bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of microbiological diagnosis on the clinical course of spondylodiscitis
Authors: Stangenberg Martin , Mende Klaus Christian , Mohme Malte , Krätzig Theresa , Viezens Lennart , Both Anna , Rohde Holger , Dreimann Marc
Published: July 2021

Purpose

This study sought to recognize differences in clinical disease manifestations of spondylodiscitis depending on the causative bacterial species.

Methods

We performed an evaluation of all spondylodiscitis cases in our clinic from 2013–2018. 211 patients were included, in whom a causative bacterial pathogen was identified in 80.6% (170/211). We collected the following data; disease complications, comorbidities, laboratory parameters, abscess occurrence, localization of the infection (cervical, thoracic, lumbar, disseminated), length of hospital stay and 30-day mortality rates depending on the causative bacterial species. Differences between bacterial detection in blood culture and intraoperative samples were also recorded.

Results

The detection rate of bacterial pathogens through intraoperative sampling was 66.3% and could be increased by the results of the blood cultures to a total of 80.6% (n = 170/211). S. aureus was the most frequently detected pathogen in blood culture and intraoperative specimens and and was isolated in a higher percentage cervically than in other locations of the spine. Bacteremic S. aureus infections were associated with an increased mortality (31.4% vs. overall mortality of 13.7%, p = 0.001), more frequently developing complications, such as shock, pneumonia, and myocardial infarction. Comorbidities, abscesses, length of stay, sex, and laboratory parameters all showed no differences depending on the bacterial species.

Conclusion

Blood culture significantly improved the diagnostic yield, thus underscoring the need for a structured diagnostic approach. MSSA spondylodiscitis was associated with increased mortality and a higher incidence of complications.
Avoid, Trap, and Mitigate: Development of an Evidence-Based Crisis Management Framework in Surgery
Authors: Gogalniceanu Petrut , Karydis Nikolaos , Loukopoulos Ioannis , Kessaris Nicos , Sevdalis Nick , Mamode Nizam
Published: July 2021

BACKGROUND:

Increasingly, surgeons are adopting broader roles in emergency response, on both clinical and executive levels. These have highlighted the need to develop healthcare-specific crisis management systems. Cross-professional research between safety-critical industries is a valuable method for learning crisis control. Commercial aviation, in particular, has been used to drive innovation in surgical safety. This study aimed to identify, adapt, and operationalize a surgical crisis management framework based on current practice in commercial aviation.

STUDY DESIGN:

A multimethod qualitative study interrogated safety experts in commercial aviation and healthcare. Stage I used immersive observational fieldwork in commercial aviation practice. Stage II performed semi-structured interviews with senior airline pilots. “Snowball” sampling targeted professional networks, recruiting 17 pilots from 4 airlines. Thematic analysis was used to derive a model of crisis management. Stage III undertook 3 focus groups with 5 pilots and 5 healthcare safety specialists. Expert consensus methods were used to adapt the model to clinical practice.

RESULTS:

Interview data provided 2,698 verbatim quotes on crisis management from aviation experts with a combined flying experience of 188,000 hours. Aviation crisis management was structured in 3 phases: avoid, trap, and mitigate. Adapted to clinical practice, these translated to crisis preparedness, recovery, and containment interventions. Additionally, the study identified 7 types of implementation tools and 9 crisis management skills that could be used to operationalize this framework in surgical practice.

CONCLUSIONS:

Surgical crisis management can follow the avoid, trap, and mitigate framework used in commercial aviation. Implementation relies on the combined use of crisis skills and performance tools. Crisis management should be delivered as part of a systems-based approach that relies on well-integrated failure management models. Simulation and in-situ validation of this framework is needed.
Outbreak of Burkholderia contaminans endophthalmitis traced to a clinic ventilation system
Authors: Spilker Theodore , Kratholm Jens , Depoorter Eliza , Vandamme Peter , LiPuma John J.
Published: July 2021

We describe the follow-up investigation of an outbreak of endophthalmitis due to Burkholderia contaminans following cataract surgery in a single clinic. Whole-genome sequence analysis of bacteria recovered from affected patients and the clinic identified the clinic’s ventilation system as the source of infection.
Modelling the Vadret da Tschierva, Switzerland: calibration with the historical length record and future response to climate change
Authors: Oerlemans Johannes , Keller Felix
Published: July 2021

The Vadret da Tschierva (Vd Tschierva) is a 4 km long glacier in the Swiss Alps spanning an altitude range of 2400–4049 m a.s.l. Length observations since 1855 show steady retreat interrupted by a period of advance from 1965 until 1985. The total retreat is ~2200 m (period 1855–2018). We have studied the Vd Tschierva with a flowline model, combined with ‘buckets’ that represent steep hanging glaciers and ice-free rock faces delivering mass to the main stream. The model is calibrated by a control method, in which an ELA history is objectively determined by finding the best match between observed and simulated glacier length. There is a modest correlation between the reconstructed ELA and an ELA record based on meteorological observations at Segl-Maria (only 8 km away from the glacier). It is difficult to reproduce the observed length record when the glacier model is driven by climate model output (Coupled Model Intercomparison Project 5). We have calculated the future evolution of the Vd Tschierva for different rates of ELA rise. For a constant rise of 4 ${\rm m\;}{\rm a}^{ \hbox{-} 1}$, we predict that the glacier length will change from the current 3.2 km to ~1.7 km in the year 2100.
Workplace Contact and Support for Anti-Immigration Parties
Authors: ANDERSSON HENRIK , DEHDARI SIRUS H.
Published: July 2021

