bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of hemagglutinin and neuraminidase amplicon-based high-throughput sequencing with variant analysis to detect co-infection and resolve identical consensus sequences of seasonal influenza in a university setting
Authors: Faleye Temitope O. C. , Adams Deborah , Adhikari Sangeet , Sandrolini Helen , Halden Rolf U. , Varsani Arvind , Scotch Matthew 
Published: August 2021

Abstract
Background
Local transmission of seasonal influenza viruses (IVs) can be difficult to resolve. Here, we study if coupling high-throughput sequencing (HTS) of hemagglutinin (HA) and neuraminidase (NA) genes with variant analysis can resolve strains from local transmission that have identical consensus genome. We analyzed 24 samples collected over four days in January 2020 at a large university in the US. We amplified complete hemagglutinin (HA) and neuraminidase (NA) genomic segments followed by Illumina sequencing. We identified consensus complete HA and NA segments using BLASTn and performed variant analysis on strains whose HA and NA segments were 100% similar.

Results
Twelve of the 24 samples were PCR positive, and we detected complete HA and/or NA segments by de novo assembly in 83.33% (10/12) of them. Similarity and phylogenetic analysis showed that 70% (7/10) of the strains were distinct while the remaining 30% had identical consensus sequences. These three samples also had IAV and IBV co-infection. However, subsequent variant analysis showed that they had distinct variant profiles. While the IAV HA of one sample had no variant, another had a T663C mutation and another had both C1379T and C1589A.

Conclusion
In this study, we showed that HTS coupled with variant analysis of only HA and NA genes can help resolve variants that are closely related. We also provide evidence that during a short time period in the 2019–2020 season, co-infection of IAV and IBV occurred on the university campus and both 2020/2021 and 2021/2022 WHO recommended H1N1 vaccine strains were co-circulating.
Hemophagocytic syndrome secondary to SARS-Cov-2 infection: a case report
Authors: Meazza Prina Marco , Martini Francesca , Bracchi Federico , Di Mauro Daniela , Fargnoli Anna , Motta Marco , Giussani Cristina , Gobbin Giovanni , Taverna Monica , D’Alessio Andrea 
Published: August 2021

Abstract
Background
Hemophagocytic syndrome (HPS) is a severe hyperinflammatory disease, whose diagnosis is based on the HLH-2004 criteria. In secondary forms of HLH (sHLH), the primary goal is treating the triggering factors such as COVID-19 (Coronavirus disease 2019). The link between the cytokine storm related to COVID-19 and development of sHLH has already been reported since the onset of pandemic, but little is known about clinical manifestations of HLH which develop after the patient’s recovery from mild symptomatic or asymptomatic Sars-CoV-2 infection.

Case presentation
We describe the case of a woman diagnosed with sHLH related to previous Sars-CoV-2 infection and successfully treated with steroids, colchicine, etoposide and ruxolitinib.

Conclusions
Our report suggests that HLH-like syndrome might be secondary to Sars-CoV-2 infection, even if the patient utterly recovered from the mildly symptomatic viral infection. In addition, we underline the treatment with low dose ruxolitinib plus etoposide as a potential choice for Sars-CoV-2 infection related HLH.
An artifıcial ıntelligence approach to automatic tooth detection and numbering in panoramic radiographs
Authors: Bilgir Elif , Bayrakdar İbrahim Şevki , Çelik Özer , Orhan Kaan , Akkoca Fatma , Sağlam Hande , Odabaş Alper , Aslan Ahmet Faruk , Ozcetin Cemre , Kıllı Musa , Rozylo-Kalinowska Ingrid 
Published: August 2021

