bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of North Pacific and North Atlantic Tropical Cyclones by Tropical Transbasin Variability and ENSO during May–October
Authors: Chen Shaohua , Zhao Haikun , Raga Graciela B. , Klotzbach Philip J. 
Published: December 2020

AbstractThis study highlights the distinct modulation of May–October tropical cyclones (TCs) in the western North Pacific (WNP), eastern North Pacific (ENP), and North Atlantic (NATL) Ocean basins by tropical transbasin variability (TBV) and ENSO. The pure TBV significantly modulates total TC counts in all three basins, with more TCs in the WNP and ENP and fewer TCs in the NATL during warm TBV years and fewer TCs in the WNP and ENP and more TCs in the NATL during cold TBV years. By contrast, the pure ENSO signal shows no impact on total TC count over any of the three basins. These results are consistent with changes in large-scale factors associated with TBV and ENSO. Low-level relative vorticity (VOR) is an important driver of WNP TC genesis frequency, with broad agreement between the observed spatial distribution of TC genesis and TBV/ENSO-associated VOR anomalies. TBV significantly affects ENP TC frequency as a result of changes in basinwide vertical wind shear and sea surface temperatures, whereas the modulation in TC frequency by ENSO is primarily caused by a north–south dipole modulation of large-scale atmospheric and oceanic factors. The pure TBV-related low-level VOR changes appear to be the most important factor modulating NATL TC frequency. Changes in large-scale factors compare well with the budget of synoptic-scale eddy kinetic energy. Possible physical processes associated with pure TBV and pure ENSO that modulate TC frequency are further discussed. This study contributes to the understanding of TC interannual variability and could thus be helpful for seasonal TC forecasting.
Subseasonal Precipitation Prediction for Africa: Forecast Evaluation and Sources of Predictability
Authors: de Andrade Felipe M. , Young Matthew P. , MacLeod David , Hirons Linda C. , Woolnough Steven J. , Black Emily 
Published: December 2020

AbstractThis paper evaluates subseasonal precipitation forecasts for Africa using hindcasts from three models (ECMWF, UKMO, and NCEP) participating in the Subseasonal to Seasonal (S2S) prediction project. A variety of verification metrics are employed to assess weekly precipitation forecast quality at lead times of one to four weeks ahead (weeks 1–4) during different seasons. Overall, forecast evaluation indicates more skillful predictions for ECMWF over other models and for East Africa over other regions. Deterministic forecasts show substantial skill reduction in weeks 3–4 linked to lower association and larger underestimation of predicted variance compared to weeks 1–2. Tercile-based probabilistic forecasts reveal similar characteristics for extreme categories and low quality in the near-normal category. Although discrimination is low in weeks 3–4, probabilistic forecasts still have reasonable skill, especially in wet regions during particular rainy seasons. Forecasts are found to be overconfident for all weeks, indicating the need to apply calibration for more reliable predictions. Forecast quality within the ECMWF model is also linked to the strength of climate drivers’ teleconnections, namely, El Niño–Southern Oscillation, Indian Ocean dipole, and the Madden–Julian oscillation. The impact of removing all driver-related precipitation regression patterns from observations and hindcasts shows reduction of forecast quality compared to including all drivers’ signals, with more robust effects in regions where the driver strongly relates to precipitation variability. Calibrating forecasts by adding observed regression patterns to hindcasts provides improved forecast associations particularly linked to the Madden–Julian oscillation. Results from this study can be used to guide decision-makers and forecasters in disseminating valuable forecasting information for different societal activities in Africa.
Development and Calibration of Seasonal Probabilistic Forecasts of Ice-Free Dates and Freeze-Up Dates
Authors: Dirkson Arlan , Denis Bertrand , Sigmond Michael , Merryfield William J. 
Published: December 2020

