed a therapeutic patient education program and were also followed-up via telephone after 1, 2, 4, 5, 7, 8, 9, 10, and 11 months to monitor asthma medication adherence and collect asthma-related information.

Results

Within the 1-year study period, a total of 23 exacerbations were recorded in 14 patients, seven of whom required emergency treatment and two of whom were hospitalized. Twelve months after the standardized therapeutic patient education program, pulmonary function and fractional exhaled nitric oxide levels improved significantly in all 40 patients. Moreover, the scores from three standardized asthma questionnaires and indices suggested improved quality of life in these patients with severe uncontrolled asthma. Serum levels of biomarkers reflecting asthma immune responses did not change between baseline and the 1-year follow-up time point.

Conclusions

Therapeutic patient education is effective in improving asthma control and decreasing exacerbations in patients with severe uncontrolled asthma.
Corporate Social Responsibility (CSR): motivations and challenges of a Multinational Enterprise (MNE) subsidiary’s engagement with host communities in Ghana
Authors: Awuah Lyon Salia , Amoako Kwame Oduro , Yeboah Stephen , Marfo Emmanuel Opoku , Ansu-Mensah Peter
Published: July 2021

This paper aims to explore the motivations and challenges of engaging host communities in CSR practices within the context of Newmont Ahafo Mines (NAM), a subsidiary of a Multinational Mining Enterprise (MNE) operating in Ghana’s mining sector. This paper draws insights from stakeholder theory and interviews conducted with internal stakeholders (management and employees) and stakeholders in host communities (traditional rulers and community members). The findings indicate that effective decision-making, gaining legitimacy, cost savings, management of risks, and accountability are some of the perceived motivations of NAM’s stakeholder engagement in CSR. Nonetheless, the most critical challenges to NAM in improving stakeholder engagement in CSR practices are the lack of community members’ support in CSR projects, communities’ high expectations of NAM on development projects and over-dependency on NAM on the part of host communities. Therefore, it is reasonable for MNEs in emerging economies to attune engagement practices to the host community’s context. This will enable CSR practices and policies to fully exploit the latent benefits of CSR in the mining sector.
Measurement of individual differences in face-identity processing abilities in older adults
Authors: Boutet Isabelle , Meinhardt-Injac Bozana
Published: July 2021

Background

Face-identity processing declines with age. Few studies have examined whether face-identity processing abilities can be measured independently from general cognitive abilities in older adults (OA). This question has practical implications for the assessment of face-identity processing abilities in OA and theoretical implications for the notion of face processing as a specific ability. The present study examined the specificity of face memory and face matching abilities in OA aged 50 + .

Methods

Performance of younger adults (YA) and OA was measured on face tasks: Cambridge Face Memory Task (CFMT), the Glasgow Face Matching Task (GFMT), holistic processing; and tasks of general cognition: fluid intelligence, selective attention, and mental rotation. Data were analyzed using multiple regression models encompassing (i) the CFMT/GFMT and measures of general cognition; and (ii) all face processing tasks.

Results

Across the two age groups, models encompassing all face tasks were significant and accounted for more variance in the data than models encompassing the CFMT/GFMT and measures of general cognition. General cognitive abilities accounted for 17% of variance for the GFMT (p < 0.01) and 3% for the CFMT (p > 0.05).

Discussion

Our results suggest that face memory can be measured independently from general cognition using the CFMT in OA. Implications for the notion of a general face processing factor across the adult lifespan are discussed.
Face mask type affects audiovisual speech intelligibility and subjective listening effort in young and older adults
Authors: Brown Violet A. , Van Engen Kristin J. , Peelle Jonathan E.
Published: July 2021

