bluuebunny/crossref_metadata_2025_split huggingface dataset:
A large-scale comparative study on peptide encodings for biomedical classification
Authors: Spänig Sebastian , Mohsen Siba , Hattab Georges , Hauschild Anne-Christin , Heider Dominik 
Published: May 2021

Abstract
Owing to the great variety of distinct peptide encodings, working on a biomedical classification task at hand is challenging. Researchers have to determine encodings capable to represent underlying patterns as numerical input for the subsequent machine learning. A general guideline is lacking in the literature, thus, we present here the first large-scale comprehensive study to investigate the performance of a wide range of encodings on multiple datasets from different biomedical domains. For the sake of completeness, we added additional sequence- and structure-based encodings. In particular, we collected 50 biomedical datasets and defined a fixed parameter space for 48 encoding groups, leading to a total of 397 700 encoded datasets. Our results demonstrate that none of the encodings are superior for all biomedical domains. Nevertheless, some encodings often outperform others, thus reducing the initial encoding selection substantially. Our work offers researchers to objectively compare novel encodings to the state of the art. Our findings pave the way for a more sophisticated encoding optimization, for example, as part of automated machine learning pipelines. The work presented here is implemented as a large-scale, end-to-end workflow designed for easy reproducibility and extensibility. All standardized datasets and results are available for download to comply with FAIR standards.
A map of the SARS-CoV-2 RNA structurome
Authors: Andrews Ryan J , O’Leary Collin A , Tompkins Van S , Peterson Jake M , Haniff Hafeez S , Williams Christopher , Disney Matthew D , Moss Walter N 
Published: May 2021

AbstractSARS-CoV-2 has exploded throughout the human population. To facilitate efforts to gain insights into SARS-CoV-2 biology and to target the virus therapeutically, it is essential to have a roadmap of likely functional regions embedded in its RNA genome. In this report, we used a bioinformatics approach, ScanFold, to deduce the local RNA structural landscape of the SARS-CoV-2 genome with the highest likelihood of being functional. We recapitulate previously-known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a large reservoir of potential drug targets for RNA-binding small molecules. Results are enhanced via the re-analyses of publicly-available genome-wide biochemical structure probing datasets that are broadly in agreement with our models. Additionally, ScanFold was updated to incorporate experimental data as constraints in the analysis to facilitate comparisons between ScanFold and other RNA modelling approaches. Ultimately, ScanFold was able to identify eight highly structured/conserved motifs in SARS-CoV-2 that agree with experimental data, without explicitly using these data. All results are made available via a public database (the RNAStructuromeDB: https://structurome.bb.iastate.edu/sars-cov-2) and model comparisons are readily viewable at https://structurome.bb.iastate.edu/sars-cov-2-global-model-comparisons.
Assessing the functional relevance of splice isoforms
Authors: Pozo Fernando , Martinez-Gomez Laura , Walsh Thomas A , Rodriguez José Manuel , Di Domenico Tomas , Abascal Federico , Vazquez Jesús , Tress Michael L 
Published: May 2021

AbstractAlternative splicing of messenger RNA can generate an array of mature transcripts, but it is not clear how many go on to produce functionally relevant protein isoforms. There is only limited evidence for alternative proteins in proteomics analyses and data from population genetic variation studies indicate that most alternative exons are evolving neutrally. Determining which transcripts produce biologically important isoforms is key to understanding isoform function and to interpreting the real impact of somatic mutations and germline variations. Here we have developed a method, TRIFID, to classify the functional importance of splice isoforms. TRIFID was trained on isoforms detected in large-scale proteomics analyses and distinguishes these biologically important splice isoforms with high confidence. Isoforms predicted as functionally important by the algorithm had measurable cross species conservation and significantly fewer broken functional domains. Additionally, exons that code for these functionally important protein isoforms are under purifying selection, while exons from low scoring transcripts largely appear to be evolving neutrally. TRIFID has been developed for the human genome, but it could in principle be applied to other well-annotated species. We believe that this method will generate valuable insights into the cellular importance of alternative splicing.
IgG Antibody Responses Are Preferential Compared With IgM for Use as Serological Markers for Detecting Recent Exposure to Plasmodium vivax Infection
Authors: Longley Rhea J , White Michael T , Brewster Jessica , Liu Zoe S J , Bourke Caitlin , Takashima Eizo , Harbers Matthias , Tham Wai-Hong , Healer Julie , Chitnis Chetan E , Monteiro Wuelton , Lacerda Marcus , Sattabongkot Jetsumon , Tsuboi Takafumi , Mueller Ivo 
Published: May 2021