AbstractDynamical forecasting systems are being used to skillfully predict deterministic ice-free and freeze-up date events in the Arctic. This paper extends such forecasts to a probabilistic framework and tests two calibration models to correct systematic biases and improve the statistical reliability of the event dates: trend-adjusted quantile mapping (TAQM) and nonhomogeneous censored Gaussian regression (NCGR). TAQM is a probability distribution mapping method that corrects the forecast for climatological biases, whereas NCGR relates the calibrated parametric forecast distribution to the raw ensemble forecast through a regression model framework. For NCGR, the observed event trend and ensemble-mean event date are used to predict the central tendency of the predictive distribution. For modeling forecast uncertainty, we find that the ensemble-mean event date, which is related to forecast lead time, performs better than the ensemble variance itself. Using a multidecadal hindcast record from the Canadian Seasonal to Interannual Prediction System (CanSIPS), TAQM and NCGR are applied to produce categorical forecasts quantifying the probabilities for early, normal, and late ice retreat and advance. While TAQM performs better than adjusting the raw forecast for mean and linear trend bias, NCGR is shown to outperform TAQM in terms of reliability, skill, and an improved tendency for forecast probabilities to be no worse than climatology. Testing various cross-validation setups, we find that NCGR remains useful when shorter hindcast records (~20 years) are available. By applying NCGR to operational forecasts, stakeholders can be more confident in using seasonal forecasts of sea ice event timing for planning purposes.
Bilateral Auditory Brainstem Implants in Patients With Neurofibromatosis 2
Authors: Noonan Kathryn Y. , Rock Jordan , Barnard Zach , Lekovic Gregory P. , Brackmann Derald E. , Wilkinson Eric P. 
Published: December 2020

ObjectiveTo discuss indications for bilateral auditory brainstem implants (ABIs), compare audiometric outcomes of unilateral vs bilateral ABIs, and determine if patients have improved outcomes with addition of a second‐side implant.Study DesignRetrospective review of 24 patients with neurofibromatosis 2 (NF2) who underwent sequential placement of ABIs from 1989 to 2019.SettingTertiary referral center.MethodsCharts were reviewed for indication for second‐side surgery, use of implants, and audiometric outcomes. Implants placed in the past 30 years were included in the study. Northwestern University Children’s Perception of Speech (NU‐CHIPS) and/or City University of New York (CUNY) sentence scores were compared in unilateral and bilateral conditions.ResultsIndications for a second‐side implant included first‐side implants with severe nonauditory symptoms (11), marginal audiometric results (9), outdated technology (2), or deterioration of first side (2). Seven patients are bilateral users and 1 patient discontinued bilateral use after a year due to no significant improvement over unilateral use. One patient with initial bilateral use was lost to follow‐up. Thirteen patients are unilateral users due to nonaudiometric side effects or poor audiometric outcomes with the first side. Two patients are complete nonusers. Seventy‐five percent had improved audiometric outcomes after the second‐side implant, and 20% had stable findings.ConclusionsSecond‐side ABIs should be consider in patients with poor performance from a first‐side implant. Most patients demonstrate subjective improvement with the second ABI. More research is needed for better objective assessments of improvements.
Prevalence and Characteristics of Taste Disorders in Cases of COVID‐19: A Meta‐analysis of 29,349 Patients
Authors: Saniasiaya Jeyasakthy , Islam Md Asiful , Abdullah Baharudin 
Published: December 2020

ObjectiveThe purpose of this meta‐analysis is to assess the pooled prevalence of taste disorders and their subtypes in patients with COVID‐19.Data SourcesPubMed, Scopus, Web of Science, Embase, and Google Scholar databases were searched to identify studies published between December 1, 2019, and June 23, 2020, without language restrictions. There was no restriction on the study design; therefore, observational studies, clinical trials, and case series were included. In addition, preprints were considered if data of interest were reported.Review MethodsTwo authors independently screened articles for eligibility. A random effects model was used to estimate the pooled prevalence with 95% CIs. Quality assessment was done with critical appraisal tools of the Joanna Briggs Institute. The robustness of the pooled estimates was checked by subgroup and sensitivity analyses.ResultsFifty‐nine studies were included (N = 29,349 patients, 64.4% female). The pooled prevalence of taste disorders in patients with COVID‐19 was 48.1% (95% CI, 41.3%‐54.8%). The prevalence of taste disorders in studies with objective assessments was higher as compared with subjective assessments (59.2% vs 47.3%). The disorders were observed in 55.2% of European patients; 61.0%, North American; 27.1%, Asian; 29.5%, South American; and 25.0%, Australian. Ageusia, hypogeusia, and dysgeusia were detected in 28.0%, 33.5%, and 41.3% of patients with COVID‐19. We identified 91.5% of the included studies as high quality.ConclusionsThe prevalence of taste disorders in patients with COVID‐19 was 48.1%. Objective assessments have higher prevalence than subjective assessments. Dysgeusia is the most common subtype, followed by ageusia and hypogeusia.
A novel conditioning-free hematopoietic stem cell transplantation model in zebrafish
Authors: Fraint Ellen , Feliz Norberto María , Bowman Teresa V. 
Published: December 2020