Identifying speech requires that listeners make rapid use of fine-grained acoustic cues—a process that is facilitated by being able to see the talker’s face. Face masks present a challenge to this process because they can both alter acoustic information and conceal the talker’s mouth. Here, we investigated the degree to which different types of face masks and noise levels affect speech intelligibility and subjective listening effort for young (N = 180) and older (N = 180) adult listeners. We found that in quiet, mask type had little influence on speech intelligibility relative to speech produced without a mask for both young and older adults. However, with the addition of moderate (− 5 dB SNR) and high (− 9 dB SNR) levels of background noise, intelligibility dropped substantially for all types of face masks in both age groups. Across noise levels, transparent face masks and cloth face masks with filters impaired performance the most, and surgical face masks had the smallest influence on intelligibility. Participants also rated speech produced with a face mask as more effortful than unmasked speech, particularly in background noise. Although young and older adults were similarly affected by face masks and noise in terms of intelligibility and subjective listening effort, older adults showed poorer intelligibility overall and rated the speech as more effortful to process relative to young adults. This research will help individuals make more informed decisions about which types of masks to wear in various communicative settings.
BIOlogical Factors that Limit sustAined Remission in rhEumatoid arthritis (the BIO-FLARE study): protocol for a non-randomised longitudinal cohort study
Authors: Rayner Fiona , Anderson Amy E. , Baker Kenneth F. , Buckley Christopher D. , Dyke Bernard , Fenton Sally , Filer Andrew , Goodyear Carl S. , Hilkens Catharien M. U. , Hiu Shaun , Kerrigan Sean , Kurowska-Stolarska Mariola , Matthews Fiona , McInnes Iain , Ng Wan-Fai , Pratt Arthur G. , Prichard Jonathan , Raza Karim , Siebert Stefan , Stocken Deborah , Teare M. Dawn , Young Stephen , Isaacs John D.
Published: July 2021

Background

Our knowledge of immune-mediated inflammatory disease (IMID) aetiology and pathogenesis has improved greatly over recent years, however, very little is known of the factors that trigger disease relapses (flares), converting diseases from inactive to active states. Focussing on rheumatoid arthritis (RA), the challenge that we will address is why IMIDs remit and relapse. Extrapolating from pathogenetic factors involved in disease initiation, new episodes of inflammation could be triggered by recurrent systemic immune dysregulation or locally by factors within the joint, either of which could be endorsed by overarching epigenetic factors or changes in systemic or localised metabolism.

Methods

The BIO-FLARE study is a non-randomised longitudinal cohort study that aims to enrol 150 patients with RA in remission on a stable dose of non-biologic disease-modifying anti-rheumatic drugs (DMARDs), who consent to discontinue treatment. Participants stop their DMARDs at time 0 and are offered an optional ultrasound-guided synovial biopsy. They are studied intensively, with blood sampling and clinical evaluation at weeks 0, 2, 5, 8, 12 and 24. It is anticipated that 50% of participants will have a disease flare, whilst 50% remain in drug-free remission for the study duration (24 weeks). Flaring participants undergo an ultrasound-guided synovial biopsy before reinstatement of previous treatment. Blood samples will be used to investigate immune cell subsets, their activation status and their cytokine profile, autoantibody profiles and epigenetic profiles. Synovial biopsies will be examined to profile cell lineages and subtypes present at flare. Blood, urine and synovium will be examined to determine metabolic profiles. Taking into account all generated data, multivariate statistical techniques will be employed to develop a model to predict impending flare in RA, highlighting therapeutic pathways and informative biomarkers. Despite initial recruitment to time and target, the SARS-CoV-2 pandemic has impacted significantly, and a decision was taken to close recruitment at 118 participants with complete data.

Discussion

This study aims to investigate the pathogenesis of flare in rheumatoid arthritis, which is a significant knowledge gap in our understanding, addressing a major unmet patient need.

Trial registration

The study was retrospectively registered on 27/06/2019 in the ISRCTN registry 16371380.
On the virulence of two Beauveria bassiana strains against the fall webworm, Hyphantria cunea (Durry) (Lepidoptera: Erebidae), larvae and their biological properties in relation to different abiotic factors
Authors: Hu Ruirui , Bai Penghua , Liu Baosheng , Yu Jinping
Published: July 2021

Background

The genus Beauveria is frequently used as a mycoinsecticides in many countries to control insect pests in agriculture, it is being very effective against the fall webworm, Hyphantria cunea (Durry) (Lepidoptera: Erebidae), which is a pest of trees in forests and orchards. Multiple abiotic factors during fungal growth are well known to influence mycelial growth and several physiological adaptations in the conidia produced.

