bluuebunny/crossref_metadata_2025 huggingface dataset:
Vibrations in finitely deformed residual stressed circular cylindrical tubes
Authors: Kanan Anas , Kaliske Michael , Dorfmann Luis
Published: June 2022

A residually stressed thick-walled tube is subject to a combination of internal or external pressure and axial stretch to maintain its circular cylindrical geometry. A small incremental motion is then superimposed on the finitely deformed configuration. We summarize the basic elements of the theory of hyperelasticity with initial stress, together with the corresponding incremental forms. Equations are derived and used to evaluate the dependence of the axial load, of the vibration frequency and of the circumferential stress, on the inner and outer curved boundaries, on the residual stress and on various geometric quantities. The theory is applied to a simple neo-Hookean model with two material parameters and a parameter to scale the magnitude of the residual stress. The static response to small incremental deformations is obtained as a special case when the vibration frequency vanishes.
‘Look at me!’ Post-mastectomy transformative politics
Authors: Davis Kathy
Published: June 2022

Breast cancer received little attention until the 1990s when women began to criticize the lack of public awareness as well as research funding. Breast cancer activism emerged across the globe, ranging from feminist grass-roots movements, to initiatives by health organizations to corporate activities, the most famous being Pink Ribbon. Feminists have been critical of Pink Ribbon, decrying what they call the ‘pink-washing’ of breast cancer through consumerism and the insistence that breast cancer survivors should ‘look good in order to feel good’. In this article, I explore activism that makes breast cancer visible without silencing its traumas. This activism takes the form of artistic projects – fashion, art, photography, and other forms of aesthetic expression. Drawing upon the work of the queer theorist Dina Georgis, I ultimately turn to the SCAR Project as example of a ‘better story’ about living with the post-mastectomy body and show how it can inspire a transformative feminist politics of the body.
Tourism, urbanization, and urban income inequality in China
Authors: Zhang Jiekuan
Published: June 2022

Despite the persisting interest in the nexus of tourism and income inequality, the relationships between tourism and urban income inequality remain unknown. In the past few decades, tourism, urbanization, and urban income inequality are all prominent social and economic phenomena in China. This study investigates such relationships and the underlying influence mechanism of urbanization based on provincial panel data in China between 1995 and 2019. The results show that tourism significantly increases urban income inequality. Moreover, there exists a Kuznets curve between tourism and urban income inequality. When the ratio of tourism revenue to GDP reaches the value of 0.416, the positive influence of tourism on urban income inequality reaches its maximum. Most of China’s provinces currently face the positive influence of tourism on urban income inequality. Besides, urbanization partially mediates tourism’s effects on urban income inequality. Heterogeneity analysis indicates that in high-urbanization, high-income, and low economic levels regions, tourism increases urban income inequality to a greater extent. This article enriches the knowledge of the association between tourism and income distribution.
Bile leakage and the number of metal clips on the cystic duct during laparoscopic cholecystectomy
Authors: Gustafsson Arvid , Enochsson Lars , Tingstedt Bobby , Olsson Greger
Published: June 2022

Background and objective:

The most common way of closing the cystic duct in laparoscopic cholecystectomy is by using metal clips (>80%). Nevertheless, bile leakage occurs in 0.4%–2.0% of cases, and thus causes significant morbidity. However, the optimal number of clips needed to avoid bile leakage has not been determined. The primary aim of this study was to evaluate bile leakage and post-procedural adverse events after laparoscopic cholecystectomy concerning whether two or three clips were used to seal the cystic duct.

Methods:

Using a retrospective observational design, we gathered data from the Swedish Registry for Gallstone Surgery and Endoscopic Retrograde Cholangiopancreatography (ERCP) (GallRiks). From 2006 until 2019, 124,818 patients were eligible for inclusion. These were nested to cohorts of 75,322 (60.3%) for uncomplicated gallstone disease and 49,496 (39.7%) with complicated gallstone disease. The cohorts were grouped by the number (i.e. two or three) of metal clips applied to the proximal cystic duct. The main outcome was 30-day bile leakage and post-procedural adverse events.

Results:

No significant differences surfaced in the rate of bile leakage (0.8% vs 0.8%; P = .87) or post-procedural adverse events (three clips, 5.7% vs two clips, 5.4%; P = .16) for uncomplicated gallstone disease. However, for complicated disease, bile leakage (1.4% vs 1.0%; P < .001) and post-procedural adverse events (10.2% vs 8.6%; P < .001) significantly increased when the cystic duct was sealed with three clips compared with two.

