bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised explainable AI for molecular evolutionary study of forty thousand SARS-CoV-2 genomes
Authors: Iwasaki Yuki , Abe Takashi , Wada Kennosuke , Wada Yoshiko , Ikemura Toshimichi 
Published: March 2022

Abstract
Background
Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes.

Results
While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. Additionally, BLSOM also provided information concerning the special genomic region possibly undergoing RNA modifications.

Conclusions
The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes, and it can complement phylogenetic methods based on sequence alignment.
The fate of indeterminate liver lesions: What proportion are precursors of hepatocellular carcinoma?
Authors: Cococcia Sara , Dutta Priti , Moghim Melika , Hogan Brian , Tanwar Sudeep , Marshall Aileen , Macdonald Douglas , Yu Dominic , O’Beirne James , Rosenberg William M. , Trembling Paul M. 
Published: March 2022

Abstract
Background
The natural history and incidence of hepatocellular carcinoma (HCC) arising from indeterminate liver lesions are not well described. We aimed to define the incidence of HCC in a cohort of patients undergoing surveillance by magnetic resonance imaging (MRI) and estimate any associations with incident HCC.

Methods
We performed a retrospective follow-up study, identifying MRI scans in which indeterminate lesions had been reported between January 2006 and January 2017. Subsequent MRI scan reports were reviewed for incident HCC arising from indeterminate lesions, data were extracted from electronic patient records and survival analysis performed to estimate associations with baseline factors.

Results
One hundred and nine patients with indeterminate lesions on MRI were identified. HCC developed in 19 (17%) patients over mean follow up of 4.6 years. Univariate Cox proportional hazards analysis found incident HCC to be significantly associated with baseline low platelet count (hazard ratio (HR) = 7.3 (95% confidence intervals (CI) 2.1–24.9), high serum alpha-fetoprotein level (HR = 2.7 (95% CI 1.0–7.1)) and alcohol consumption above fourteen units weekly (HR = 3.1 (95% CI 1.1–8.7)). Multivariate analysis, however, found that only low platelet count was independently associated with HCC (HR = 5.5 (95% CI 0.6–5.1)).

Conclusions
HCC arises in approximately one fifth of indeterminate liver lesions over 4.6 years and is associated with a low platelet count at the time of first diagnosis of an indeterminate lesion. Incidence of HCC was more common in people with viral hepatitis and in those consuming > 14 units of alcohol per week. Our data may be used to support a strategy of enhanced surveillance in patients with indeterminate lesions.
Gastrointestinal symptoms are associated with a lower risk of hospitalization and mortality and outcomes in COVID-19
Authors: Delavari Alireza , Asgari Samaneh , Alimohamadi Yousef , Vosoogh-Moghaddam Abbass , Sadeghi Anahita , Shahrousvand Shokouh , Zakeri Armin , Moradzadeh Rahmatollah , Akbarpour Samaneh 
Published: March 2022

Abstract
Background
We aimed to find the association between gastrointestinal (GI) and respiratory symptoms with mortality and hospitalization among COVID-19 patients.

Methods
We analyzed the registered data of COVID-19 patients from February 20, 2020, to March 10, 2021. Depending on the patients’ disease symptoms, four categories were defined: patients with only GI symptoms, patients with only respiratory symptoms, patients with both symptoms, and patients with other symptoms. Logistic regression analysis was used to assess the association of groups with outcomes.

Results
A total of 42,964 patients from 23 hospitals were included, of which 26.5% patients had at least one or more GI symptoms. Of total patients, 51.58% patients were hospitalized among which 22.8% had at least one or more GI symptoms. GI symptoms significantly decreased the odds of mortality (OR 0.72, 95% CI 0.56–0.92), but respiratory symptoms increased the odds for mortality (1.36: 1.24–1.50), compared with patients with other symptoms. Moreover, the odds ratio of patients who had both respiratory and GI symptoms increased (1.52: 1.31–1.78) compared with patients with other symptoms. The same results were observed for hospitalization as the outcome.