Results

In this study, the pathogenicity of the Beauveria bassiana strains Bb10331 and Bb7725 against H. cunea was evaluated. Peptone potato dextrose agar (PPDA) was used as the medium and colony diameter, conidiation capacity, conidial germination rate were directly affected by relative humidity (RH), illumination, and the ambient pH. The LC50 values of Bb10331 and Bb7725 to H. cunea were 4.72 × 106 and 3.28 × 106 conidia·ml−1, respectively, after 120 h post treatments, while their corresponding LT50 values were 71.13 and 74.54 h at the concentration of 1 × 108 conidia/ml. The Bb7725 had a conidial germination rate than did Bb10331 at the same RH. The two strains grew faster under a dark:light (D:L) photoperiod of 12:12 h, and this particular light condition was also most suitable for their conidia production. The optimum pH for the growth and conidiation of the two strains was approximately 7.0.

Conclusions

Both strains are promising for pest control, possessing effective virulence against H. cunea, but this is slightly stronger in Bb7725 than Bb10331. The values of abiotic factors apt to promote the biological properties of each B. bassiana were different.
Informing resilience building: FAO’s Surveillance Evaluation Tool (SET) Biothreat Detection Module will help assess national capacities to detect agro-terrorism and agro-crime
Authors: Vasconcelos Gioia Gisela , Lamielle Gaël , Aguanno Ryan , ElMasry Ihab , Mouillé Béatrice , De Battisti Cristian , Angot Angélique , Ewann Fanny , Sivignon Adrien , Donachie Daniel , Rozov Orr , Bonbon Étienne , Poudevigne Frédéric , VonDobschuetz Sophie , Plée Ludovic , Kalpravidh Wantanee , Sumption Keith
Published: July 2021

Attacks using animal pathogens can have devastating socioeconomic, public health and national security consequences. The livestock sector has some inherent vulnerabilities which put it at risk to the deliberate or accidental spread of disease. The growing concern of countries about the risks of agro-terrorism and agro-crime has led to efforts to prepare against potential attacks. One recent international effort is the launch of a joint OIE, FAO and INTERPOL project in 2019 to build resilience against agro-terrorism and agro-crime targeting animal health with the financial support of the Weapons Threat Reduction Programme of Global Affairs Canada. Given the importance of strong animal health surveillance systems for the early and effective response to agro-terrorism and agro-crime, the project will use the FAO Surveillance Evaluation Tool (SET) and its new Biothreat Detection Module to evaluate beneficiary countries’ capacities to detect criminal or terrorist animal health events. This paper presents the development of the new SET Biothreat Detection Module and how it will be used to evaluate surveillance for agro-terrorism and agro-crime animal disease threats. The module will be piloted in early 2021 and, once finalized, will be used by beneficiary countries of the joint OIE-FAO-INTERPOL project. Results from evaluations using SET and its Biothreat Detection Module are expected to provide a baseline from which countries can build targeted capacity for animal disease surveillance including early detection and investigation of potential terrorist or criminal events involving zoonotic and non-zoonotic animal pathogens.
Role of multislice computed tomography 3D volumetric analysis in the assessment of the therapeutic response of hepatocellular carcinoma after transarterial chemoembolization
Authors: Osman Mohamed Fouad , Farag Ahmed Shawky Ali , Samy Haney Ahmed , El-Baz Tamer Mahmoud , Elkholy Shaima Fattouh
Published: July 2021

Background

Volumetric analysis is a novel radiological technique used in the measurement of target lesions in three dimensions in order to estimate the lesion’s volume. Recently, it has been used for evaluation of the remaining liver volume after partial hepatectomy and also for evaluation of the response of tumours to treatment. It has been proven to be more accurate than the standard one or two-dimensional measurements, and it is especially useful for the evaluation of complex tumours after radiological interventional methods when the use of standard methods is limited. In the current study, our aim was to evaluate the value of the three-dimensional (3D) volumetric method “Response Evaluation Criteria in Solid Tumours (vRECIST)” and to compare it with the non–three-dimensional methods (RECIST) and modified RECIST (mRECIST) in the assessment of the therapeutic response of hepatocellular carcinoma (HCC) after transarterial chemoembolization (TACE).