Conclusions:

Because no differences in the rates of bile leakage or adverse events emerged in uncomplicated gallstone disease when a third clip was applied, a third clip for additional safety is not recommended in such cases. On the contrary, bile leakage and adverse events increased when a third clip was used in patients with complicated gallstone disease. This finding probably indicates a more difficult cholecystectomy rather than being caused by the third clip itself.
“Write it down! I am an Arab”: The role of reader comments in the formation of networked counterpublics
Authors: Lowenstein-Barkai Hila
Published: June 2022

Various literature has examined how affordances of online media such as openness and connectivity have constituted digital counterpublics, that is, discursive arenas where members of subordinate social groups invent and circulate oppositional interpretations of their identities. At the same time, and in sharp contrast to the bilateral nature of online media, most of this literature has focused on content produced by the group members only, without addressing neither its acceptance by the hegemonic public nor the internal discursive negotiations surrounding it. Using the Facebook page “Write it down! I’m an Arab” as a case study, the current study examines the role played by reader comments in the formation of networked counterpublics. We found that reader comments expand the counterpublic sphere in two directions: vertical and horizontal. Vertically, they produce an interface between the dominant public sphere and the counterpublic sphere. Horizontally, they function as a discursive arena within the group members.
How the social robot Sophia is mediated by a YouTube video
Authors: Fortunati Leopoldina , Manganelli Anna Maria , Höflich Joachim , Ferrin Giovanni
Published: June 2022

In robotics, a field of research still populated by prototypes, much of the research is made through videos and pictures of robots. We study how the highly human-like robot Sophia is perceived through a YouTube video. Often researchers take for granted in their experiments that people perceive humanoids as such. With this study we wanted to understand to what extent a convenience sample of university students perceive Sophia’s human-likeness; second, we investigated which mental capabilities and emotions they attribute to her; and third, we explored the possible uses of Sophia they imagine. Our findings suggest that the morphological human-likeness of Sophia, through the video, is not salient in the Sophia’s representations of these participants. Only some mental functions are attributed to Sophia and no emotions. Finally, uses of Sophia turned out to be connected to the gender stereotypes that characterize stereotyped women’s professions and occupations but not completely.
When ethnographic work turns into distant screen visits: A note on flexible inflexibility during the COVID-19 pandemic
Authors: Sandberg Helena , Sundin Ebba , Sjöberg Ulrika
Published: June 2022

This colloquium shares experiences from doing ethnographic fieldwork with young children and the challenges that followed due to the COVID-19 pandemic. The project DIGIKIDS Sweden has its focus on very young children (birth to three years) and their engagement with digital media technologies in their homes. The pandemic put the project on hold, but in the families where the fieldwork had already started, the authors decided to change the methods of data collection. Digital screen visits were introduced and, at first, this seemed to be flexible, and they adjusted to the new environment. At the same time, this flexibility also became an inflexible experience due to the use of technology.
Decolonization and qualitative epistemology: Toward reconciliation in the academy
Authors: Au Anson
Published: June 2022

The subject of (de)colonization in the academy has witnessed an upsurge in attention over the past two decades across the social sciences and the Global North-South divide. This article critically examines central themes that have guided the conceptualization of decolonization thus far and foregrounds the convergences that decolonization shares with the epistemology of qualitative research methodology and pedagogy. In so doing, this article articulates the objective of reconciliation and demonstrates the ways in which reconciliation has been and can be enacted in the academy, limning the themes of (a) attention to physical context; (b) inclusion of Indigenous voices; (c) and decolonization of Indigenous and non-Indigenous minds. This article argues for better aligning the epistemology and conduct of qualitative research with Indigenous values—and concludes by calling for attention to Indigenous intersectionality and calling against a growing trend of decontextualizing decolonization.
Professor John Eirwyn Ffowcs Williams FREng: Engineer, educator, researcher and entrepreneur, Cambridge Professor and Master of Emmanuel College 25 May 1935–12 December 2020
Authors: Dowling Ann P
Published: June 2022

I first met Shôn in October 1973. I had just started Part III of the Cambridge Mathematical Tripos – a post-graduate course that was retrospectively awarded a Masters’ Degree in Mathematics. After a summer job working with Ted Broadbent on aircraft noise at the Royal Aircraft Establishment in Farnborough, I had decided do a PhD in Aeroacoustics. I asked Sir James Lighthill for advice and he told me that he was now focused on biomechanics but a new professor had recently arrived in the Cambridge Department of Engineering and that I should ask him. I made contact with Shôn, saw him in his office that afternoon, and he agreed to supervise me for a PhD. As quickly and simply as that, I was on a path that for me was transformational, not only an exciting research future, but the start of my transition from mathematics into engineering. Throughout my career, Shôn continued to be a major influence on me as he has for many others.
Outcomes in Ballistic Injuries to the Hand: Fractures and Nerve/Tendon Damage as Predictors of Poor Outcomes
Authors: Dugom Patrick M. , Jester Mitchell P. , Archie William H. , Huynh Duy M. , Scarcella Josh F. , Guo Yifan
Published: June 2022

Background:

Gunshot injuries can be devasting, regardless of their location. However, ballistic injuries involving the upper extremity have not been thoroughly investigated. The goal of this study is to evaluate the injury patterns and outcomes of patients who sustained gunshot injuries to the hand.

Methods:

A retrospective chart review of patients with gunshot injuries to the upper extremity at a single, level 1 trauma center between January 2016 and December 2017 was performed. Patient demographics and mechanisms of injuries were reviewed. The injury patterns, location, tendon/nerve involvement, and bony involvement were analyzed. Surgical interventions and long-term outcomes were reviewed. Outcomes were compared using the presence of fractures and nerve/tendon injuries as independent variables.