How does an increased presence of immigrants in the workplace affect anti-immigration voting behavior? While cooperative interactions between natives and immigrants can reduce intergroup prejudice, immigrant coworkers might be regarded as a threat to native-born workers’ labor market position. We combine detailed Swedish workplace data with precinct-level election outcomes for a large anti-immigration party (the Sweden Democrats) to study how the share of non-Europeans in the workplace affects opposition to immigration. We show that the share of non-Europeans in the workplace has a negative effect on support for the Sweden Democrats and that this effect is solely driven by same-skill contact in small workplaces. We interpret these results as supporting the so-called contact hypothesis: that increased interactions with minorities can reduce opposition to immigration among native-born voters, which, in turn, leads to lower support for anti-immigration parties.
ON HIGHER FROBENIUS–SCHUR INDICATORS
Authors: LIU YANJUN , WILLEMS WOLFGANG
Published: July 2021

Similarly to the Frobenius–Schur indicator of irreducible characters, we consider higher Frobenius–Schur indicators$\nu _{p^n}(\chi ) = |G|^{-1} \sum _{g \in G} \chi (g^{p^n})$for primespand$n \in \mathbb {N}$, whereGis a finite group and$\chi $is a generalised character ofG. These invariants give answers to interesting questions in representation theory. In particular, we give several characterisations of groups via higher Frobenius–Schur indicators.
Ketogenic diets, physical activity and body composition: a review
Authors: Ashtary-Larky Damoon , Bagheri Reza , Bavi Hoda , Baker Julien S. , Moro Tatiana , Mancin Laura , Paoli Antonio
Published: July 2021

Obesity remains a serious relevant public health concern throughout the world despite related countermeasures being well understood (i.e. mainly physical activity and an adjusted diet). Among different nutritional approaches, there is a growing interest in ketogenic diets (KD) to manipulate body mass (BM) and to enhance fat mass loss. KD reduce the daily amount of carbohydrate intake drastically. This results in increased fatty acid utilisation, leading to an increase in blood ketone bodies (acetoacetate, 3-β-hydroxybutyrate and acetone) and therefore metabolic ketosis. For many years, nutritional intervention studies have focused on reducing dietary fat with little or conflicting positive results over the long term. Moreover, current nutritional guidelines for athletes propose carbohydrate-based diets to augment muscular adaptations. This review discusses the physiological basis of KD and their effects on BM reduction and body composition improvements in sedentary individuals combined with different types of exercise (resistance training or endurance training) in individuals with obesity and athletes. Ultimately, we discuss the strengths and the weaknesses of these nutritional interventions together with precautionary measures that should be observed in both individuals with obesity and athletic populations. A literature search from 1921 to April 2021 using Medline, Google Scholar, PubMed, Web of Science, Scopus and Sportdiscus Databases was used to identify relevant studies. In summary, based on the current evidence, KD are an efficient method to reduce BM and body fat in both individuals with obesity and athletes. However, these positive impacts are mainly because of the appetite suppressive effects of KD, which can decrease daily energy intake. Therefore, KD do not have any superior benefits to non-KD in BM and body fat loss in individuals with obesity and athletic populations in an isoenergetic situation. In sedentary individuals with obesity, it seems that fat-free mass (FFM) changes appear to be as great, if not greater, than decreases following a low-fat diet. In terms of lean mass, it seems that following a KD can cause FFM loss in resistance-trained individuals. In contrast, the FFM-preserving effects of KD are more efficient in endurance-trained compared with resistance-trained individuals.
Seroprevalence of Strongyloides stercoralis among patients with leptospirosis in northern Iran: a descriptive cross-sectional study
Authors: Varzegar P. , Bayani M. , Kalantari N. , Nasiri-kenari M. , Amini Navaie B. , Mollalo A. , Rostami A.
Published: July 2021

Strongyloidiasis and leptospirosis are neglected tropical diseases that have affected many countries across the world. In this study, we evaluated the seroprevalence of Strongyloides stercoralis among patients with leptospirosis in northern Iran. We evaluated 156 laboratory- or clinically confirmed leptospirosis cases. The overall seroprevalence of S. stercoralis was 32.0% (95% confidence interval (CI): 27.4–36.5%, 50/156). Seropositivity was significantly associated with agricultural activities (odds ratio (OR): 2.84, 95% CI: 1.0–8.77) and gastrointestinal disorders (OR: 2.4, 95% CI: 1.1–4.9). Laboratory findings indicated that seropositivity of S. stercoralis was significantly associated with decreased levels of platelet and elevated levels of creatinine, alanine aminotransferase and aspartate aminotransferase (P < 0.05). Our findings suggested a higher exposure to S. stercoralis larvae among patients with leptospirosis. The public health and medical communities may benefit from this research through preventive measures to improve farmers’ knowledge and awareness regarding strongyloidiasis and leptospirosis and the associated risk factors.
A daily diary study into the effects on mental health of COVID-19 pandemic-related behaviors
Authors: Shaw Philip , Blizzard Sam , Shastri Gauri , Kundzicz Paul , Curtis Brenda , Ungar Lyle , Koehly Laura
Published: July 2021

Background

Recommendations for promoting mental health during the COVID-19 pandemic include maintaining social contact, through virtual rather than physical contact, moderating substance/alcohol use, and limiting news and media exposure. We seek to understand if these pandemic-related behaviors impact subsequent mental health.