AbstractBackgroundPanoramic radiography is an imaging method for displaying maxillary and mandibular teeth together with their supporting structures. Panoramic radiography is frequently used in dental imaging due to its relatively low radiation dose, short imaging time, and low burden to the patient. We verified the diagnostic performance of an artificial intelligence (AI) system based on a deep convolutional neural network method to detect and number teeth on panoramic radiographs.MethodsThe data set included 2482 anonymized panoramic radiographs from adults from the archive of Eskisehir Osmangazi University, Faculty of Dentistry, Department of Oral and Maxillofacial Radiology. A Faster R-CNN Inception v2 model was used to develop an AI algorithm (CranioCatch, Eskisehir, Turkey) to automatically detect and number teeth on panoramic radiographs. Human observation and AI methods were compared on a test data set consisting of 249 panoramic radiographs. True positive, false positive, and false negative rates were calculated for each quadrant of the jaws. The sensitivity, precision, and F-measure values were estimated using a confusion matrix.ResultsThe total numbers of true positive, false positive, and false negative results were 6940, 250, and 320 for all quadrants, respectively. Consequently, the estimated sensitivity, precision, and F-measure were 0.9559, 0.9652, and 0.9606, respectively.ConclusionsThe deep convolutional neural network system was successful in detecting and numbering teeth. Clinicians can use AI systems to detect and number teeth on panoramic radiographs, which may eventually replace evaluation by human observers and support decision making.
What underlies the difference between self-reported health and disability after stroke? A qualitative study in the UK
Authors: Mavaddat Nahal , Sadler Euan , Lim Lisa , Williams Kate , Warburton Elizabeth , Kinmonth Ann Louise , Mckevitt Chris , Mant Jonathan 
Published: August 2021

Abstract
Background
Levels of self-reported health do not always correlate with levels of physical disability in stroke survivors. We aimed to explore what underlies the difference between subjective self-reported health and objectively measured disability among stroke survivors.

Methods
Face to face semi-structured interviews were conducted with stroke survivors recruited from a stroke clinic or rehabilitation ward in the UK. Fifteen stroke survivors purposively sampled from the clinic who had discordant self-rated health and levels of disability i.e. reported health as ‘excellent’ or ‘good’ despite significant physical disability (eight), or as ‘fair’ or ‘poor’ despite minimal disability (seven) were compared to each other, and to a control group of 13 stroke survivors with concordant self-rated health and disability levels. Interviews were conducted 4 to 6 months after stroke and data analysed using the constant comparative method informed by Albrecht and Devlieger’s concept of ‘disability paradox’.

Results
Individuals with ‘excellent’ or ‘good’ self-rated health reported a sense of self-reliance and control over their bodies, focussed on their physical rehabilitation and lifestyle changes and reported few bodily and post-stroke symptoms regardless of level of disability. They also frequently described a positive affect and optimism towards recovery. Some, especially those with ‘good’ self-rated health and significant disability also found meaning from their stroke, reporting a spiritual outlook including practicing daily gratitude and acceptance of limitations. Individuals with minimal disability reporting ‘fair’ or ‘poor’ self-rated health on the other hand frequently referred to their post-stroke physical symptoms and comorbidities and indicated anxiety about future recovery. These differences in psychological outlook clustered with differences in perception of relational and social context including support offered by family and healthcare professionals.

Conclusions
The disability paradox may be illuminated by patterns of individual attributes and relational dynamics observed among stroke survivors. Harnessing these wider understandings can inform new models of post-stroke care for evaluation.
Estimating the causal effect of embryo transfer day on clinical in vitro fertilization outcomes using propensity score matching
Authors: Hsieh Han-Chih , Lee Chun-I , Lai En-Yu , Su Jia-Ying , Huang Yi-Ting , Zheng Wei-Lin , Chen Chien-Hong , Huang Chun-Chia , Lin Pin-Yao , Lee Maw-Sheng , Liu Mark , Huang Yen-Tsung 
Published: August 2021