Conclusions
Our study showed that the presence of GI symptoms in COVID-19 at the time of admission was associated with a lower odds of hospitalization and mortality; however, this association had higher odds for respiratory symptoms.
Characterization of short-chain fatty acids in patients with ulcerative colitis: a meta-analysis
Authors: Xu Hao-Ming , Zhao Hai-Lan , Guo Gong-Jing , Xu Jing , Zhou You-Lian , Huang Hong-Li , Nie Yu-Qiang 
Published: March 2022

Abstract
Background
Studies investigating the changes in short-chain fatty acids (SCFAs) in patients with ulcerative colitis (UC) have yielded inconsistent results. We performed a meta-analysis of studies that investigated the alterations in different SCFAs among UC patients to assess their role in the development of UC.

Methods
Three databases were searched for relevant studies published as of April 2021. Results are presented as standardized mean difference (SMD) with 95% confidence interval (95% CI).

Results
Eleven studies were included in the meta-analysis. Compared to healthy subjects, UC patients had significantly lower concentrations of total SCFAs (SMD = − 0.88, 95%CI − 1.44, − 0.33; P < 0.001), acetate (SMD = − 0.54, 95% CI − 0.91, − 0.17; P = 0.004), propionate, (SMD = − 0.37, 95% CI − 0.66, − 0.07; P = 0.016), and valerate (SMD = − 0.91, 95% CI − 1.45, − 0.38; P < 0.001). On subgroup analysis based on disease status, patients with active UC had reduced concentrations of acetate (SMD = − 1.83, 95% CI − 3.32, − 0.35; P = 0.015), propionate (SMD = − 2.51, 95% CI − 4.41, − 0.61; P = 0.009), and valerate (SMD = − 0.91, 95% CI − 1.45, − 0.38; P < 0.001), while UC patients in remission had similar concentrations with healthy subjects. Patients with active UC had lower butyrate level (SMD = − 2.09, 95% CI − 3.56, − 0.62; P = 0.005) while UC patients in remission had higher butyrate level (SMD = 0.71, 95% CI 0.33, 1.10; P < 0.001) compared with healthy subjects.

Conclusion
UC patients had significantly decreased concentrations of total SCFAs, acetate, propionate, and valerate compared with healthy subjects. In addition, inconsistent changes of certain special SCFAs were observed in UC patients with different disease status.
An evaluation of injurious falls and Fall-Risk-Increasing-Drug (FRID) prescribing in ambulatory care in older adults
Authors: Elliott Taylor R. , Westneat Susan , Karanth Shama D. , Abner Erin L. , Kucharska-Newton Anna M. , Moga Daniela C. 
Published: March 2022

Abstract
Background
Falls are a major public health problem affecting millions of older adults each year. Little is known about FRID prescribing behaviors after injurious falls occur. The primary objective of this study was to investigate whether an injurious fall is associated with being prescribed a new FRID.

Methods
We conducted a cross-sectional analysis using data from the National Ambulatory Medical Care Survey (2016). We included visits from patients age ≥ 65 years and classified visits based on presence of an injurious fall. The outcome of interest was prescription of new FRID between those with and without an injurious fall. Multivariable logistic regression weighted for sampling and adjusted for demographics, health history and other medications was used. Age and Alzheimer’s disease were examined as potential effect measure modifiers. Odds ratios and 95% confidence intervals were reported. Bayes factor upper bounds were also reported to quantify whether the data were better predicted by the null hypothesis or the alternative hypothesis.

Results
The sample included 239,016,482 ambulatory care visits. 5,095,734 (2.1%) of the visits were related to an injurious fall. An injurious fall was associated with a non-statistically significant increase in odds of at least one new FRID prescription: adjusted OR = 1.6 (95% CI 0.6, 4.0). However, there was non-statistically significant evidence that the association depended on patient age, with OR = 2.6 (95% CI 0.9, 7.4) for ages 65–74 versus OR = 0.4 (95% CI 0.1, 1.6) for ages ≥ 75. In addition to age, Alzheimer’s disease was also identified as a statistically significant effect measure modifier, but stratum specific estimates were not determined due to small sample sizes.