Results:

In all, 32 patients met our inclusion criteria. Of these, 15 patients had gunshots to the hand, 10 patients to the fingers, and 7 patients involving both the finger and hand. In patients with isolated hand injuries, 60% had fractures and 53% had nerve/tendon injuries. The presence of fractures was associated with a 7.9-fold increase in tendon and nerve injuries ( P = .032). Patients who sustained tendon/nerve injuries had significantly higher rates of permanent disability ( P = .01). The presence of a fracture leads to a higher likelihood of long-term complications, although not statistically significant ( P = .13).

Conclusion:

Ballistic injuries to the hand are frequently associated with fractures and neurovascular and tendon injuries. The presence of fractures is associated with a higher incidence of nerve and tendon injuries. Involvement of these structures is linked to an increased risk of long-term disability.
Efficacy and safety of SOFIA aspiration catheter for mechanical thrombectomy via ADAPT and Solumbra echniques in acute ischemic stroke: A systematic review and meta-analysis
Authors: Essibayi Muhammed Amir , Brinjikji Waleed
Published: June 2022

Introduction

SOFIA catheter is a relatively new and recently FDA-approved aspiration catheter. This systematic review aims to investigate the safety and efficacy of SOFIA catheter for treatment of acute ischemic stroke (AIS) via ADAPT and Solumbra techniques.

Methods

Search of all studies evaluating the SOFIA catheter for mechanical thrombectomy (MT) for treatment of AIS via ADAPT and Solumbra techniques from inception through 2020 on Pubmed, PMC, and Embase was performed. We analyzed the angiographic and clinical outcomes of both techniques with SOFIA catheter using the random-effects model.

Results

From 18 studies, 1836 patients were included with 1365 receiving MT using ADAPT and 471 with solumbra technique. The mean age was 69.8 years and 51.1% of the patients were women. The rate of rescue therapy was 30%. The outcomes rates of ADAPT group were as follows; mFPE (59.3%), FPE (34.4%) final TICI 2b/3 (89.3%), procedural complications (8%), embolization to new territory (ENT) (2.3%), symptomatic ICH (5.4%), mean NIHSS (8.97), 90-day-mRS 0–2 (48.8%), and mortality (15.3%). The outcomes rates of Solumbra group were as follows; mFPE (60.5%), FPE (46.7%), final TICI 2b/3 (93%), procedural complications (6.4%), ENT (2%), symptomatic ICH (6%), mean NIHSS (7.59), mRS 0–2 (53.8%), and mortality (10.8%). ICA and posterior circulation strokes, and tandem lesions had worse outcomes (P < .005). MCA strokes were associated with better outcomes (P = .005). ASPECT scores’ association with the clinical outcomes was found statistically significant.

Conclusion

SOFIA catheter is effective and safe to treat acute ischemic stroke regardless of applied MT technique.
Exploring the Expansive Properties of Interpretive Description: An Invitation to Anti-oppressive Researchers
Authors: Ocean Mia , Montgomery Rose , Jamison Zoe , Hicks Karon , Thorne Sally
Published: June 2022

There is an ever-present need to challenge, create, and expand upon qualitative research approaches in the applied and practice disciplines to avoid repeating mistakes of the past and to realize a research agenda for socially just practice. Toward these goals, anti-oppressive researchers engage with a variety of methodologies to co-produce accounts that reflect a comprehensive understanding of social problems with the people who experience them and to enact solutions for real world change. In this article, we reflect on the manner in which Interpretive Description may be a useful option for anti-oppressive researchers to consider as a methodological approach in meeting these philosophical and practical aspirations. We find that Interpretive Description offers guidance toward building the foundation, bringing your whole self to the research, remaining responsive to people, valuing people’s expert perspective of their own experience, using power and privilege wisely, broadening contributors and consumers of research, embracing complications and variations, and enacting change. To illustrate this, we share examples from a participatory, anti-oppressive Interpretive Description study conducted by a team comprised of an inter-racial coalition of students, alumni, and faculty. Collectively, we investigated Black graduate student experiences of racism, inclusion, and expansion within a historically and primarily White university. This case example illustrates our contention that, as our commitment to anti-oppressive research and practice in the applied disciplines intensifies, Interpretive Description is well situated to help us advance practice knowledge in a manner that is transparent, equitable and credible.
‘The likes of me running and walking? No chance’: Exploring the perceptions of adult patients with bronchiectasis towards exercise
Authors: Royle Holly , Kelly Carol
Published: June 2022

Objective: To explore the views and experiences of adult patients with bronchiectasis towards exercise. Methods: Semi-structured interviews with ten patients with bronchiectasis were conducted to explore perceptions of exercise, potential barriers and facilitators of exercise. Inductive thematic analysis was used to identify key themes. Findings: Five main themes: 1. The language of exercise 2. Facilitators to exercise 3. Barriers to exercise 4. Exercise has a positive impact on health and life expectancy 5. Grief regarding loss of ability Discussion: Participants perceived exercise as positive, but there was variance regarding what this entailed. Findings suggest healthcare professionals should consider the language used when prescribing exercise and provide clarity for patients and reflect on their own role in advising on exercise. There were both common and differing barriers and facilitators to exercise between participants. Holistic needs and the identification of these potential barriers and facilitators to exercise could aid compliance. Further research is needed to explore generalisability and the effectiveness of behaviour change models to improve engagement with exercise.
Targeting IL12/23 in ulcerative colitis: update on the role of ustekinumab
Authors: Pugliese Daniela , Privitera Giuseppe , Fiorani Marcello , Parisio Laura , Calvez Valentin , Papa Alfredo , Gasbarrini Antonio , Armuzzi Alessandro
Published: June 2022