Methods

Daily online survey data were collected on adults during May/June 2020. Measures were of daily physical and virtual (online) contact with others; substance and media use; and indices of psychological striving, struggling and COVID-related worry. Using random-intercept cross-lagged panel analysis, dynamic within-person cross-lagged effects were separated from more static individual differences.

Results

In total, 1148 participants completed daily surveys [657 (57.2%) females, 484 (42.1%) males; mean age 40.6 (s.d.12.4) years]. Daily increases in news consumed increased COVID-related worrying the next day [cross-lagged estimate = 0.034 (95% CI 0.018–0.049), FDR-adjustedp= 0.00005] andvice versa[0.03 (0.012–0.048), FDR-adjustedp= 0.0017]. Increased media consumption also exacerbated subsequent psychological struggling [0.064 (0.03–0.098), FDR-adjustedp= 0.0005]. There were no significant cross-lagged effects of daily changes in social distancing or virtual contact on later mental health.

Conclusions

We delineate a cycle wherein a daily increase in media consumption results in a subsequent increase in COVID-related worries, which in turn increases daily media consumption. Moreover, the adverse impact of news extended to broader measures of psychological struggling. A similar dynamic did not unfold between the daily amount of physical or virtual contact and subsequent mental health. Findings are consistent with current recommendations to moderate news and media consumption in order to promote mental health.
Do employment promotion policies affect employment or job transfer among older adults? Evidence from Japan
Authors: Jiang Mingyu
Published: July 2021

In most rapidly ageing industrialised countries, ageing problems have become an important social issue. In Japan, owing to the rapidly ageing population, the government has been intervening in both the demand side and supply side of labour to increase employment of older adults. This study examines labour supply responses to the increasing pension eligibility age and labour demand responses to company expansion and the abolition of the employee selection mechanism. This study is based on Japanese longitudinal survey data (Keio Household Panel Survey) from 2008 to 2018. Since employment law revisions and social security revisions are inextricably linked, one way to examine the effect of revisions to both simultaneously is to investigate them by cohort. The difference-in-difference model was used to compare revision-affected cohorts born between April 1953 and January 1956 and unaffected cohorts born between April 1949 and March 1953. It was found that the revisions had almost no impact on the employment of older adults and their receipt of pensions. However, they did have significant positive effects on job transfers and resignations. Hence, although the system was modified, it also gave companies the option of placing older adults in associated companies and of retaining some routes for older adults to retire, much as before the revisions.
Changes in Multiple Birth Rates and Parental Demographic Factors in South Korea During the Last Four Decades: 1981–2019
Authors: Hur Yoon-Mi
Published: July 2021

Over the previous decades, twinning rates worldwide have increased remarkably. This study aimed to describe changes in multiple birth rates and related demographic characteristics, such as maternal age and the level of education of parents in South Korea from 1981 to 2019. This study analyzed birth data obtained from the Korean Statistical Information Service. From 1981 to 2019, the total twinning rate increased from 5 to 22.5 pairs per 1000 births. This rapid increase was due to an increase in dizygotic twin births, which mainly occurred in mothers aged between 30 and 39 years. The average maternal age of multiples increased from 26.06 years in 1981 to 33.98 years in 2019, suggesting that a delay in childbearing contributed to the increase in the twinning rate. The percentage of mothers of multiples who completed a college or higher degree (CHD) increased by 1000% from 1981 to 2019, indicating that a sharp increase in the level of education of females in part explains the delay in childbearing. The percentages of individuals who completed a CHD were higher among parents of multiples than among those of singletons in recent years when public funding arrangements for fertility treatments were available. This result suggested that completion of higher education may be associated with increased use of assisted reproductive technology (ART) independent of the financial status of couples. Taken together, the analysis suggested that increased maternal age, ART and the increased number of females who completed CHD may be responsible for the remarkable increase in the rates of multiple births in South Korea in the last four decades.
Evaluation of panicle removal methods and crop topping applications as supplemental tools for wild oat (Avena fatua) management
Authors: Tidemann Breanne D. , Harker K. Neil , Shirtliffe Steve J. , Willenborg Christian J. , Johnson Eric N. , Sroka Elizabeth , Zuidhof Jennifer , Duddu Hema
Published: July 2021