AbstractBackgroundFor women undergoing in vitro fertilization (IVF), the clinical benefit of embryo transfer at the blastocyst stage (Day 5) versus cleavage stage (Day 3) remains controversial. The purpose of this study is to compare the implantation rate, clinical pregnancy rate and odds of live birth of Day 3 and Day 5 embryo transfer, and more importantly, to address the issue that patients were chosen to receive either transfer protocol due to their underlying clinical characteristics, i.e., confounding by indication.MethodsWe conducted a retrospective cohort study of 9,090 IVF cycles collected by Lee Women’s Hospital in Taichung, Taiwan from 1998 to 2014. We utilized the method of propensity score matching to mimic a randomized controlled trial (RCT) where each patient with Day 5 transfer was matched by another patient with Day 3 transfer with respect to other clinical characteristics. Implantation rate, clinical pregnancy rate, and odds of live birth were compared for women underwent Day 5 transfer and Day 3 transfer to estimate the causal effects. We further investigated the causal effects in subgroups by stratifying age and anti-Mullerian hormone (AMH).ResultsOur analyses uncovered an evidence of a significant difference in implantation rate (p=0.04) favoring Day 5 transfer, and showed that Day 3 and Day 5 transfers made no difference in both odds of live birth (p=0.27) and clinical pregnancy rate (p=0.11). With the increase of gestational age, the trend toward non-significance of embryo transfer day in our result appeared to be consistent for subgroups stratified by age and AMH, while all analyses stratified by age and AMH were not statistically significant.ConclusionsWe conclude that for women without strong indications for Day 3 or Day 5 transfer, there is a small significant difference in implantation rate in favor of Day 5 transfer. However, the two protocols have indistinguishable outcomes on odds of live birth and clinical pregnancy rate.
Breastfeeding support and barriers to women with gestational diabetes mellitus: a nationwide cross-sectional survey of hospitals in Japan
Authors: Matsunaga Mayumi , Kataoka Yaeko , Igarashi Yumiko , Fukui Toshiko , Imura Masumi , Horiuchi Shigeko 
Published: August 2021

Abstract
Background
Despite the benefits of breastfeeding for women with Gestational Diabetes Mellitus (GDM) and their infants, breastfeeding is less likely to be performed by this group. This study aimed to examine the current levels of implementation of breastfeeding support to women with GDM in Japan and to clarify barriers to promoting breastfeeding among this population.

Methods
A 25-item questionnaire was developed by the authors to investigate the current levels of implementation of breastfeeding support for women with GDM provided in hospitals, and to explore barriers for promoting breastfeeding among these women. The questionnaire was sent to all 1046 hospitals facilitating childbirth in Japan. Descriptive statistics were used to analyze the quantitative data, and content analysis was used to analyze qualitative data from the open-ended questions.

Results
All 296 respondents were included in this study. Regarding breastfeeding support, 95.2% of the respondents provided general information on breastfeeding to GDM women during antenatal midwife consultations. However, the benefits of breastfeeding for preventing type 2 diabetes were addressed by only 48.0%. Likewise, although follow-up services (e.g., telephone support or breastfeeding consultations) were conducted in 88.9% of hospitals, only 50.7% of hospitals informed women that breastfeeding decreases the risk of developing type 2 diabetes after GDM. Regarding barriers, seven categories and 20 subcategories about promoting breastfeeding for women with GDM were extracted and abstracted into the following three themes: Barriers associated with mother and infant, Barriers associated with health professionals, and Organizational barriers.

Conclusions
In Japan, most hospitals that responded provided general breastfeeding support from the antenatal to postpartum periods. However, the benefits of breastfeeding in terms of preventing the incidence of type 2 diabetes following GDM were insufficiently communicated to women with GDM. Furthermore, there were numerous barriers to promoting breastfeeding among women with GDM.
Precision treatment exploration of breast cancer based on heterogeneity analysis of lncRNAs at the single-cell level
Authors: Zhang Yan , Zhang Denan , Meng Qingkang , Liu Ziqi , Xie Hongbo , Liu Lei , Xu Fei , Chen Xiujie 
Published: August 2021

AbstractBackgroundBreast cancer (BC) is a complex disease with high heterogeneity, which often leads to great differences in treatment results. Current common molecular typing method is PAM50, which shows positive results for precision medicine; however, room for improvement still remains because of the different prognoses of subtypes. Therefore, in this article, we used lncRNAs, which are more tissue-specific and developmental stage-specific than other RNAs, as typing markers and combined single-cell expression profiles to retype BC, to provide a new method for BC classification and explore new precise therapeutic strategies based on this method.MethodsBased on lncRNA expression profiles of 317 single cells from 11 BC patients, SC3 was used to retype BC, and differential expression analysis and enrichment analysis were performed to identify biological characteristics of new subtypes. The results were validated for survival analysis using data from TCGA. Then, the downstream regulatory genes of lncRNA markers of each subtype were searched by expression correlation analysis, and these genes were used as targets to screen therapeutic drugs, thus proposing new precision treatment strategies according to the different subtype compositions of patients.ResultsSeven lncRNA subtypes and their specific biological characteristics are obtained. Then, 57 targets and 210 drugs of 7 subtypes were acquired. New precision medicine strategies were proposed according to the different compositions of patient subtypes.ConclusionsFor patients with different subtype compositions, we propose a strategy to select different drugs for different patients, which means using drugs targeting multi subtype or combinations of drugs targeting a single subtype to simultaneously kill different cancer cells by personalized treatment, thus reducing the possibility of drug resistance and even recurrence.
Sniffer dogs can identify lung cancer patients from breath and urine samples
Authors: Feil Charlotte , Staib Frank , Berger Martin R. , Stein Thorsten , Schmidtmann Irene , Forster Andreas , Schimanski Carl C. 
Published: August 2021