As our comprehension of the pathogenic mechanisms of inflammatory bowel disease (IBD) increases, the therapeutic armamentarium for its treatment can expand, and novel target therapies join the treatment pipeline. Interleukin (IL)-12 and IL23 are two key cytokines responsible for promoting and perpetuating bowel inflammation in IBD. Ustekinumab is a monoclonal antibody directed against the shared p40 subunit of both cytokines, and it was recently approved for the treatment of ulcerative colitis (UC). In the pivotal phase III UNIFI trial, ustekinumab showed a superiority over placebo in both clinical and endoscopic outcomes; furthermore, it was characterized by a favorable safety profile, with a similar rate of adverse events as compared with placebo. Recent evidence from real-life experiences have started accumulating, generally confirming the effectiveness and safety figures emerged from the registration studies. However, most of these observational studies enrolled multirefractory patients; moreover, comparative data with other target therapies are lacking, leaving physicians without clear indications about the appropriate positioning of ustekinumab in the therapeutic pipeline for UC. This review examines the basis of targeting IL12-23 in UC therapy and summarizes the data from both clinical trials and real-life studies, to highlight the main evidence already available and the research gaps that need to be filled for the optimal usage of ustekinumab in UC.
YouTube as a Source of Patient Information for Ankle Arthroplasty: Quantitative Analysis of Video Reliability, Quality, and Content
Authors: Hartnett Davis A. , Yang Daniel S. , Lama Christopher J. , McDonald Christopher L. , Daniels Alan H. , Blankenhorn Brad D.
Published: June 2022

Background. There are limited data on the quality and content of videos discussing total ankle arthroplasty (TAA) on the YouTube video platform. Methods. The first 60 unique YouTube videos resulting from the keyword query “ankle arthroplasty” and “ankle replacement” were analyzed for comprehensiveness and quality. Content was assessed using the Journal of American Medical Association (JAMA) benchmark criteria, DISCERN, Global Quality Scale (GQS), and an arthroplasty-specific score. Results. Videos demonstrated low mean DISCERN (49.2/80), GQS (3.2/5), and arthroplasty-specific scores (4.3/12) with substantial variability between videos. Most of the content was produced by nonacademic physicians (46.7%) and academic sources (21.7%). Academic videos saw significantly higher mean JAMA scores ( P = .013) but were otherwise comparable to non-academic physicians. Commercial content demonstrated significantly low-quality scores compared to academic ( P = .012) and physician ( P = .008) sources despite the highest mean viewership. Conclusions. Information on TAA on the YouTube platform is highly variable based on video source, with generally poor quality and content.

Level of Evidence: Level V, systemic review of non-peer reviewed resources
Long Non-Coding RNA DUXAP8 Acts as an Oncogene in Sinonasal Squamous Cell Carcinoma Through miR-584-5p/FNDC3B Pathway
Authors: Chen Xuan , Li Guidi , Zhong Guanzhong , Chen Junyong , Feng Lijun , Zhang Tao , Tang Zhi
Published: June 2022

Sinonasal squamous cell carcinoma (SNSCC) is one of the least frequent carcinomas in the head and neck and accounts for 60% to 75% of sinonasal malignancies. The role of long non-coding RNAs (lncRNAs) in cancer development has drawn great attention over the years. The current study intended to assess the role and specific mechanism of lncRNA double homeobox A pseudogene 8 (DUXAP8) in SNSCC. Quantitative real-time PCR (qRT-PCR) analysis was implemented to assess the expression level of DUXAP8, microRNA-584-5p (miR-584-5p), and fibronectin type III domain containing 3B (FNDC3B). Proliferation assays included colony formation assay, Cell Counting Kit-8 (CCK-8) assay, and 5-ethynyl-2′-deoxyuridine (EdU) assay. Transwell assays were implemented to monitor cell migration and invasion. Cell apoptosis was evaluated via terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling (TUNEL) and JC-1 experiments. Mechanism experiments included RNA pull-down assay, RNA binding protein immunoprecipitation (RIP) assay, and luciferase reporter assay. DUXAP8 is overexpressed in SNSCC cells. Functionally, DUXAP8 silencing suppresses the malignant progression of SNSCC. Furthermore, DUXAP8 up-regulates the expression of FNDC3B via sponging miR-584-5p. Rescue experiments demonstrated that DUXAP8 mediates the progression of SNSCC via up-regulating FNDC3B expression. In conclusion, DUXAP8 acts as an oncogene in SNSCC, which may be a new molecular marker for SNSCC.
Winging it: a qualitative study of knowledge-acquisition experiences for early adopting providers of medical assistance in dying
Authors: Winters Janine Penfield , Pickering Neil , Jaye Chrystal
Published: June 2022

Background:

Medical Assistance in Dying (MAID) was legalized in Canada without a designated period for implementation. Providers did not have access to customary alternatives for training and mentorship during the first 1–3 years after legalization.

Objective:

To report on how doctors prepared for their first provision of MAID in the early period after legalization in Canada.