Conclusions
Ambulatory care visits involving an injurious fall showed a non-statistically significant increase in odds of generating a new FRID prescription, but this association may depend on age.
Health care system and patient costs associated with receipt of minimally adequate treatment for depression and anxiety disorders in older adults
Authors: Lamoureux-Lamarche Catherine , Berbiche Djamal , Vasiliadis Helen-Maria 
Published: March 2022

AbstractBackgroundDepression and anxiety disorders in older adults are associated with a great burden. Research has shown that less than 50% of adults receive adequate treatment in primary care settings for these disorders. Rare are the studies however assessing adequate treatment in older adults and associated costs from the societal perspective. Given the episodic nature of common mental disorders, this study aims to assess the three-year costs from a restricted societal perspective (including health system and patient perspectives) associated with receipt of minimally adequate treatment for depression and anxiety disorders in older adults consulting in primary care.MethodsThis primary care cohort study included 358 older adults aged 65 years and older with either a self-reported or physician diagnosis of depression or an anxiety disorder covered under Quebec’s public drug plan. Receipt of minimally adequate treatment was assessed according to Canadian guidelines and relevant reports. Outpatient and inpatient service use, medication costs and physician billing fees were obtained from provincial administrative databases. Unit costs were calculated using provincial financial and activity reports and relevant literature. A propensity score was created to estimate the probability of receiving minimally adequate treatment and the inverse probability was used as a weight in analyses. Generalized linear models, with gamma distribution and log link, were conducted to assess the association between receipt of minimally adequate treatment and costs.ResultsOverall, receipt of minimally adequate treatment was associated with increased three-year costs averaging $5752, $536, $6266 for the health system, patient and societal perspectives, respectively, compared to those not receiving minimally adequate treatment. From the health system perspective, participants receiving minimally adequate treatment had higher costs related to emergency department (ED) (difference: $457,p = 0.001) and outpatient visits (difference: $620,p < 0.001), inpatient stays (difference: $2564,p = 0.025), drug prescriptions (difference: $1243,p = 0.002) and physician fees (difference: $1224,p < 0.001). From the patient perspective, receipt of minimally adequate treatment was associated with higher costs related to loss of productivity related to ED (difference: $213,p < 0.001) and outpatient visits (difference: $89,p < 0.001).ConclusionsOlder adults receiving minimally adequate treatment for depression and anxiety disorders incurred higher societal costs reaching $2089 annually compared to older adults not receiving minimally adequate treatment. The main cost drivers were attributable to hospitalizations and prescription drug costs.
Engagement with protective behaviours in the UK during the COVID-19 pandemic: a series of cross-sectional surveys (the COVID-19 rapid survey of adherence to interventions and responses [CORSAIR] study)
Authors: Smith Louise E. , Potts Henry W. W. , Amlȏt Richard , Fear Nicola T. , Michie Susan , Rubin G. James 
Published: March 2022

Abstract
Background
Behaviour is key to suppressing the COVID-19 pandemic. Maintaining behaviour change can be difficult. We investigated engagement with hand cleaning, reducing the number of outings, and wearing a face covering over the course of the pandemic.

Methods
We used a series of 64 cross-sectional surveys between 10 February 2020 and 20 January 2022 (n ≈ 2000 per wave). Surveys investigated uptake of hand cleaning behaviours, out of home activity (England only, n ≈ 1700 per wave) and wearing a face covering (England only, restricted to those who reported going out shopping in the last week, n ≈ 1400 per wave).

Results
Reported hand cleaning has been high throughout the pandemic period (85 to 90% of participants consistently reporting washing their hands thoroughly and regularly with soap and water frequently or very frequently). Out of home activity has mirrored the easing and re-introduction of restrictive measures. Total number of outings were higher in the second national lockdown than in the first and third lockdowns. Wearing a face covering increased steadily between April to August 2020, plateauing until the end of measurement in May 2021, with approximately 80% of those who had been out shopping in the previous week reporting wearing a face covering frequently or very frequently.