Abstract
Transplantation is the most common assay for measuring the in vivo functionality of hematopoietic stem cells (HSCs). Although various HSC transplantation strategies have been developed in zebrafish, they are underutilized because of challenges related to immune matching and preconditioning toxicity. To circumvent these limitations, we developed a simple and robust transplantation model using HSC-deficient hosts. Homozygous runx1W84X mutants are devoid of definitive hematopoietic cells, including HSCs and adaptive immune cells; thus, they require no preconditioning regimen for transplantation. Marrow cell transplantation into runx1-mutant zebrafish 2 days after fertilization significantly improved their survival to adulthood and resulted in robust, multilineage, long-lasting, serially repopulating engraftment. Furthermore, we demonstrated that engraftment into runx1 homozygous mutants was significantly higher than into runx1 heterozygotes, demonstrating that the improved transplantation success is attributable to the empty HSC niche in mutants and not just the embryonic environment. Competitive transplantation of marrow cells into runx1 mutants revealed a stem cell frequency similar to that of murine marrow cells, which demonstrates the utility of this model for quantifying HSC function. The streamlined approach and robustness of this assay will help broaden its feasibility for future high-throughput transplantation experiments in zebrafish and will enable further novel discoveries in the biology of HSCs.
Regional patterns and trends of hearing loss in England: evidence from the English longitudinal study of ageing (ELSA) and implications for health policy
Authors: Tsimpida Dialechti , Kontopantelis Evangelos , Ashcroft Darren M. , Panagioti Maria 
Published: December 2020

Abstract
Background
Hearing loss (HL) is a significant public health concern globally and is estimated to affect over nine million people in England. The aim of this research was to explore the regional patterns and trends of HL in a representative longitudinal prospective cohort study of the English population aged 50 and over.

Methods
We used the full dataset (74,699 person-years) of self-reported hearing data from all eight Waves of the English Longitudinal Study of Ageing (ELSA) (2002–2017). We examined the geographical identifiers of the participants at the Government Office Region (GOR) level and the geographically based Index of Multiple Deprivation (IMD). The primary outcome measure was self-reported HL; it consisted of a merged category of people who rated their hearing as fair or poor on a five-point Likert scale (excellent, very good, good, fair or poor) or responded positively when asked whether they find it difficult to follow a conversation if there is background noise (e.g. noise from a TV, a radio or children playing).

Results
A marked elevation in HL prevalence (10.2%) independent of the age of the participants was observed in England in 2002–2017. The mean HL prevalence increased from 38.50 (95%CI 37.37–39.14) in Wave 1 to 48.66 (95%CI 47.11–49.54) in Wave 8. We identified three critical patterns of findings concerning regional trends: the highest HL prevalence among samples with equal means of age was observed in GORs with the highest prevalence of participants in the most deprived (IMD) quintile, in routine or manual occupations and misusing alcohol. The adjusted HL predictions at the means (APMs) showed marked regional variability and hearing health inequalities between Northern and Southern England that were previously unknown.