Design:

Qualitative research design within an interpretive phenomenological theoretical framework. We asked participants to describe their experiences preparing for first MAID provision. Analysis of transcripts elicited themes regarding training and information desired by early adopters for provision of newly legalized MAID.

Participants:

Twenty-one early adopting physician-providers in five Canadian provinces were interviewed.

Results:

Few formal training opportunities were available. Many early-adopting providers learned about the procedure from novel sources using innovative methods. They employed a variety of strategies to meet their needs, including self-training and organizing provider education groups. They acknowledged and reflected on uncertainty and knowledge gained from unexpected experiences and missteps. Key phrases from participants indicated a desire for early training and mentorship.

Limitations:

This study included only the perspective of physicians who were providers of MAID. It does not address the training needs for all health practitioners who receive requests for assisted death nor report the patient/family experience.

Conclusion:

The Canadian experience demonstrates the importance of establishing accessible guidance and training opportunities for providers at the outset of implementation of newly legalized assisted dying.
Poly-(vinyl alcohol) composite films reinforced with carboxylated functional microcrystalline cellulose from jute fiber
Authors: Hasan Md Zahid , Arafat Yeasin , Bashar M Mahbubul , Niloy Md Nabi Newaz , Islam Md Imranul , Khandaker Shahjalal , Chowdhury AM Sarwaruddin
Published: June 2022

Bio-based materials have attracted ample research interest due to their intrinsic beneficial impact on human society. Microcrystalline cellulose (MCC) extracted from a variety of bioresources is one of the most prominent candidate in this regard. Herein, the MCC was synthesized from jute fiber by a facile ammonium persulfate (APS) oxidation method resulting in carboxylic functional groups on the fiber surface. The carboxylated MCC was utilized to develop polyvinyl alcohol (PVA) composite films in a solution casting method. The surface chemistry, thermal properties, and surface morphology of MCC and MCC-PVA composite films were studied by FT-IR spectroscopy, thermogravimetric analysis, and scanning electron microscopy. The SEM images confirmed the rod-like MCC with average particle diameter 4.6 μm and length in 48.4 μm. The FT-IR spectroscopy suggested the complete removal of lignin and hemicellulose from jute fiber. A peak at 1730 cm−1 was introduced in MCC due to oxidation with APS. The MCC was readily dispersible in water, and chemical interaction with –OH group of PVA was spontaneous due to the carboxylation in MCC. The absorption peak of –OH groups in MCC-PVA composite films were shifted, somewhat disappeared and weakened due to the intra and intermolecular hydrogen bonding of MCC and OH groups in PVA. Thermogravimetric analysis expressed the thermal behavior of MCC and MCC-PVA composite films. The char formation at 500°C of the two different composite films was 15% and 16%, respectively. The stability of MCC-PVA composite films at elevated temperatures is the indication of potential application as flame retardant material.
CARE 2.0: reducing false-positive sequencing error corrections using machine learning
Authors: Kallenborn Felix , Cascitti Julian , Schmidt Bertil
Published: June 2022

Background

Next-generation sequencing pipelines often perform error correction as a preprocessing step to obtain cleaned input data. State-of-the-art error correction programs are able to reliably detect and correct the majority of sequencing errors. However, they also introduce new errors by making false-positive corrections. These correction mistakes can have negative impact on downstream analysis, such ask-mer statistics, de-novo assembly, and variant calling. This motivates the need for more precise error correction tools.

Results

We present CARE 2.0, a context-aware read error correction tool based on multiple sequence alignment targeting Illumina datasets. In addition to a number of newly introduced optimizations its most significant change is the replacement of CARE 1.0’s hand-crafted correction conditions with a novel classifier based on random decision forests trained on Illumina data. This results in up to two orders-of-magnitude fewer false-positive corrections compared to other state-of-the-art error correction software. At the same time, CARE 2.0 is able to achieve high numbers of true-positive corrections comparable to its competitors. On a simulated full human dataset with 914M reads CARE 2.0 generates only 1.2M false positives (FPs) (and 801.4M true positives (TPs)) at a highly competitive runtime while the best corrections achieved by other state-of-the-art tools contain at least 3.9M FPs and at most 814.5M TPs. Better de-novo assembly and improvedk-mer analysis show the applicability of CARE 2.0 to real-world data.

Conclusion

False-positive corrections can negatively influence down-stream analysis. The precision of CARE 2.0 greatly reduces the number of those corrections compared to other state-of-the-art programs including BFC, Karect, Musket, Bcool, SGA, and Lighter. Thus, higher-quality datasets are produced which improvek-mer analysis and de-novo assembly in real-world datasets which demonstrates the applicability of machine learning techniques in the context of sequencing read error correction. CARE 2.0 is written in C++/CUDA for Linux systems and can be run on the CPU as well as on CUDA-enabled GPUs. It is available athttps://github.com/fkallen/CARE.
CancerNet: a unified deep learning network for pan-cancer diagnostics
Authors: Gore Steven , Azad Rajeev K.
Published: June 2022

Background

Despite remarkable advances in cancer research, cancer remains one of the leading causes of death worldwide. Early detection of cancer and localization of the tissue of its origin are key to effective treatment. Here, we leverage technological advances in machine learning or artificial intelligence to design a novel framework for cancer diagnostics. Our proposed framework detects cancers and their tissues of origin using a unified model of cancers encompassing 33 cancers represented in The Cancer Genome Atlas (TCGA). Our model exploits the learned features of different cancers reflected in the respective dysregulated epigenomes, which arise early in carcinogenesis and differ remarkably between different cancer types or subtypes, thus holding a great promise in early cancer detection.

