bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the economic well‐being in the context of Africa
Authors: Konou Comlanvi Martin , Mensah Edwin Clifford 
Published: April 2022

AbstractEconomists rely on the gross domestic product (GDP) to assess the economic performance of a country. This paper, however, argues that in Africa, the GDP alone cannot be used as a sufficient macroeconomic indicator in accounting for poverty rates and the overall health of the economy. Existing alternatives to GDP also fail to account adequately for relevant factors that are vital in determining the well‐being of individuals in Africa. The current study, therefore, proposes an inclusive macroeconomic performance index (IMPI) computed for 45 African countries with data from 2002 to 2015. Using the dynamic panel system generalised method of moments estimation method, we evaluate the impact of governance (i.e. the quality of institutions), social and growth‐related factors on the IMPI developed. Our results show that growth‐related variables such as trade have a positive impact while FDI had a negative and significant impact on the index. Education also has a positive and significant effect on the index. Social factors such as civil war, ethnic and religious fractionalisations on the other hand significantly impacted the index negatively. This study contributes to the literature by introducing a new economic performance index which combines both poverty and per capita GDP into a single index to assess the well‐being of individuals in Africa.
Perioperative Cardiometabolic Targets and Coronary Artery Bypass Surgery Mortality in Patients With Diabetes
Authors: Skendelas John P. , Phan Donna K. , Friedmann Patricia , Rodriguez Carlos J. , Stein Daniel , Arbab‐Zadeh Armin , Forest Stephen J. , Slipczuk Leandro 
Published: April 2022

Background
Coronary artery bypass graft (CABG) surgery represents the preferred revascularization strategy for most patients with diabetes and multivessel disease. We aimed to evaluate the role of optimized, perioperative cardiometabolic targets on long‐term survival in patients who underwent CABG.

Methods and Results

Single‐institution retrospective study was conducted in patients with diabetes who underwent CABG between January 2010 and June 2018. Demographic, surgical, and cardiometabolic determinants were identified during the perioperative period. Clinical characteristics and longitudinal survival outcomes data were obtained. A total of 1534 patients with CABG were considered for analysis and 1273 met inclusion criteria. The mean age of patients was 63.3 years (95% CI, 62.7–63.8 years), and most were men (65%) and Hispanic or Latino (47%). Comorbidities included hypertension (95%) and dyslipidemia (88%). In total, 490 patients (52%) had a low‐density lipoprotein cholesterol level >70 mg/dL. Furthermore, 390 patients (31%) had uncontrolled systolic blood pressure >130 mm Hg. Last, only 386 patients (29%) had a hemoglobin A
1c
level between 6% and 7%. At 5 years, 121 patients (10%) died. Failure to achieve goal systolic blood pressure was associated with all‐cause (hazard ratio [HR], 1.573; 95% CI, 1.048–2.362 [
P
=0.029]) and cardiovascular (HR, 2.023; 95% CI, 1.196–3.422 [
P
=0.009]) mortality at 5 years post‐CABG. In contrast, prescription of a statin during the perioperative interval demonstrated a protective effect for all‐cause (HR, 0.484; 95% CI, 0.286–0.819 [
P
=0.007]) and cardiovascular (HR, 0.459; 95% CI, 0.229–0.920 [
P
=0.028]) mortality. There was no association between achievement of low‐density lipoprotein cholesterol, triglycerides, non–high‐density lipoprotein cholesterol, or hemoglobin A
1c
level goals and mortality risk at 5 years.