Conclusions
A sociospatial approach is crucial for planning sustainable models of hearing care based on actual needs and reducing hearing health inequalities. The Clinical Commissioning Groups (CCGs) currently responsible for the NHS audiology services in England should not consider HL an inevitable accompaniment of older age; instead, they should incorporate socio-economic factors and modifiable lifestyle behaviours for HL within their spatial patterning in England.
Primary hepatic neuroendocrine carcinoma: report of two cases and literature review
Authors: Zhao Zi-Ming , Wang Jin , Ugwuowo Ugochukwu C. , Wang Liming , Townsend Jeffrey P. 
Published: December 2020

Abstract
Background
Primary hepatic neuroendocrine carcinoma (PHNEC) is extremely rare. The diagnosis of PHNEC remains challenging—partly due to its rarity, and partly due to its lack of unique clinical features. Available treatment options for PHNEC include surgical resection of the liver tumor(s), radiotherapy, liver transplant, transcatheter arterial chemoembolization (TACE), and administration of somatostatin analogues.

Case presentation
We report two male PHNEC cases and discuss the diagnosis and treatment options. Both cases presented with abdominal pain; case two also presented with symptoms of jaundice. The initial diagnosis for both cases was poorly differentiated grade 3 small-cell neuroendocrine carcinoma, based on imaging characteristics and the pathology of liver biopsies. Final diagnoses of PHNEC were arrived at by ruling out non-hepatic origins. Case one presented with a large tumor in the right liver lobe, and the patient was treated with TACE. Case two presented with tumors in both liver lobes, invasions into the left branch of hepatic portal vein, and metastasis in the hepatic hilar lymph node. This patient was ineligible for TACE and was allergic to the somatostatin analogue octreotide. This limited treatment options to supportive therapies such as albumin supplementation for liver protection. Patient one and two died at 61 and 109 days, respectively, following initial hospital admission.

Conclusions
We diagnosed both cases with poorly differentiated grade 3 small-cell PHNEC through imaging characteristics, immunohistochemical staining of liver biopsies, and examinations to eliminate non-hepatic origins. Neither TACE nor liver protection appeared to significantly extend survival time of the two patients, suggesting these treatments may be inadequate to improve survival of patients with poorly differentiated grade 3 small-cell PHNEC. The prognosis of poorly differentiated grade 3 small-cell PHNEC is poor due to limited and ineffective treatment options.
Evaluation of lexical clarification by patients reading their clinical notes: a quasi-experimental interview study
Authors: van Mens Hugo J. T. , van Eysden Mirte M. , Nienhuis Remko , van Delden Johannes J. M. , de Keizer Nicolette F. , Cornet Ronald 
Published: December 2020

Abstract
Background
Patients benefit from access to their medical records. However, clinical notes and letters are often difficult to comprehend for most lay people. Therefore, functionality was implemented in the patient portal of a Dutch university medical centre (UMC) to clarify medical terms in free-text data. The clarifications consisted of synonyms and definitions from a Dutch medical terminology system. We aimed to evaluate to what extent these lexical clarifications match the information needs of the patients. Secondarily, we evaluated how the clarifications and the functionality could be improved.

Methods
We invited participants from the patient panel of the UMC to read their own clinical notes. They marked terms they found difficult and rated the ease of these terms. After the functionality was activated, participants rated the clarifications provided by the functionality, and the functionality itself regarding ease and usefulness. Ratings were on a scale from 0 (very difficult) to 100 (very easy). We calculated the median number of terms not understood per participant, the number of terms with a clarification, the overlap between these numbers (coverage), and the precision and recall.

Results
We included 15 participants from the patient panel. They marked a median of 21 (IQR 19.5–31) terms as difficult in their text files, while only a median of 2 (IQR 1–4) of these terms were clarified by the functionality. The median precision was 6.5% (IQR 2.3–14.25%) and the median recall 8.3% (IQR 4.7–13.5%) per participant. However, participants rated the functionality with median ease of 98 (IQR 93.5–99) and a median usefulness of 79 (IQR 52.5–97). Participants found that many easy terms were unnecessarily clarified, that some clarifications were difficult, and that some clarifications contained mistakes.