AbstractBackgroundLung cancer is the most common oncological cause of death in the Western world. Early diagnosis is critical for successful treatment. However, no effective screening methods exist. A promising approach could be the use of volatile organic compounds as diagnostic biomarkers. To date there are several studies, in which dogs were trained to discriminate cancer samples from controls. In this study we evaluated the abilities of specifically trained dogs to distinguish samples derived from lung cancer patients of various tumor stages from matched healthy controls.MethodsThis single center, double-blind clinical trial was approved by the local ethics committee, project no FF20/2016. The dog was conditioned with urine and breath samples of 36 cancer patients and 150 controls; afterwards, further 246 patients were included: 41 lung cancer patients comprising all stages and 205 healthy controls. From each patient two breath and urine samples were collected and shock frozen. Only samples from new subjects were presented to the dog during study phase randomized, double-blinded. This resulted in a specific conditioned reaction pointing to the cancer sample.ResultsUsing a combination of urine and breath samples, the dog correctly predicted 40 out of 41 cancer samples, corresponding to an overall detection rate of cancer samples of 97.6% (95% CI [87.1, 99.9%]). Using urine samples only the dog achieved a detection rate of 87.8% (95% CI [73.8, 95.9%]). With breath samples, the dog correctly identified cancer in 32 of 41 samples, resulting in a detection rate of 78% (95% CI [62.4, 89.4%]).ConclusionsIt is known from current literature that breath and urine samples carry VOCs pointing to cancer growth. We conclude that olfactory detection of lung cancer by specifically trained dogs is highly suggestive to be a simple and non-invasive tool to detect lung cancer. To translate this approach into practice further target compounds need to be identified.
Acute limb ischemia in a cancer patient has high morbidity, high mortality, and atypical presentation: a tertiary cancer center’s retrospective study
Authors: Bryce Yolanda , Emmanuel Amoateng , Agrusa Christopher , Ziv Etay , Harnain Christopher , Huq Samantha , Martin Ernesto Santos 
Published: August 2021

Abstract
Background
Acute Limb Ischemia (ALI) carries a high morbidity and mortality rate that is compounded in the cancer patient. Though it is a relatively uncommon event, it is of extremely high adverse impact and carries poor awareness among clinicians.

Methods
Retrospective review of electronic medical records was performed of cancer patients presenting with acute limb ischemia (ALI) to the tertiary cancer center’s urgent care center or as inpatient between January 1, 2014 and January 1, 2020.

Results
Out of the 29 cancer patients with ALI, 12 (41%) died within 3 month and 9 (31%) patients died within 1 months of ALI diagnosis. 65% had long term adverse outcome after ALI – 31% with death in 1 month, 2 (7%) with an amputation, 5 (17%) with lifestyle-limiting claudication, and 3 (10%) with subsequent wound ulceration or gangrene. Patients not eligible for standard of care (12 patients, 41%) (RR 2.33 95% CI [1.27–4.27], p <  0.01) and heparin administration ≥6 h from presentation (19 patients, 65%) (RR 2.81 [1.07–7.38], p = 0.04) were at increased risk of adverse outcome. Atypical/confounded presentation of ALI (13 patients, 45%) (RR 1.84 95% CI [1.03–3.29], p = 0.04), pulse exam not documented (12 patients, 41.4%) (RR 1.95 [95% CI [1.14–3.32], p = 0.01), and patients with services other than a vascular specialist initially consulted (8 patients, 27.6%) (RR 1.91 95% CI [1.27–2.87], p <  0.01) were significant risk factors for heparin administered ≥6 h from presentation.