Results

Our comprehensive assessment of the proposed model on the 33 different tissues of origin demonstrates its ability to detect and classify cancers to a high accuracy (> 99% overall F-measure). Furthermore, our model distinguishes cancers from pre-cancerous lesions to metastatic tumors and discriminates between hypomethylation changes due to age related epigenetic drift and true cancer.

Conclusions

Beyond detection of primary cancers, our proposed computational model also robustly detects tissues of origin of secondary cancers, including metastatic cancers, second primary cancers, and cancers of unknown primaries. Our assessment revealed the ability of this model to characterize pre-cancer samples, a significant step forward in early cancer detection. Deployed broadly this model can deliver accurate diagnosis for a greatly expanded target patient population.
Fluoride mitigates aluminum-toxicity in barley: morpho-physiological responses and biochemical mechanisms
Authors: Dawood Mona F. A. , Tahjib-Ul-Arif Md. , Sohag Abdullah Al Mamun , Abdel Latef Arafat Abdel Hamed
Published: June 2022

Background

To our knowledge, the role of exogenous fluoride (F–) on aluminum (Al)-stress mitigation in plants has not been investigated yet. In this experiment, barley (Hordeum vulgaris) seedlings were exposed to excessive Al3+ concentrations (aluminum chloride, 0.5, 1.0, 2.0, 3.0, and 4.0 mM) with and without fluoride (0.025% sodium fluoride) to explore the possible roles of fluoride on the alleviation of Al-toxicity.

Results

Overall, Al-stress caused inhibition of growth and the production of photosynthetic pigments. Principal component analysis showed that the growth inhibitory effects were driven by increased oxidative stress and the interruption of water balance in barley under Al-stress. Fluoride priming, on the other hand, enhanced growth traits, chlorophyll a and b content, as well as invigorated the protection against oxidative damage by enhancing overall antioxidant capacity. Fluoride also improved osmotic balance by protecting the plasma membrane. Fluoride reduced endogenous Al3+ content, restored Al-induced inhibition of glutathione-S-transferase, and increased  the contents of phytochelatins and metallothioneins, suggesting that fluoride reduced Al3+ uptake and improved chelation of Al3+.

Conclusions

Aluminum chloride-induced harmful effects are abridged by sodium fluoride on barely via enhancing antioxidative responses, the chelation mechanism causing reduction of Al uptake and accumulation of barely tissues. Advanced investigations are necessary to uncover the putative mechanisms underpinning fluoride-induced Al-stress tolerance in barley and other economically significant crops, where our results might serve as a solid reference.
Molecular epidemiology and outcome of carbapenem-resistant Enterobacterales in Saudi Arabia
Authors: Alraddadi Basem M. , Heaphy Emily L. G. , Aljishi Yamama , Ahmed Waleed , Eljaaly Khalid , Al-Turkistani Hanan H. , Alshukairi Abeer N. , Qutub Mohammed O. , Alodini Kholoud , Alosaimi Roaa , Hassan Waseem , Attalah Dalya , Alswaiel Rakan , Saeedi Mohammed F. , Al-Hamzi Mohammed A. , Hefni Lama K. , Almaghrabi Reem S. , Anani Mushira , Althaqafi Abdulhakeem
Published: June 2022

Background

The burden of carbapenem resistance is not well studied in the Middle East. We aimed to describe the molecular epidemiology and outcome of carbapenem-resistant Enterobacterales (CRE) infections from several Saudi Arabian Centers.

Methods

This is a multicenter prospective cohort study conducted over a 28-month period. Patients older than 14 years of age with a positive CRE Escherichia coli or Klebsiella pneumoniae culture and a clinically established infection were included in this study. Univariate and multivariable logistic models were constructed to assess the relationship between the outcome of 30-day all-cause mortality and possible continuous and categorical predictor variables.

Results

A total of 189 patients were included. The median patient age was 62.8 years and 54.0% were male. The most common CRE infections were nosocomial pneumonia (23.8%) and complicated urinary tract infection (23.8%) and 77 patients (40.7%) had CRE bacteremia. OXA-48 was the most prevalent gene (69.3%). While 100 patients (52.9%) had a clinical cure, 57 patients (30.2%) had died within 30 days and 23 patients (12.2%) relapsed. Univariate analysis to predict 30-day mortality revealed that the following variables are associated with mortality: older age, high Charlson comorbidity index, increased Pitt bacteremia score, nosocomial pneumonia, CRE bacteremia and diabetes mellitus. In multivariable analysis, CRE bacteremia remained as an independent predictor of 30 day all-cause mortality [AOR and 95% CI = 2.81(1.26–6.24), p = 0.01].