Conclusions
Patients found the functionality easy to use and useful. However, in its current form it only helped patients to understand few terms they did not understand, patients found some clarifications to be difficult, and some to be incorrect. This shows that lexical clarification is feasible even when limited terms are available, but needs further development to fully use its potential.
Extending import detection algorithms for concept import from two to three biomedical terminologies
Authors: Keloth Vipina K. , Geller James , Chen Yan , Xu Julia 
Published: December 2020

Abstract
Background
While enrichment of terminologies can be achieved in different ways, filling gaps in the IS-A hierarchy backbone of a terminology appears especially promising. To avoid difficult manual inspection, we started a research program in 2014, investigating terminology densities, where the comparison of terminologies leads to the algorithmic discovery of potentially missing concepts in a target terminology. While candidate concepts have to be approved for import by an expert, the human effort is greatly reduced by algorithmic generation of candidates. In previous studies, a single source terminology was used with one target terminology.

Methods
In this paper, we are extending the algorithmic detection of “candidate concepts for import” from one source terminology to two source terminologies used in tandem. We show that the combination of two source terminologies relative to one target terminology leads to the discovery of candidate concepts for import that could not be found with the same “reliability” when comparing one source terminology alone to the target terminology. We investigate which triples of UMLS terminologies can be gainfully used for the described purpose and how many candidate concepts can be found for each individual triple of terminologies.

Results
The analysis revealed a specific configuration of concepts, overlapping two source and one target terminology, for which we coined the name “fire ladder” pattern. The three terminologies in this pattern are tied together by a kind of “transitivity.” We provide a quantitative analysis of the discovered fire ladder patterns and we report on the inter-rater agreement concerning the decision of importing candidate concepts from source terminologies into the target terminology. We algorithmically identified 55 instances of the fire ladder pattern and two domain experts agreed on import for 39 instances. In total, 48 concepts were approved by at least one expert. In addition, 105 import candidate concepts from a single source terminology into the target terminology were also detected, as a “beneficial side-effect” of this method, increasing the cardinality of the result.

Conclusion
We showed that pairs of biomedical source terminologies can be transitively chained to suggest possible imports of concepts into a target terminology.
Texture features in the Shearlet domain for histopathological image classification
Authors: Alinsaif Sadiq , Lang Jochen 
Published: December 2020

AbstractBackgroundA various number of imaging modalities are available (e.g., magnetic resonance, x-ray, ultrasound, and biopsy) where each modality can reveal different structural aspects of tissues. However, the analysis of histological slide images that are captured using a biopsy is considered the gold standard to determine whether cancer exists. Furthermore, it can reveal the stage of cancer. Therefore, supervised machine learning can be used to classify histopathological tissues. Several computational techniques have been proposed to study histopathological images with varying levels of success. Often handcrafted techniques based on texture analysis are proposed to classify histopathological tissues which can be used with supervised machine learning.MethodsIn this paper, we construct a novel feature space to automate the classification of tissues in histology images. Our feature representation is to integrate various features sets into a new texture feature representation. All of our descriptors are computed in the complex Shearlet domain. With complex coefficients, we investigate not only the use of magnitude coefficients, but also study the effectiveness of incorporating the relative phase (RP) coefficients to create the input feature vector. In our study, four texture-based descriptors are extracted from the Shearlet coefficients: co-occurrence texture features, Local Binary Patterns, Local Oriented Statistic Information Booster, and segmentation-based Fractal Texture Analysis. Each set of these attributes captures significant local and global statistics. Therefore, we study them individually, but additionally integrate them to boost the accuracy of classifying the histopathology tissues while being fed to classical classifiers. To tackle the problem of high-dimensionality, our proposed feature space is reduced using principal component analysis. In our study, we use two classifiers to indicate the success of our proposed feature representation: Support Vector Machine (SVM) and Decision Tree Bagger (DTB).ResultsOur feature representation delivered high performance when used on four public datasets. As such, the best achieved accuracy: multi-class Kather (i.e., 92.56%), BreakHis (i.e., 91.73%), Epistroma (i.e., 98.04%), Warwick-QU (i.e., 96.29%).ConclusionsOur proposed method in the Shearlet domain for the classification of histopathological images proved to be effective when it was investigated on four different datasets that exhibit different levels of complexity.