Abstract
To achieve malaria elimination, new tools are required to explicitly target Plasmodium vivax. Recently, a novel panel of P. vivax proteins were identified and validated as serological markers for detecting recent exposure to P. vivax within the last 9 months. In order to improve the sensitivity and specificity of these markers, immunoglobulin M (IgM) in addition to immunoglobulin G (IgG) antibody responses were compared with a down-selected panel of 20 P. vivax proteins. IgM was tested using archival plasma samples from observational cohort studies conducted in malaria-endemic regions of Thailand and Brazil. IgM responses to these proteins generally had poorer classification performance than IgG.
Infra-Occipital Supra-Tentorial Approach for Resection of Low-Grade Tumor of the Left Lingual Gyrus: 2-Dimensional Operative Video
Authors: De Benedictis Alessandro , de Palma Luca , Herur-Raman Aalap , Pepi Chiara , Colafati Giovanna Stefania , Carboni Alessia , Randi Franco , Savioli Alessandra , Ricci Giuseppe , Mastronuzzi Angela , Carai Andrea , Specchio Nicola , Marras Carlo Efisio 
Published: May 2021

Abstract
Surgical treatment of lesions involving the postero-medial occipito-temporal region is challenging because of high risk of morbidity due to damage or excessive retraction of critical neuro-vascular structures, especially within the dominant hemisphere.
1-3

Here, we describe the case of a 17-yr-old patient who underwent resection of an epileptogenic low-grade tumor located within the left-dominant lingual gyrus. Seizures were characterized, as a first symptom, by right-sided simple visual hallucination that pointed to the left pericalcarine region, corresponding to the lesion location. No signs of primary involvement of anterior temporo-mesial structures (hippocampus/amygdala) were found. As the anatomo-electroclinical correlation was concordant, direct tumor removal was indicated through an infra-occipital supratentorial approach.
This route allowed direct access to the target through a safe extra-axial corridor, which limits intraparenchymal dissection until the tumor margin is identified and avoids critical vascular structures, such as the vein of Labbé.
4,5
An external cerebrospinal fluid (CSF) drainage was used to facilitate brain relaxation, minimizing brain and venous retraction and, consequently, reducing the risk of postoperative neurological complications, especially for vision. Postoperative magnetic resonance imaging (MRI) demonstrated no surgical complications. Pathological examination revealed a ganglioglioma. At 9-mo follow-up, the neurological examination was normal, antiepileptic therapy was stopped, and the patient was seizure-free.
The video describes the main surgical steps, using both intraoperative videos and advanced 3-dimensional modeling of neuroimaging pictures.
Informed consent was obtained for surgery and video recording.
Lymphoid stromal cells—more than just a highway to humoral immunity
Authors: Cinti Isabella , Denton Alice E 
Published: May 2021

Abstract
The generation of high-affinity long-lived antibody responses is dependent on the differentiation of plasma cells and memory B cells, which are themselves the product of the germinal centre (GC) response. The GC forms in secondary lymphoid organs in response to antigenic stimulation and is dependent on the coordinated interactions between many types of leucocytes. These leucocytes are brought together on an interconnected network of specialized lymphoid stromal cells, which provide physical and chemical guidance to immune cells that are essential for the GC response. In this review we will highlight recent advancements in lymphoid stromal cell immunobiology and their role in regulating the GC, and discuss the contribution of lymphoid stromal cells to age-associated immunosenescence.
The history and future of AI
Authors: Russell Stuart 
Published: May 2021

Abstract
The standard model for developing AI systems assumes a fixed, known objective that the AI system is required to optimize through its actions. Systems developed within the standard model have been increasingly successful. I briefly summarize the state of the art and its likely evolution over the next decade. Substantial breakthroughs leading to general-purpose AI are much harder to predict, but they will have an enormous impact on the global economy and on human roles therein. At the same time, I expect that the standard model will become increasingly untenable in real-world applications because of the difficulty of specifying objectives completely and correctly. I propose a new model for AI development in which the machine’s uncertainty about the true objective leads to qualitatively new modes of behaviour that are more robust, controllable, and deferential.
A time to act: Anti-racist paediatric research
Authors: Smile Sharon , Williams Alison 
Published: May 2021

Abstract
Research offers the potential for new treatments, programs and services, and underlies decisions about funding that can have profound implications for people’s lives. When racism in research is not addressed, children and their families will be unjustly impacted by systemic discrimination, exclusion, and inequity. With a growing acknowledgement that racism is a social determinant of health, and as COVID-19 reveals staggering racial disparities, we believe now is the time for intentional anti-racism initiatives throughout the research ecosystem to prevent further harms in patient care and the lives and futures of children. We aim to highlight this need for justice, and conclude with a series of practical recommendations, ranging from the collection and use of race-based data, to equity, diversity, and inclusion (EDI) education, to mentorship opportunities.
Back So Soon? A Community Hospital Creates New Ways to Prevent Readmission
Authors: Wrotny Cathy 
Published: May 2021