Conclusions
Engagement with protective behaviours increased at the start of the pandemic and has remained high since. The greatest variations in behaviour reflected changes to Government rules. Despite the duration of restrictions, people have continued to adopt personal protective behaviours that were intended to prevent the spread of COVID-19.
Muscle architecture, growth, and biological Remodelling in cerebral palsy: a narrative review
Authors: Handsfield Geoffrey G. , Williams Sîan , Khuu Stephanie , Lichtwark Glen , Stott N. Susan 
Published: March 2022

AbstractCerebral palsy (CP) is caused by a static lesion to the brain occurring in utero or up to the first 2 years of life; it often manifests as musculoskeletal impairments and movement disorders including spasticity and contractures. Variable manifestation of the pathology across individuals, coupled with differing mechanics and treatments, leads to a heterogeneous collection of clinical phenotypes that affect muscles and individuals differently. Growth of muscles in CP deviates from typical development, evident as early as 15 months of age. Muscles in CP may be reduced in volume by as much as 40%, may be shorter in length, present longer tendons, and may have fewer sarcomeres in series that are overstretched compared to typical. Macroscale and functional deficits are likely mediated by dysfunction at the cellular level, which manifests as impaired growth. Within muscle fibres, satellite cells are decreased by as much as 40–70% and the regenerative capacity of remaining satellite cells appears compromised. Impaired muscle regeneration in CP is coupled with extracellular matrix expansion and increased pro-inflammatory gene expression; resultant muscles are smaller, stiffer, and weaker than typical muscle. These differences may contribute to individuals with CP participating in less physical activity, thus decreasing opportunities for mechanical loading, commencing a vicious cycle of muscle disuse and secondary sarcopenia. This narrative review describes the effects of CP on skeletal muscles encompassing substantive changes from whole muscle function to cell-level effects and the effects of common treatments. We discuss growth and mechanics of skeletal muscles in CP and propose areas where future work is needed to understand these interactions, particularly the link between neural insult and cell-level manifestation of CP.
Suppurative thyroiditis caused by ingested fish bone in the thyroid gland: a case report on its diagnostics and surgical therapy
Authors: Hendricks Anne , Meir Michael , Hankir Mohammed , Lenschow Christina , Germer Christoph-Thomas , Schneider Michael , Wiegering Armin , Schlegel Nicolas 
Published: March 2022

Abstract
Background
Accidental ingestion of fish bone is a common cause of otolaryngological emergency. Migration of the ingested bone into the thyroid gland, however, occurs very rarely. The associated clinical presentation, symptoms and duration of discomfort are also highly variable between patients and can be diagnostically challenging.

Case presentation
Here, we report the case of a 71-year-old female patient presenting with an ingested fish bone that migrated into the right thyroid lobe as a rare cause of suppurative thyroiditis with the clinical features of sepsis. We outline the diagnostic approach, peri- and intraoperative management as well as complications. It is proposed that besides endoscopy, imaging methods such as ultrasound or computed tomography may be necessary to verify the diagnosis and location of an ingested fish bone. Prompt surgical removal of the foreign body and resection of the infectious focus is recommended to minimize the risk of local inflammation, recurrent nerve lesions and septic complications arising from the spread of infection.

Conclusion
Fish bone migration into the thyroid gland is an extremely rare event, the successful detection and surgical management of which can be achieved through a careful interdisciplinary approach.
Syndrome of inappropriate secretion of antidiuretic hormone following high dose rate brachytherapy for prostate cancer: a case report
Authors: Ayoola Adeoluwa , Sodji Quaovi H. , Chin Sharon , Panousis Periklis , Bagshaw Hilary P. , Buyyounouski Mark K. 
Published: March 2022

Abstract
Background
The syndrome of inappropriate secretion of antidiuretic hormone is a disorder characterized by the excess release of antidiuretic hormone and can result in hyponatremia. If managed inappropriately, severe hyponatremia can cause seizures, cerebral edema, and even death. There are various known causes of this inappropriate release of antidiuretic hormone, including malignancy, CNS disorders, and disturbances in the hypothalamic-pituitary-renal axis. However, reports of syndrome of inappropriate secretion of antidiuretic hormone after brachytherapy for prostate cancer are exceedingly rare.