Increased frequency and occurrence of herbicide-resistant biotypes heightens the need for alternative wild oat management strategies. This study aimed to exploit the height differential between wild oat and crops by targeting wild oat between panicle emergence and seed shed timing. Two field studies were conducted either in Lacombe, AB, or Lacombe, AB and Saskatoon, SK, from 2015 to 2017. In the first study, we compared panicle removal methods: hand clipping, use of a hedge trimmer, and a selective herbicide crop topping application to a weedy check and an industry standard in-crop herbicide application in wheat. These treatments were tested early (at panicle emergence), late (at initiation of seed shed), or in combination at one location over 3 yr. In the second study, we investigated optimal timing of panicle removal via a hedge trimmer with weekly removals in comparison to a weedy check in wheat and lentil. This study was conducted at two locations, Lacombe, AB, and Saskatoon, SK, over 3 yr. Among all the tested methods, the early crop topping treatment consistently had the largest impact on wild oat density, dockage, seedbank, and subsequent year crop yield. The early (at panicle emergence) or combination of early and late (at initiation of seed shed) treatments tended to reduce wild oat populations the following season the most compared to the late treatments. Subsequent wild oat populations were not influenced by panicle removal timing, but only by crop and location interactions. Panicle removal timing did significantly affect wild oat dockage in the year of treatment, but no consistent optimal timing could be identified. However, the two studies together highlight additional questions to be investigated, as well as the opportunity to manage wild oat seedbank inputs at the panicle emergence stage of the wild oat lifecycle.
Getting to the Bottom of Trawling’s Carbon Emissions
Authors: Averett Nancy
Published: July 2021

A new model shows that bottom trawling, which stirs up marine sediments as weighted nets scrape the ocean floor, may be releasing more than a billion metric tons of carbon every year.
The zinc finger transcription factor, KLF2, protects against COVID-19 associated endothelial dysfunction
Authors: Xu Suowen , Liu Yujie , Ding Yu , Luo Sihui , Zheng Xueying , Wu Xiumei , Liu Zhenghong , Ilyas Iqra , Chen Suyu , Han Shuxin , Little Peter J. , Jain Mukesh K. , Weng Jianping
Published: July 2021

Coronavirus disease 2019 (COVID-19) is regarded as an endothelial disease (endothelialitis) with its patho-mechanism being incompletely understood. Emerging evidence has demonstrated that endothelial dysfunction precipitates COVID-19 and its accompanying multi-organ injuries. Thus, pharmacotherapies targeting endothelial dysfunction have potential to ameliorate COVID-19 and its cardiovascular complications. The objective of the present study is to evaluate whether kruppel-like factor 2 (KLF2), a master regulator of vascular homeostasis, represents a therapeutic target for COVID-19-induced endothelial dysfunction. Here, we demonstrate that the expression of KLF2 was reduced and monocyte adhesion was increased in endothelial cells treated with COVID-19 patient serum due to elevated levels of pro-adhesive molecules, ICAM1 and VCAM1. IL-1β and TNF-α, two cytokines elevated in cytokine release syndrome in COVID-19 patients, decreased KLF2 gene expression. Pharmacologic (atorvastatin and tannic acid) and genetic (adenoviral overexpression) approaches to augment KLF2 levels attenuated COVID-19-serum-induced increase in endothelial inflammation and monocyte adhesion. Next-generation RNA-sequencing data showed that atorvastatin treatment leads to a cardiovascular protective transcriptome associated with improved endothelial function (vasodilation, anti-inflammation, antioxidant status, anti-thrombosis/-coagulation, anti-fibrosis, and reduced angiogenesis). Finally, knockdown of KLF2 partially reversed the ameliorative effect of atorvastatin on COVID-19-serum-induced endothelial inflammation and monocyte adhesion. Collectively, the present study implicates loss of KLF2 as an important molecular event in the development of COVID-19-induced vascular disease and suggests that efforts to augment KLF2 levels may be therapeutically beneficial.
Identification of a seven-long non-coding RNA signature associated with Jab1/CSN5 in predicting hepatocellular carcinoma
Authors: Ma Weijie , Yao Ye , Xu Gang , Wu Xiaoling , Li Jinghua , Wang Ganggang , Chen Xi , Wang Kunlei , Chen Yirang , Guo Yonghua , Li Yongsheng , Tan Deli , Guo Hui , Liu Zhisu , Yuan Yufeng , Claret Francois X.
Published: July 2021

Hepatocellular carcinoma (HCC) is a leading cause of cancer death worldwide, accounting for over 700,000 deaths each year. The lack of predictive and prognostic biomarkers for HCC, with effective therapy, remains a significant challenge for HCC management. Long non-coding RNAs (lncRNAs) play a key role in tumorigenesis and have clinical value as potential biomarkers in the early diagnosis and prediction of HCC. Jun activation domain-binding protein 1 (Jab1, also known as COP9 signalosome subunit 5, CSN5) is a potential oncogene that plays a critical role in the occurrence of HCC. Here, we performed a comprehensive analysis for Jab1/CSN5-associated lncRNAs to predict the prognosis of HCC. The differentially expressed (DE) lncRNAs between in HCC were analyzed based on the TCGA RNA-seq data. We detected 1031 upregulated lncRNAs in 371 HCC tissues and identified a seven-lncRNA signature strongly correlated with Jab1/CSN5 (SNHG6, CTD3065J16.9, LINC01604, CTD3025N20.3, KB-1460A1.5, RP13-582O9.7, and RP11-29520.2). We further evaluated the prognostic significance of these lncRNAs by GEPIA (http://gepia.cancer-pku.cn/). The expression data in 364 liver tumors indicated that this seven-lncRNA signature could better predict worse survival in HCC patients. Moreover, 35 clinical HCC samples were evaluated to assess the validity and reproducibility of the bioinformatic analysis. We found that the targeted lncRNAs were upregulated, with a strong association with Jab1/CSN5 and prognostic value in HCC. Functional enrichment analysis by Gene Ontology (GO) showed that these seven prognostic lncRNAs exhibit oncogenic properties and are associated with prominent hallmarks of cancer. Overall, our findings demonstrate the clinical implication of Jab1/CSN5 with the seven‐lncRNAs in predicting survival for patients with HCC.
Visualizing the strongly reshaped skyrmion Hall effect in multilayer wire devices
Authors: Tan Anthony K. C. , Ho Pin , Lourembam James , Huang Lisen , Tan Hang Khume , Reichhardt Cynthia J. O. , Reichhardt Charles , Soumyanarayanan Anjan
Published: July 2021