Conclusions
ALI is devastating in cancer patients, with a high number presenting with atypical/confounded signs and symptoms which delays treatment. Heparin administered ≥6 h from presentation is associated with adverse outcome.
Acceptability of a digital return-to-work intervention for common mental disorders: a qualitative study on service user perspectives
Authors: Engdahl Patrik , Svedberg Petra , Bejerholm Ulrika 
Published: August 2021

AbstractBackgroundThere is an evident discrepancy between need and provision of evidence-based return-to-work (RTW) interventions in existing mental health services. Online dissemination of evidence-based interventions is presumed to reduce this gap. However, there is almost no knowledge available on perceived acceptability of digital RTW interventions among service users, which are factors that might influence the development and implementation of future interventions. The aim of this study was to develop knowledge of service user acceptability of mWorks, a proposed digital RTW solution.MethodsParticipants (n = 18) with experience of common mental disorder and sick leave were recruited with a purposive snowball sampling method. Semi-structured interviews (n = 12) and one focus group interview (n = 6) were conducted. A deductive thematic analysis was performed according to the Theoretical Framework of Acceptability.ResultsDigital RTW interventions were perceived as acceptable and aligned with participant value. Participants expressed positive attitudes toward having access to support, regardless of time and place. A certain ambiguity between a decline in social interactions and opportunities to RTW in a safe space was reported. Participants were confident in their ability to use digital RTW solutions, but reported the need to reduce stressful elements of using smartphones. Overly demanding digital solutions, i.e. ones requiring high cognitive effort, were described as burdensome.ConclusionsFor digital RTW solutions to be acceptable, they need to complement traditional services by providing accessible and person-centred support throughout the RTW process. They should be designed to reduce the need for cognitive effort. Future research should explore how to balance user autonomy with other support components in digital interventions.
“Burnt by the scorching sun”: climate-induced livelihood transformations, reproductive health, and fertility trajectories in drought-affected communities of Zambia
Authors: Rosen Joseph G. , Mulenga Drosin , Phiri Lyson , Okpara Natasha , Brander Caila , Chelwa Nachela , Mbizvo Michael T. 
Published: August 2021

AbstractBackgroundClimate-induced disruptions like drought can destabilize household and community livelihoods, particularly in low- and middle-income countries. This qualitative study explores the impact of severe and prolonged droughts on gendered livelihood transitions, women’s social and financial wellbeing, and sexual and reproductive health (SRH) outcomes in two Zambian provinces.MethodsIn September 2020, in-depth interviews (n = 20) and focus group discussions (n = 16) with 165 adult women and men in five drought-affected districts, as well as key informant interviews (n = 16) with civic leaders and healthcare providers, were conducted. A team-based thematic analysis approach, guided by the Framework Method, was used to code transcript text segments, facilitating identification and interpretation of salient thematic patterns.ResultsAcross districts, participants emphasized the toll drought had taken on their livelihoods and communities, leaving farming households with reduced income and food, with many turning to alternative income sources. Female-headed households were perceived as particularly vulnerable to drought, as women’s breadwinning and caregiving responsibilities increased, especially in households where women’s partners out-migrated in search of employment prospects. As household incomes declined, women and girls’ vulnerabilities increased: young children increasingly entered the workforce, and young girls were married when families could not afford school fees and struggled to support them financially. With less income due to drought, many participants could not afford travel to health facilities or would resort to purchasing health commodities, including family planning, from private retail pharmacies when unavailable from government facilities. Most participants described changes in fertility intentions motivated by drought: women, in particular, expressed desires for smaller families, fearing drought would constrain their capacity to support larger families. While participants cited some ongoing activities in their communities to support climate change adaptation, most acknowledged current interventions were insufficient.ConclusionsDrought highlighted persistent and unaddressed vulnerabilities in women, increasing demand for health services while shrinking household resources to access those services. Policy solutions are proposed to mitigate drought-induced challenges meaningfully and sustainably, and foster climate resilience.