Conclusions

These data highlight the molecular epidemiology and outcomes of CRE infection in Saudi Arabia and will inform future studies to address preventive and management interventions.
Targeting inflammation for the treatment of Diabetic Kidney Disease: a five-compartment mechanistic model
Authors: Hofherr Alexis , Williams Julie , Gan Li-Ming , Söderberg Magnus , Hansen Pernille B. L. , Woollard Kevin J.
Published: June 2022

Diabetic kidney disease (DKD) is the leading cause of kidney failure worldwide. Mortality and morbidity associated with DKD are increasing with the global prevalence of type 2 diabetes. Chronic, sub-clinical, non-resolving inflammation contributes to the pathophysiology of renal and cardiovascular disease associated with diabetes. Inflammatory biomarkers correlate with poor renal outcomes and mortality in patients with DKD. Targeting chronic inflammation may therefore offer a route to novel therapeutics for DKD. However, the DKD patient population is highly heterogeneous, with varying etiology, presentation and disease progression. This heterogeneity is a challenge for clinical trials of novel anti-inflammatory therapies. Here, we present a conceptual model of how chronic inflammation affects kidney function in five compartments: immune cell recruitment and activation; filtration; resorption and secretion; extracellular matrix regulation; and perfusion. We believe that the rigorous alignment of pathophysiological insights, appropriate animal models and pathology-specific biomarkers may facilitate a mechanism-based shift from recruiting ‘all comers’ with DKD to stratification of patients based on the principal compartments of inflammatory disease activity.
Exploring association of mobile phone access with positive health outcomes and behaviors amongst post-partum mothers in rural Malawi
Authors: Anto-Ocrah Martina , Latulipe Ryan J. , Mark Tiffany E. , Adler David , Zaihra Tasneem , Lanning Joseph W.
Published: June 2022

Background

Access to mass media and emerging technologies (e.g., cell phones, the internet, and social media) is a social determinant of health that has been shown to profoundly influence women’s health outcomes. In the African region, where women in rural settings with limited access to care are most vulnerable to maternal mortality and other pregnancy-related morbidities, mobile phone access can be an important and life-saving health determinant.

Objective

The goal of this study was to examine the association between mobile/cellular phone ownership and health behaviors of post-partum mothers in rural Malawi.

Methods

In this cross-sectional study, we recruited and consented a convenient sample of 174 post-partum mothers of 4- and 5-month-olds who were attending well-child clinics in Gowa, situated in the rural Ntcheu district of Malawi. Using logistic regression models, we hypothesized that compared to non-cell phone owners, mobile phone ownership will be predictive (greater odds) of antenatal visit frequency, exclusive breastfeeding knowledge and practices, health-seeking behaviors, and involvement in motherhood support groups; and protective (lower odds) of infant illnesses, breastfeeding challenges, and post-partum depressive symptoms.

Results

Mobile phones were highly prevalent in this rural setting, with 45% (n = 79) of post-partum women indicating they owned at least one cell phone. Cell phone owners tended to have higher levels of education (p < 0.012) and wealth (p < 0.001). Interestingly, mobile phone ownership was only associated with exclusive breastfeeding practices; and phone owners had 75% lower odds of exclusively breastfeeding (adj. OR 0.25; 95% CI: 0.07–0.92, p = 0.038) in multivariable models. Though not statistically significant but clinically meaningful, cell phone ownership was associated with fewer depressive symptoms (adj. OR 0.84; 95% CI: 0.39–1.84, p = 0.67) and more social support (adj. OR 1.14; 95% CI: 0.61–2.13, p = 0.70).

Conclusions

Digital literacy and internet connectivity are social determinants of health, thus delving deeper into mothers’ digital experiences to identify and ameliorate their unique barriers to full digital access will be crucial to successful implementation of digital interventions to address post-partum challenges for women in hard-to-reach settings such as ours. Such interventions are of even greater relevance as the Covid-19 pandemic has increased the urgency of reaching vulnerable, marginalized populations.
Does dropout from school matter in taking antenatal care visits among women in Bangladesh? An application of marginalized poisson-poisson mixture model
Authors: Haque M. Ershadul , Mallick Taslim Sazzad , Bari Wasimul
Published: June 2022

Background

There exists a lack of research in explaining the link between dropout from school and antenatal care (ANC) visits of women during pregnancy in Bangladesh. The aim of this study is to investigate how the drop out from school influences the ANC visits after controlling the relevant covariates using an appropriate count regression model.

Methods

The association between the explanatory variables and the outcome of interest, ANC visits, have been performed using one-way analysis of variance/independent sample t-test. To examine the adjusted effects of covariates on the marginal mean of count data, Marginalized Poison-Poisson mixture regression model has been fitted.

Results

The estimated incidence rate of antenatal care visits was 10.6% lower for the mothers who were not continued their education after marriage but had at least 10 years of schooling (p-value <0.01) and 20.2% lower for the drop-outed mothers (p-value <0.01) than the mothers who got continued their education after marriage.