Magnetic skyrmions are nanoscale spin textures touted as next-generation computing elements. When subjected to lateral currents, skyrmions move at considerable speeds. Their topological charge results in an additional transverse deflection known as the skyrmion Hall effect (SkHE). While promising, their dynamic phenomenology with current, skyrmion size, geometric effects and disorder remain to be established. Here we report on the ensemble dynamics of individual skyrmions forming dense arrays in Pt/Co/MgO wires by examining over 20,000 instances of motion across currents and fields. The skyrmion speed reaches 24 m/s in the plastic flow regime and is surprisingly robust to positional and size variations. Meanwhile, the SkHE saturates at ∼22∘, is substantially reshaped by the wire edge, and crucially increases weakly with skyrmion size. Particle model simulations suggest that the SkHE size dependence — contrary to analytical predictions — arises from the interplay of intrinsic and pinning-driven effects. These results establish a robust framework to harness SkHE and achieve high-throughput skyrmion motion in wire devices.
Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease
Authors: Sahoo Debashis , Swanson Lee , Sayed Ibrahim M. , Katkar Gajanan D. , Ibeawuchi Stella-Rita , Mittal Yash , Pranadinata Rama F. , Tindle Courtney , Fuller Mackenzie , Stec Dominik L. , Chang John T. , Sandborn William J. , Das Soumita , Ghosh Pradipta
Published: July 2021

Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents.
Morphological screening of mesenchymal mammary tumor organoids to identify drugs that reverse epithelial-mesenchymal transition
Authors: Zhao Na , Powell Reid T. , Yuan Xueying , Bae Goeun , Roarty Kevin P. , Stossi Fabio , Strempfl Martina , Toneff Michael J. , Johnson Hannah L. , Mani Sendurai A. , Jones Philip , Stephan Clifford C. , Rosen Jeffrey M.
Published: July 2021

The epithelial-mesenchymal transition (EMT) has been implicated in conferring stem cell properties and therapeutic resistance to cancer cells. Therefore, identification of drugs that can reprogram EMT may provide new therapeutic strategies. Here, we report that cells derived from claudin-low mammary tumors, a mesenchymal subtype of triple-negative breast cancer, exhibit a distinctive organoid structure with extended “spikes” in 3D matrices. Upon a miR-200 induced mesenchymal-epithelial transition (MET), the organoids switch to a smoother round morphology. Based on these observations, we developed a morphological screening method with accompanying analytical pipelines that leverage deep neural networks and nearest neighborhood classification to screen for EMT-reversing drugs. Through screening of a targeted epigenetic drug library, we identified multiple class I HDAC inhibitors and Bromodomain inhibitors that reverse EMT. These data support the use of morphological screening of mesenchymal mammary tumor organoids as a platform to identify drugs that reverse EMT.
Self-supplied drinking water in low- and middle-income countries in the Asia-Pacific
Authors: Foster Tim , Priadi Cindy , Kotra Krishna Kumar , Odagiri Mitsunori , Rand Emily Christensen , Willetts Juliet
Published: July 2021

There is increasing awareness of household self-supply and the role it can play in securing water for domestic needs in low- and middle-income countries (LMICs), but its scale across the Asia-Pacific has not previously been quantified. This study analysed 77 datasets from 26 countries to estimate the prevalence of self-supplied drinking water, and its associated trends in LMICs in South Asia, Southeast Asia and the Pacific. When factoring in temporal trends, results suggest that >760 million people—or 31% of the population—relied on self-supply for their drinking water in these regions in 2018, with the number of users increasing by >9 million each year. Reliance on self-supply for drinking water is greater in rural areas than in urban areas (37% of rural population vs 20% of urban population), though results vary considerably between countries. Groundwater sources constitute the most common form of self-supply in South Asia and Southeast Asia, while rainwater collection is dominant in the Pacific. The results confirm the significance of self-supply in the Asia-Pacific and suggest that households are a major but often overlooked source of financing within the water sector. The findings raise important questions about how policy and practice should respond to this widespread phenomenon.
The impact of the COVID-19 epidemic on hospital admissions for alcohol-related liver disease and pancreatitis in Japan
Authors: Itoshima Hisashi , Shin Jung-ho , Takada Daisuke , Morishita Tetsuji , Kunisawa Susumu , Imanaka Yuichi
Published: July 2021