Purpose/Objectives:
Readmission prevention is part of the hospital's strategic plan. Why? Reducing hospital readmissions decreases patient suffering. It also reduces the Centers for Medicare & Medicaid Services financial penalty. But how do you do it? The hospital received a 2-year grant/“investment” from the Massachusetts Health Policy Commission to develop and implement creative, innovative ways of reducing readmissions. The goal was to reduce the 30-day readmission rate for two groups by 20%—adult high utilizers (4 or more admissions within a 12-month period) and adult discharges to post-acute care (PAC) services (skilled nursing facilities and home care agencies).

Primary Practice Settings:
The primary practice settings for the initiative were the hospital, skilled nursing facilities, a short-term rehabilitation hospital, and the patients' homes. The patients were initially selected according to risk criteria determined by the hospital and then followed in the post-acute venue via telephone call and/or visit.

Findings/Conclusions:
Enrollment consisted of 2,860 patients. The readmission rate for adult high utilizers fell from 40.1% to 24.6% (a 39% reduction). The PAC readmissions for both skilled nursing facilities and home health agencies fell from 12.9% to 12.5%—a small decrease. However, the overall PAC readmission rate for the CHART (Community Hospital Acceleration, Revitalization, and Transformation) program is significantly lower than the state's—the rate for home health agencies is 17.2% and for skilled nursing facilities is 20.0%—making the effort to reduce the readmission rate all the more challenging. The significant reduction in hospital readmissions is attributed to the work of the Readmission Prevention Team, which met daily to discuss patients. Team members shared perceptions on patient education, medication management, communication, and end-of-life care. The team developed innovative practices and protocols, which were then applied to the patients' care.

Implications for Readmission Specialists Practice/Case Management:
Back So Soon? Part 2
Authors: Wrotny Cathy , Bradley Dona , Brulé Maurice 
Published: May 2021

Purpose/Objectives:
Readmission prevention strategies are the focus of many hospitals, but despite these efforts, unplanned, all-payer hospital readmission rates are increasing. The purpose of this study was to use root cause analysis (RCA) to explore the main cause (medical, behavioral health, and/or social) for the unplanned 30-day readmissions that the Readmission Prevention Team followed up and then to use this data to change and/or refine discharge planning interventions.

Primary Practice Setting:
The primary practice setting was the 229-bed study hospital where subjects with 30-day unplanned readmissions who were followed up by the Readmission Prevention Team were admitted. The venues that subjects were readmitted from were noted as home without services, home with home care, skilled nursing facility (SNF), acute rehab, physician office, hospice/palliative care, and refused care.

Methodology and Sample:
Using a descriptive, correlational, qualitative design, demographic data (age, gender, days between discharge and readmission, and the venue from which the patient was readmitted) were collected from the RCA worksheets of each subject with an unplanned hospital readmission within 30 days.

Results:
Among the 150 subjects, the main cause for readmission was medical (92%), with 19 of the subjects (13%) demonstrating multiple root causes. Women were readmitted more frequently than men, and the prominent age range was the 70s and 80s. The two main readmission venues were home with home care (54.7%) and skilled nursing facilities (23.3%).

Implications for Case Management:
Medical was the chief cause of readmissions in this study, with many case management interventions noted in the literature to address these issues. Behavioral health and social issues were responsible for 13% of the readmissions. These issues are more complex, and hospitals should review the interventions that they have in place and develop others that are needed to decrease these types of readmissions.
Home with home care was the main venue of readmission, with return from a skilled nursing facility (SNF) being the second. Potential interventions to decrease these unplanned hospital readmissions might include developing a backup discharge plan (Option B) and developing improved communication avenues between the hospital emergency department and the SNF that might lead to the patient returning to the SNF versus being admitted.
Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
Authors: Stüder François , Petit Jean-Louis , Engelen Stefan , Mendoza-Parra Marco Antonio 
Published: May 2021