Conclusions

To ensure the WHO recommended 8+ ANC visits for the pregnant women of Bangladesh, it is essential to promote maternal education so that at least ten years of schooling should be completed by a woman and dropout from school after marriage should be prevented.
Quantitative and qualitative changes in platelet traits of sunitinib-treated patients with renal cell carcinoma in relation to circulating sunitinib levels: a proof-of-concept study
Authors: Tullemans Bibian M. E. , Brouns Sanne L. N. , Swieringa Frauke , Sabrkhany Siamack , van den Berkmortel Franchette W. P. J. , Peters Natascha A. J. B. , de Bruijn Peter , Koolen Stijn L. W. , Heemskerk Johan W. M. , Aarts Maureen J. B. , Kuijpers Marijke J. E.
Published: June 2022

Background

Tyrosine kinase inhibitors (TKIs), such as sunitinib, are used for cancer treatment, but may also affect platelet count and function with possible hemostatic consequences. Here, we investigated whether patient treatment with the TKI sunitinib affected quantitative and qualitative platelet traits as a function of the sunitinib level and the occurrence of bleeding.

Methods

Blood was collected from 20 metastatic renal cell carcinoma (mRCC) patients before treatment, and at 2 weeks, 4 weeks and 3 months after sunitinib administration. We measured blood cell counts, platelet aggregation, and concentrations of sunitinib as well as its N-desethyl metabolite in plasma, serum and isolated platelets. Progression of disease (PD) and bleeding were monitored after 3 months.

Results

In sunitinib-treated mRCC patients, concentrations of (N-desethyl-)sunitinib in plasma and serum were highly correlated. In the patients’ platelets the active metabolite levels were relatively increased as compared to sunitinib. On average, a sustained reduction in platelet count was observed on-treatment, which was significantly related to the inhibitor levels in plasma/serum. Principal component and correlational analysis showed that the (N-desethyl-)sunitinib levels in plasma/serum were linked to a reduction in both platelet count and collagen-induced platelet aggregation. The reduced aggregation associated in part with reported bleeding, but did not correlate to PD.

Conclusion

The sunitinib-induced reduction in quantitative and qualitative platelet traits may reflect the effective sunitinib levels in the patient. These novel results may serve as a proof-of-principle for other TKI-related drugs, where both platelet count and functions are affected, which could be used for therapeutic drug monitoring.
Integrative medicine during the intensive phase of chemotherapy in pediatric oncology in Germany: a randomized controlled trial with 5-year follow up
Authors: Seifert Georg , Blakeslee Sarah B. , Calaminus Gabriele , Kandil Farid I. , Barth Andrea , Bernig Toralf , Classen Carl Friedrich , Corbacioglu Selim , Föll Jürgen , Gottschling Sven , Gruhn Bernd , vom Hoff-Heise Claudia , Lode Holger N. , Martin David , Nathrath Michaela , Neunhoeffer Felix , Pekrun Arnulf , Wulff Beate , Zuzak Tycho , Henze Günter , Längler Alfred
Published: June 2022

Background

Integrative medicine is used frequently alongside chemotherapy treatment in pediatric oncology, but little is known about the influence on toxicity. This German, multi-center, open-label, randomized controlled trial assessed the effects of complementary treatments on toxicity related to intensive-phase chemotherapy treatment in children aged 1–18 with the primary outcome of the toxicity sum score. Secondary outcomes were chemotherapy-related toxicity, overall and event-free survival after 5 years in study patients.

Methods

Intervention and control were given standard chemotherapy according to malignancy & tumor type. The intervention arm was provided with anthroposophic supportive treatment (AST); given as anthroposophic base medication (AMP), as a base medication for all patients and additional on-demand treatment tailored to the intervention malignancy groups. The control was given no AMP. The toxicity sum score (TSS) was assessed using NCI-CTC scales.

Results

Data of 288 patients could be analyzed. Analysis did not reveal any statistically significant differences between the AST and the control group for the primary endpoint or the toxicity measures (secondary endpoints). Furthermore, groups did not differ significantly in the five-year overall and event-free survival follow up.

Discussion

In this trial findings showed that AST was able to be safely administered in a clinical setting, although no beneficial effects of AST between group toxicity scores, overall or event-free survival were shown.
Development and validation of a novel mitophagy-related gene prognostic signature for glioblastoma multiforme
Authors: Wang Jinghua , Qiu Xinqi , Huang Jiayu , Zhuo Zewei , Chen Hao , Zeng Ruijie , Wu Huihuan , Guo Kehang , Yang Qi , Ye Huiling , Huang Wei , Luo Yujun
Published: June 2022

Background

Glioblastoma multiforme (GBM) is one of the most malignant tumors in brain with high morbidity and mortality. Mitophagy plays a significant role in carcinogenesis, metastasis, and invasion. In our study, we aim to construct a mitophagy-related risk model to predict prognosis in GBM.

Methods

RNA-seq data combined with clinical information were downloaded from TCGA. The 4-gene risk model and nomograph was then constructed and validated in external cohort. Evaluation of immune infiltration, functional enrichment and tumor microenvironment (TME) were then performed.

Result

A mitophagy-related risk model was established and patients in TCGA and CGGA were classified into low-risk and high-risk groups. In both cohorts, patients in low-risk group had improved survival, while high-risk group had poor prognosis. Also, the risk model was identified as an independent factor for predicting overall survival via Cox regression. Furthermore, a prognostic nomogram including mitophagy signatures was established with excellent predictive performance. In addition, the risk model was closely associated with regulation of immune infiltration as well as TME.

Conclusion

In conclusion, our study constructed a mitophagy-related risk model, which can be utilized for the clinical prognostic prediction in GBM.