During the coronavirus disease 2019 (COVID-19) pandemic, there have been health concerns related to alcohol use and misuse. We aimed to examine the population-level change in cases of alcohol-related liver disease and pancreatitis that required admission during the COVID-19 epidemic by interrupted time series (ITS) analysis using claims data. We defined the period from April 2020, when the Japanese government declared a state of emergency, as the beginning of the COVID-19 epidemic. This ITS analysis included 3,026,389 overall admissions and 10,242 admissions for alcohol-related liver disease or pancreatitis from 257 hospitals between July 2018 and June 2020. The rate of admissions per 1000 admissions during the COVID-19 epidemic period (April 2020–June 2020) was 1.2 times (rate ratio: 1.22, 95% confidence interval: 1.12–1.33) compared to the pre-epidemic period. Analyses stratified by sex revealed that the increases in admission rates of alcohol-related liver disease or pancreatitis for females were higher than for males during the COVID-19 epidemic period. The COVID-19 epidemic in Japan might associates an increase in hospital admissions for alcohol-related liver disease and pancreatitis. Our study could support the concern of alcohol consumption and health problems during the COVID-19 pandemic.
Interpretable deep learning for the remote characterisation of ambulation in multiple sclerosis using smartphones
Authors: Creagh Andrew P. , Lipsmeier Florian , Lindemann Michael , Vos Maarten De
Published: July 2021

The emergence of digital technologies such as smartphones in healthcare applications have demonstrated the possibility of developing rich, continuous, and objective measures of multiple sclerosis (MS) disability that can be administered remotely and out-of-clinic. Deep Convolutional Neural Networks (DCNN) may capture a richer representation of healthy and MS-related ambulatory characteristics from the raw smartphone-based inertial sensor data than standard feature-based methodologies. To overcome the typical limitations associated with remotely generated health data, such as low subject numbers, sparsity, and heterogeneous data, a transfer learning (TL) model from similar large open-source datasets was proposed. Our TL framework leveraged the ambulatory information learned on human activity recognition (HAR) tasks collected from wearable smartphone sensor data. It was demonstrated that fine-tuning TL DCNN HAR models towards MS disease recognition tasks outperformed previous Support Vector Machine (SVM) feature-based methods, as well as DCNN models trained end-to-end, by upwards of 8–15%. A lack of transparency of “black-box” deep networks remains one of the largest stumbling blocks to the wider acceptance of deep learning for clinical applications. Ensuing work therefore aimed to visualise DCNN decisions attributed by relevance heatmaps using Layer-Wise Relevance Propagation (LRP). Through the LRP framework, the patterns captured from smartphone-based inertial sensor data that were reflective of those who are healthy versus people with MS (PwMS) could begin to be established and understood. Interpretations suggested that cadence-based measures, gait speed, and ambulation-related signal perturbations were distinct characteristics that distinguished MS disability from healthy participants. Robust and interpretable outcomes, generated from high-frequency out-of-clinic assessments, could greatly augment the current in-clinic assessment picture for PwMS, to inform better disease management techniques, and enable the development of better therapeutic interventions.
Designing magnetic field sensor based on tapered photonic crystal fibre assisted by a ferrofluid
Authors: Taghizadeh Mostafa , Bozorgzadeh Forough , Ghorbani Marjan
Published: July 2021

A novel magnetic field sensor is proposed based on the combination of in-line tapered photonic crystal fibre (PCF) Mach–Zehnder interferometer and magnetic nanoparticles. The sensor is theoretically investigated and experimentally realized. The effect of the mechanical strain and the magnetic field on the sensitivity of the sensor is studied. It is found that the proposed sensor shows a wavelength-sensitivity of $$-\,0.072\,\text {nm/mT}$$

-

0.072

nm/mT

and a strain-sensitivity of $$1\,\text {pm/}\upmu \,\epsilon \,$$

1

pm/
μ

ϵ

. To evaluate the effect of the magnetic nanoparticles on the output light intensity, the sensitivity response of the device has been measured under different magnetic field strengths for different length scales. The experimental results show refractive index changes of the magnetic nanoparticles-infiltrated PCF—acting as fibre cladding—under the applied magnetic field leads to variations of the interferometric output. The sensitivity of magnetic field measurement with the sensor with $$30\,\text {mm}$$

30

mm

and $$40\,\text {mm}$$

40

mm

PCF could reach up to $$0.021\,\text {dB/mT}$$

0.021

dB/mT

and $$0.017\,\text {dB/mT}$$

0.017

dB/mT

, respectively. The results show a very good linear response that is an essential requirement for the practical sensors. The proposed magnetic field sensor finds applications in various areas, such as optical sensing, military, power industry, and tunable photonic devices.
The impact of ossification spread on cervical spine function in patients with ossification of the posterior longitudinal ligament
Authors: Katsumi Keiichi , Hirai Takashi , Yoshii Toshitaka , Maki Satoshi , Mori Kanji , Nagoshi Narihito , Nishimura Soraya , Takeuchi Kazuhiro , Ushio Shuta , Furuya Takeo , Watanabe Kei , Nishida Norihiro , Watanabe Kota , Kaito Takashi , Kato Satoshi , Nagashima Katsuya , Koda Masao , Ito Kenyu , Imagama Shiro , Matsuoka Yuji , Wada Kanichiro , Kimura Atsushi , Ohba Tetsuro , Katoh Hiroyuki , Matsuyama Yukihiro , Ozawa Hiroshi , Haro Hirotaka , Takeshita Katsushi , Watanabe Masahiko , Matsumoto Morio , Nakamura Masaya , Yamazaki Masashi , Okawa Atsushi , Kawaguchi Yoshiharu
Published: July 2021