AbstractSince December 2019, the emergence of a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. As consequence, a major effort worldwide has been performed for the development of viral diagnostics strategies aiming at (i) reducing the diagnostics time, (ii) decrease the costs per assay, and (iii) providing population-scale solutions.Beyond the diagnostics requirements, the description of the B.1.1.7 strain, originated in the south of England, as a highly transmissible variant has strongly accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Since then, other extremely infectious variants, were described and unsurprisingly further others are expected to be discovered, notably due to the long period of time on which the pandemic situation is lasting.Interestingly, all currently described SARS-CoV-2 variants present systematically several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants’ tracking, our proposed strategy focuses on the SPIKE region, as a way to increase the number of candidate samples to screen at once; an essential aspect to accelerate SARS-CoV-2 diagnostics, but also improve variants’ emergence and progression surveillance.Herein we present a proof of concept study, for performing both at once, population-scale SARS-CoV-2 diagnostics and variants’ tracking. This strategy relies on (i) the use of the portable and affordable MinION DNA sequencer; (ii) a DNA barcoding strategy and a SPIKE gene-centered variant’s tracking, for largely increasing the number of candidates per assay; and (iii) a real-time diagnostics and variant’s tracking monitoring thanks to our software RETIVAD.As a whole, this strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.
Neuroprotective effect of vitamin B6 and vitamin B12 against vincristine- induced peripheral neuropathy: A randomized, double- blind, placebo controlled, multicenter trial
Authors: Jeenia Fatiha Tasmin , Sojib Ferdaush Ahmed , Rahman Md Sayedur , Ara Tasneem , Khan Rafiquzzaman , Tanin Md Jamal Uddin 
Published: May 2021

AbstractBackgroundVincristine leads to development of debilitating neuropathy in 40-45% patients with resultant compromised efficacy of chemotherapy, suboptimal treatment and worse prognostic outcome. Vitamin B6 and vitamin B12 improves non-oncological neuropathies. Therefore, this study investigated vitamin B6 and vitamin B12 to prevent vincristine- induced peripheral neuropathy (VIPN) by reducing incidence, absolute risk, relative risk, severity as well as delaying the onset.MethodsPatients with ALL undergoing induction phase were randomly assigned into intervention or placebo arm in a double- blind manner. Vitamin B6 (25 mg Pyridoxine) two tablets were given three times daily for 5 weeks. Vitamin B12 (500 μg/ml Methylcobalamin) was administered intravenously on day 1, 3 and 5 of every week for 5 weeks during induction period. Placebo arm received oral and intravenous placebo for same duration. Patients were evaluated on the outset of every week by FACT/GOG-NTX questionnaire. Severity was assessed per NCI-CTCAE grading scale.Results102 patients were enrolled. Among them 81 completed the study, where 42 received vitamin B6 and B12 and 39 received placebo. There was significant difference in incidence of neuropathy between arms (26.19% intervention arm, 56.41% placebo; P-0.01). Relative risk of neuropathy was significantly (RR-0.46) lower in intervention arm. Besides, absolute risk reduction (ARR) was 30% and relative risk reduction (RRR) was 54%. NNT was 3.33. Significant trend was observed in difference of severity of VIPN between groups (P-0.03). No significant difference observed in between arms for time to onset of neuropathy.ConclusionVitamin B6 and vitamin B12 significantly reduced the incidence, relative risk and severity of VIPN. NNT was encouraging too. Henceforth, the status of vitamin B6 and vitamin B12 as neuroprotective agent against VIPN can be recommended as a promising one. Clinicaltrials.gov ID: NCT02923388
Mechanistic model calibration and the dynamics of the COVID-19 epidemic in the UK (the past, the present and the future)
Authors: Conn Harry , Taylor Robyn , Willis Mark J. , Wright Allen , Bramfitt Victoria 
Published: May 2021

Summary▪We augment the well-known susceptible – infected – recovered – deceased (SIRD) epidemiological model to include vaccination dynamics, implemented as a piecewise continuous simulation. We calibrate this model to reported case data in the UK at a national level,▪Our modelling approach decouples the inherent characteristics of the infection from the degree of human interaction (as defined by the effective reproduction number,Re). This allows us to detect and infer a change in the characteristic of the infection, for example the emergence of the Kent variant,▪We find that that the infection rate constant (k) increases by around 89% as a result of the B.1.1.7 (Kent) COVID-19 variant in England,▪Through retrospective analysis and modelling of early epidemic case data (between March 2020 and May 2020) we estimate that ∼1.2M COVID-19 infections were unreported in the early phase of the epidemic in the UK. We also obtain an estimate of the basic reproduction number as,R0= 3.23,▪We use our model to assess the UK Government’s roadmap for easing the third national lockdown as a result of the current vaccination programme. To do this we use our estimated model parameters and a future forecast of the daily vaccination rates of the next few months,▪Our modelling predicts an increased number of daily cases as NPIs are lifted in May and June 2021,▪We quantify this increase in terms of the vaccine rollout rate and in particular the percentage vaccine uptake rate of eligible individuals, and show that a reduced take up of vaccination by eligible adults may lead to a significant increase in new infections.