Case presentation
We report a case of symptomatic hyponatremia secondary to the inappropriate secretion of antidiuretic hormone after prostate high-dose rate brachytherapy under general anesthesia in a patient with adenocarcinoma of the prostate.

Conclusions
In rare instances, inappropriate secretion of antidiuretic hormone can occur after high-dose rate brachytherapy for prostate cancer. The cause is likely multifactorial, involving pain or discomfort ensuing from the surgical procedure, the general anesthesia or intraoperative drugs administered. However, due to the potential severity of the side effects, timely diagnosis is crucial to ensure prompt, and effective management.
Collaborative learning in small groups in an online course – a case study
Authors: Haugland Mildrid Jorunn , Rosenberg Ivar , Aasekjær Katrine 
Published: March 2022

Abstract
Background
The ability to learn collaboratively and work in teams is an essential competency in both educational and healthcare settings, and collaborative student activities are acknowledged as being an important part of the pedagogical approach in higher education and teaching. The course that was the focus of this research, a 15-ECTS-credit online course in philosophy of science, ethics, and research methods, was offered online as part of 11 master’s-level health programmes at a university in Norway. Collaborative learning in combination with digital teaching tools was the preferred pedagogical approach in the online course. The aim of the study was to describe, explore and discuss how the students collaborated in small groups in an online course to learn.

Methods
We performed six focus groups and 13 individual interviews from February 2018 to May 2019, conducting a qualitative case study with a content analysis of the data collected. The participants were master students in the same faculty at a university in Norway. All the included participants had fulfilled the 15 ECTS credit course.

Results
Our study revealed that the collaboration in small groups resulted in three different working processes, depending on the students’ ability to be flexible and take responsibility for their own and common learning. The three different working processes that emerged from our data were 1. joint responsibility – flexible organization; 2. individual responsibility – flexible organization; and 3. individual responsibility – unorganized. None of the groups changed their working process during their course, even though some experienced their strategy as inadequate.

Conclusions
Our study showed that despite similar factors such as context, assignments and student autonomy, the students chose different collaboration strategies to accomplish the online course learning objectives. Each group chose their own working process, but only the strategy 1. joint responsibility – flexible organization seemed to promote collaboration, discussion, and team work to complete the complex assignments in the online course. The result from our study may be helpful in designing and planning future online courses; hence online learning requires a focus on how students collaborate and learn online, to gain knowledge and understanding through group discussion.
Using information technology to optimize the identification process for outpatients having blood drawn and improve patient satisfaction
Authors: Wu Li-Feng , Zhuang Guo-Hua , Hu Qi-Lei , Zhang Liang , Luo Zhang-Mei , Lv Yin-Jiang , Tang Jian 
Published: March 2022

Abstract
Background
This study explored the application effect of information technology in optimizing the patient identification process.

Methods
The method for optimizing the identification process involved in drawing blood among outpatients using information technology was executed from July 2020. In this paper, 959 patients who had blood drawn from January to June 2020 were included as the pre-optimization group, and 1011 patients who had blood drawn from July to December 2019 were included as the post-optimization group. The correct rate of patient identification, waiting time, and patient satisfaction before and after the optimization were statistically analyzed. The changes in these three indexes before and after the optimization implementation, as well as the application effects, were compared.

Results
The correct rate of patient identification after optimization (99.80%) was higher than before optimization (98.02%) (X2 = 13.120; P < 0.001), and the waiting time for having blood drawn was also significantly shortened (t = 8.046; P < 0.001). The satisfaction of patients was also significantly improved (X2 = 20.973; P < 0.001).

Conclusions
By combining information technology with the characteristics of blood collection in our hospital, using the call system to obtain patient information, then scan the QR code of the guide sheet for automatic verification, and finally manually reconfirm patient information, which can significantly reduce the occurrence of identification errors, improve work efficiency and improve patients' satisfaction.