Ossification of the posterior longitudinal ligament (OPLL) is a progressive disease. The bridging of ossified lesions to the vertebral body gradually increases, thereby decreasing the mobility of the cervical spine; thus, cervical spine function may decrease over time. However, cervical spine function in patients with cervical OPLL has not been evaluated in large prospective studies. Therefore, we conducted a prospective multicenter study to clarify whether ossification spread can influence cervical spine function and quality of life (QOL) in patients with cervical OPLL. In total, 238 patients (162 men, 76 women; mean age, 63.9 years) were enrolled from 16 institutions. Each patient underwent whole spine computed tomography and was evaluated for cervical spine function and QOL using the Japanese Orthopaedic Association Cervical Myelopathy Evaluation Questionnaire (JOACMEQ). In the multivariate regression analysis, a higher neck VAS score and a larger number of bridge formations of OPLL in the whole spine were significant predictors of adverse outcomes related to cervical spine function. This is the first prospective multicenter study to reveal the impact of ossification spread on cervical spine function. These findings are important to understand the natural course of OPLL and can serve as controls when evaluating postoperative cervical spine function.
Deep learning identifies antigenic determinants of severe SARS-CoV-2 infection within T-cell repertoires
Authors: Sidhom John-William , Baras Alexander S.
Published: July 2021

SARS-CoV-2 infection is characterized by a highly variable clinical course with patients experiencing asymptomatic infection all the way to requiring critical care support. This variation in clinical course has led physicians and scientists to study factors that may predispose certain individuals to more severe clinical presentations in hopes of either identifying these individuals early in their illness or improving their medical management. We sought to understand immunogenomic differences that may result in varied clinical outcomes through analysis of T-cell receptor sequencing (TCR-Seq) data in the open access ImmuneCODE database. We identified two cohorts within the database that had clinical outcomes data reflecting severity of illness and utilized DeepTCR, a multiple-instance deep learning repertoire classifier, to predict patients with severe SARS-CoV-2 infection from their repertoire sequencing. We demonstrate that patients with severe infection have repertoires with higher T-cell responses associated with SARS-CoV-2 epitopes and identify the epitopes that result in these responses. Our results provide evidence that the highly variable clinical course seen in SARS-CoV-2 infection is associated to certain antigen-specific responses.
An interpretable multiple-instance approach for the detection of referable diabetic retinopathy in fundus images
Authors: Papadopoulos Alexandros , Topouzis Fotis , Delopoulos Anastasios
Published: July 2021

Diabetic retinopathy (DR) is one of the leading causes of vision loss across the world. Yet despite its wide prevalence, the majority of affected people lack access to the specialized ophthalmologists and equipment required for monitoring their condition. This can lead to delays in the start of treatment, thereby lowering their chances for a successful outcome. Machine learning systems that automatically detect the disease in eye fundus images have been proposed as a means of facilitating access to retinopathy severity estimates for patients in remote regions or even for complementing the human expert’s diagnosis. Here we propose a machine learning system for the detection of referable diabetic retinopathy in fundus images, which is based on the paradigm of multiple-instance learning. Our method extracts local information independently from multiple rectangular image patches and combines it efficiently through an attention mechanism that focuses on the abnormal regions of the eye (i.e. those that contain DR-induced lesions), thus resulting in a final image representation that is suitable for classification. Furthermore, by leveraging the attention mechanism our algorithm can seamlessly produce informative heatmaps that highlight the regions where the lesions are located. We evaluate our approach on the publicly available Kaggle, Messidor-2 and IDRiD retinal image datasets, in which it exhibits near state-of-the-art classification performance (AUC of 0.961 in Kaggle and 0.976 in Messidor-2), while also producing valid lesion heatmaps (AUPRC of 0.869 in the 81 images of IDRiD that contain pixel-level lesion annotations). Our results suggest that the proposed approach provides an efficient and interpretable solution against the problem of automated diabetic retinopathy grading.
Optical power limiter in the femtosecond filamentation regime
Authors: Agiotis Leonidas , Meunier Michel
Published: July 2021

We present the use of a power limiting apparatus to evaluate ultrafast optical nonlinearities of transparent liquids (water and ethanol) in the femtosecond filamentation regime. The setup has been previously employed for the same purpose, however, in a longer pulsewidth (> 20 ps) regime, which leads to an ambiguous evaluation of the critical power for self-focusing. The uncertainty originates from the existence of a threshold power for optical breakdown well below the critical power for self-focusing within this timeframe. Contrarily, using the proposed apparatus in the femtosecond regime, we observe for the first time a unique optical response, which features the underlying physics of laser filamentation. Importantly, we demonstrate a dependence of the optical transmission of the power limiter on its geometrical, imaging characteristics and the conditions under which a distinct demarcation for the critical power for self-focusing can be determined. The result is supported by numerical simulations, which indicate that the features of the observed power-dependent optical response of the power limiting setup are physically related to the spontaneous transformation of the laser pulses into nonlinear conical waves.
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases
Authors: Magraner-Pardo Lorena , Laskowski Roman A. , Pons Tirso , Thornton Janet M.
Published: July 2021