Results

A retrospective study was conducted on 50 patients with confirmed radiological or pathological diagnosis of hepatocellular carcinoma (HCC) who underwent TACE as the only interventional procedure and follwed up by triphasic CT 1 and 4 months after treatment. The study revealed a significant difference between mRECIST and vRECIST in the assessment of the therapeutic response of HCC after TACE, a weak agreement was found between both methods in the detection of complete response (CR), partial response (PR), stable disease (SD) or progressive disease (PD). Also, there was no significant agreement between mRECIST and vRECIST regarding the assessment by classifying the patients into responders or nonresponders.

Conclusion

Volumetric analysis is an effective method for measuring the HCC lesions and evaluating its response to locoregional treatment with a significant difference between vRECIST and mRECIST in the assessment of therapeutic response, which in turn help the interventional radiologist to decide the future treatments and change the therapeutic plans. Based on these results, we recommend vRECIST to be an essential part of the assessment of therapeutic response after locoregional therapy.
Diagnostic dilemma of primary neonatal iliopsoas abscess
Authors: Ray Sampurna , Dey Pranab Kumar , Halder Pankaj , Ghosh Arindam
Published: July 2021

Background

Primary iliopsoas abscess is extremely rare in neonates and overlooked easily. It is potentially curable with surgical drainage and broad-spectrum antibiotics if diagnosed early.

Case presentation

A 13-day-old neonate was presented with a swelling and bluish discoloration on the left thigh and groin. There was a restriction of movement of the left lower limb, and he developed high grade fever later on, during hospital stay. In spite of a great dilemma, we could finally reach the diagnosis of primary iliopsoas abscess, performed surgical drainage, and controlled ongoing sepsis. At 3 months follow-up, the patient was doing well and there was no asymmetry in appearance of movements.

Conclusion

High index of suspicion, vigilant clinical examinations, and targeted laboratory investigations with imaging studies are of paramount importance in establishing its diagnosis. This case highlights the diagnostic difficulties and re-evaluates the representative features of neonatal iliopsoas abscess and its management.
Assessing model uncertainty for the scaling function inversion of potential fields
Authors: Chauhan Mahak Singh , Pierri Ivano , Sen Mrinal K. , Fedi Maurizio
Published: July 2021

We have used the very fast simulated annealing algorithm to invert the scaling function along selected ridges, lying in a vertical section formed by upward continuing gravity data to a set of altitudes. The scaling function is formed by the ratio of the field derivative by the field itself, and it is evaluated along the lines formed by the zeros of the horizontal field derivative at a set of altitudes. We also use the same algorithm to invert gravity anomalies only at the measurement altitude. Our goal is to analyze the different models obtained through the two different inversions and to evaluate the relative uncertainties. One main difference is that the scaling function inversion is independent of density and the unknowns are the geometric parameters of the source. The gravity data are instead inverted for the source geometry and the density simultaneously. A priori information used for both the inversions is that the source has a known depth to the top. We examine the results over the synthetic examples of a salt dome structure generated by Talwani’s approach and real gravity data sets over the Mors salt dome (Denmark) and the Decorah Basin (USA). For all of these cases, the scaling function inversion yields models with better sensitivity to specific features of the sources, such as the tilt of the body, and reduced uncertainty. Finally, we analyze the density, which is one of the unknowns for the gravity inversion, and it is estimated from the geometric model for the scaling function inversion. The histograms over the density estimated at many iterations indicate a very concentrated distribution for the scaling function, whereas the density contrast retrieved by the gravity inversion, according to the fundamental ambiguity density/volume, is widely dispersed, making it difficult to assess its best estimate.
Regularization by denoising for simultaneous source separation
Authors: Bahia Breno , Lin Rongzhi , Sacchi Mauricio
Published: July 2021