DNA-Damage Response (DDR) proteins are crucial for maintaining the integrity of the genome by identifying and repairing errors in DNA. Variants affecting their function can have severe consequences since failure to repair damaged DNA can result in cells turning cancerous. Here, we compare germline and somatic variants in DDR genes, specifically looking at their locations in the corresponding three-dimensional (3D) structures, Pfam domains, and protein–protein interaction interfaces. We show that somatic variants in metastatic cases are more likely to be found in Pfam domains and protein interaction interfaces than are pathogenic germline variants or variants of unknown significance (VUS). We also show that there are hotspots in the structures of ATM and BRCA2 proteins where pathogenic germline, and recurrent somatic variants from primary and metastatic tumours, cluster together in 3D. Moreover, in the ATM, BRCA1 and BRCA2 genes from prostate cancer patients, the distributions of germline benign, pathogenic, VUS, and recurrent somatic variants differ across Pfam domains. Together, these results provide a better characterisation of the most recurrent affected regions in DDRs and could help in the understanding of individual susceptibility to tumour development.
Poly (red DSBR)/Al-ZnO modified carbon paste electrode sensor for dopamine: a voltammetric study
Authors: Shashikumara J. K. , Swamy B. E. Kumara , Sharma S. C. , Hariprasad S. A. , Mohanty Kaustubha
Published: July 2021

In the present work, the ZnO and Al-ZnO nanoflakes (NFs) were synthesized by the co-precipitation process. The synthesized NFs were characterized by X-ray diffraction and field emission scanning electron microscopy. Energy dispersive X-ray spectrometer was explored for the elemental chemical compositions. The prepared NFs were taken for the modification of the electrode and developed the modified electrode for the electrochemical analysis of the dopamine (DOA) at pH 7.4. The Al-ZnO modified carbon paste electrode (MCPE) was electropolymerised by using textile dye red DSBR. The Po-RD/Al-ZnO MCPE exhibited good electrochemical sensor properties towards the electrochemical detection of DOA. Several factors such as the impact of speed rate (υ), pH and concentration of the DOA were analyzed at the modified electrode. The great sensitivity was established to the fast electron-transfer kinetics and surface coverage of the DOA on the electrode. The prepared electrode exhibits satisfactory stability at the ambient conditions. The detection limit of 0.58 μM was achieved for the DOA. The decorated sensor was stable, sensitive, selective, and reproducible and used in the analytical applications.
Visual outcome of endogenous endophthalmitis in Thailand
Authors: Lourthai Preeyachan , Choopong Pitipol , Dhirachaikulpanich Dhanach , Soraprajum Kunravitch , Pinitpuwadol Warinyupa , Punyayingyong Noppakhun , Ngathaweesuk Yaninsiri , Tesavibul Nattaporn , Boonsopon Sutasinee
Published: July 2021

To evaluate a 10-year visual outcome of endogenous endophthalmitis (EE) patients. A 10-year retrospective chart review of EE patients. Thirty-eight patients (40 eyes) were diagnosed with EE at the mean age of 42. Among the identifiable pathogens (71.1% culture positive), the causative agents were predominantly gram-negative bacteria (48.1%). The most common specie was Klebsiella pneumoniae (25.9%). About a quarter of the patients required surgical eye removal, and the remaining 45.7% had visual acuity (VA) worse than hand motion at one month after the infectious episode. The most common complication was ocular hypertension (52.5%). Poor initial VA was significantly associated with a worse visual outcome in the early post-treatment period (p 0.12, adjusted OR 10.20, 95% CI 1.65–62.96). Five patients continued to visit the clinic for at least ten years. One patient had gained his vision from hand motion to 6/7.5. Two patients had visual deterioration, one from corneal decompensation, and the other from chronic retinal re-detachment. Two patients developed phthisis bulbi, with either some VA perception of light or no light perception. Poor initial VA is the only prognostic factor of a poor early post-treatment visual outcome of EE.
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex
Authors: Jones Ashley R. , Iacoangeli Alfredo , Adey Brett N. , Bowles Harry , Shatunov Aleksey , Troakes Claire , Garson Jeremy A. , McCormick Adele L. , Al-Chalabi Ammar
Published: July 2021

There is increasing evidence that endogenous retroviruses (ERVs) play a significant role in central nervous system diseases, including amyotrophic lateral sclerosis (ALS). Studies of ALS have consistently identified retroviral enzyme reverse transcriptase activity in patients. Evidence indicates that ERVs are the cause of reverse transcriptase activity in ALS, but it is currently unclear whether this is due to a specific ERV locus or a family of ERVs. We employed a combination of bioinformatic methods to identify whether specific ERVs or ERV families are associated with ALS. Using the largestpost-mortemRNA-sequence datasets available we selectively identified ERVs that closely resembled full-length proviruses. In the discovery dataset there was one ERV locus (HML6_3p21.31c) that showed significant increased expression inpost-mortemmotor cortex tissue after multiple-testing correction. Using six replicationpost-mortemdatasets we found HML6_3p21.31c was consistently upregulated in ALS in motor cortex and cerebellum tissue. In addition, HML6_3p21.31c showed significant co-expression with cytokine binding and genes involved in EBV, HTLV-1 and HIV type-1 infections. There were no significant differences in ERV family expression between ALS and controls. Our results support the hypothesis that specific ERV loci are involved in ALS pathology.