Denoisers can help solve inverse problems via a recently proposed framework known as regularization by denoising (RED). The RED approach defines the regularization term of the inverse problem via explicit denoising engines. Simultaneous source separation techniques, themselves being a combination of inversion and denoising methods, provide a formidable field to explore RED. We investigate the applicability of RED to simultaneous-source data processing and introduce a deblending algorithm called REDeblending (RDB). The formulation permits developing deblending algorithms in which the user can select any denoising engine that satisfies RED conditions. Two popular denoisers are tested, but the method is not limited to them: frequency-wavenumber thresholding and singular spectrum analysis. We offer synthetically blended data examples to showcase the performance of RDB.
Regional stratigraphy and proximal-to-distal variation of lithology and porosity within a mixed carbonate-siliciclastic system, Mississippian strata of northern and central Oklahoma
Authors: Drummond Katherine A. , Pranter Matthew J. , Grammer Michael G.
Published: July 2021

Mississippian carbonate and silica-rich reservoirs of northern and central Oklahoma formed along a regionally extensive carbonate ramp to basin transect. The stratigraphy, lithology, and porosity characteristics of the Mississippian Meramec and Osage series significantly vary as older ramp carbonates prograde southward and transition into younger calcareous and quartz-rich silt deposits of the Anadarko Basin. Lithofacies identified within the northern carbonate-dominated portion of the system commonly include altered chert, skeletal grainstones, peloidal packstones-grainstones, bioturbated wackestones-packstones, bioturbated mudstones-wackestones, glauconitic sandstones, and siliceous shale. Lithofacies within the southern siliciclastic-dominated portion of the system include structureless to bioturbated sandstones, siltstones, and laminated mudstones, each with varying degrees of carbonate content. We have grouped these core-based lithofacies into dominant lithologies/rock types, which tie to well-log properties. Electrofacies classification methods including the artificial neural network (ANN) and k-means clustering predict lithologies in noncored wells. ANN yielded the highest overall prediction accuracy of 85% for lithologies. Core, well log, and lithology log data establish the regional stratigraphic framework. The Mississippian interval of interest subdivides into 16 stratigraphic zones. A depositional-dip-oriented cross section and the associated reservoir models illustrate the proximal to distal and stratigraphic variability of the lithology and porosity. Lithology trends moving from north to south, from older to younger strata, reveal a carbonate-dominated succession capped by diagenetically altered chert northward shifting into a siliciclastic-dominated interval, which increases in clay content southward. Northward, prospective conventional reservoirs developed near cycle tops within diagenetically replaced cherts and cherty limestones associated with subaerial exposure and sea-level fluctuations. Southward, higher total porosity associates with increased clay content linked to the suppression of calcite cement, forming prospective unconventional targets near the bases of depositional cycles.
Medical Oncology Patient Perceptions of Telehealth Video Visits
Authors: Granberg Rachel E. , Heyer Arianna , Rising Kristin L. , Handley Nathan R. , Gentsch Alexzandra T. , Binder Adam F.
Published: July 2021

PURPOSE

Telehealth in medical oncology has expanded secondary to the COVID-19 pandemic. However, quantitative research on medical oncology telehealth use shows conflicting results on patient satisfaction, whereas qualitative data are sparse. Our qualitative study aimed to identify the factors influencing patient acceptability of video visits for medical oncology care before and at the onset of the expansion of telehealth because of the COVID-19 pandemic.

METHODS

Semi-structured interviews were conducted between November 2019 and April 2020 with 20 patients who participated in a telehealth visit with a medical oncology provider at Thomas Jefferson University.

RESULTS

Of the 20 participants, 13 (65%) were female and 15 (75%) were White, with a mean (standard deviation) age of 60.5 years (11.8). Patients identified convenience, anxiety, COVID-19, and provider preference as positively influencing the acceptability of video visits; however, some patients noted limitations in provider connection, physical examinations, and visit length as disadvantages. Regarding receipt of serious or bad news, some preferred video visits for privacy, immediacy of results, news processing, and family comfort. Others preferred in-person encounters for provider support and the ability to receive written information and in-person referrals.

CONCLUSION

Patient-perceived factors influencing general acceptability, appropriateness of serious and bad news delivery, and future uses of telehealth were unique to each individual, but shared common themes. Understanding each patient's perspective of telehealth acceptability and tailoring use to their preferences is critical for continued utilization. Further research is needed to understand and address reasons for lack of telehealth uptake among certain patients.