Conclusions
Among patients with diabetes, blood pressure control and statin therapy were the most important perioperative cardiometabolic survival determinants 5 years after CABG.
Canonical Workflow for Machine Learning Tasks
Authors: Blanchi Christophe , Gebre Binyam , Wittenburg Peter 
Published: April 2022

Abstract
There is a huge gap between (1) the state of workflow technology on the one hand and the practices in the many labs working with data driven methods on the other and (2) the awareness of the FAIR principles and the lack of changes in practices during the last 5 years. The CWFR concept has been defined which is meant to combine these two intentions, increasing the use of workflow technology and improving FAIR compliance. In the study described in this paper we indicate how this could be applied to machine learning which is now used by almost all research disciplines with the well-known effects of a huge lack of repeatability and reproducibility.
Researchers will only change practices if they can work efficiently and are not loaded with additional tasks. A comprehensive CWFR framework would be an umbrella for all steps that need to be carried out to do machine learning on selected data collections and immediately create a comprehensive and FAIR compliant documentation. The researcher is guided by such a framework and information once entered can easily be shared and reused. The many iterations normally required in machine learning can be dealt with efficiently using CWFR methods.
Libraries of components that can be easily orchestrated using FAIR Digital Objects as a common entity to document all actions and to exchange information between steps without the researcher needing to understand anything about PIDs and FDO details is probably the way to increase efficiency in repeating research workflows. As the Galaxy project indicates, the availability of supporting tools will be important to let researchers use these methods. Other as the Galaxy framework suggests, however, it would be necessary to include all steps necessary for doing a machine learning task including those that require human interaction and to document all phases with the help of structured FDOs.
Evaluation of Application Possibilities for Packaging Technologies in Canonical Workflows
Authors: Jejkal Thomas , Chelbi Sabrine , Pfeil Andreas , Wittenburg Peter 
Published: April 2022

Abstract
In Canonical Workflow Framework for Research (CWFR) “packages” are relevant in two different directions. In data science, workflows are in general being executed on a set of files which have been aggregated for specific purposes, such as for training a model in deep learning. We call this type of “package” a data collection and its aggregation and metadata description is motivated by research interests. The other type of “packages” relevant for CWFR are supposed to represent workflows in a self-describing and self-contained way for later execution. In this paper, we will review different packaging technologies and investigate their usability in the context of CWFR. For this purpose, we draw on an exemplary use case and show how packaging technologies can support its realization. We conclude that packaging technologies of different flavors help on providing inputs and outputs for workflow steps in a machine-readable way, as well as on representing a workflow and all its artifacts in a self-describing and self-contained way.
Individual Differences in Cue Weighting in Sentence Comprehension: An Evaluation Using Approximate Bayesian Computation
Authors: Yadav Himanshu , Paape Dario , Smith Garrett , Dillon Brian W. , Vasishth Shravan 
Published: April 2022

AbstractCue-based retrieval theories of sentence processing assume that syntactic dependencies are resolved through a content-addressable search process. An important recent claim is that in certain dependency types, the retrieval cues are weighted such that one cue dominates. This cue-weighting proposal aims to explain the observed average behavior, but here we show that there is systematic individual-level variation in cue weighting. Using the Lewis and Vasishth cue-based retrieval model, we estimated individual-level parameters for reading speed and cue weighting using 13 published datasets; hierarchical approximate Bayesian computation (ABC) was used to estimate the parameters. The modeling reveals a nuanced picture of cue weighting: we find support for the idea that some participants weight cues differentially, but not all participants do. Only fast readers tend to have the predicted higher weighting for structural cues, suggesting that reading proficiency (approximated here by reading speed) might be associated with cue weighting. A broader achievement of the work is to demonstrate how individual differences can be investigated in computational models of sentence processing without compromising the complexity of the model.
How Does Sea Surface Temperature Drive the Intertropical Convergence Zone in the Southern Indian Ocean?
Authors: Zhang Honghai , Seager Richard , Xie Shang-Ping 
Published: April 2022

Abstract
The Indian Ocean has an intriguing intertropical convergence zone (ITCZ) south of the equator year-round, which remains largely unexplored. Here we investigate this Indian Ocean ITCZ and the mechanisms for its origin. With a weak semiannual cycle, this ITCZ peaks in January–February with the strongest rainfall and southernmost location and a northeast–southwest orientation from the Maritime Continent to Madagascar, reaches a minimum around May with a zonal orientation, grows until its secondary maximum around September with a northwest–southeast orientation, weakens slightly until December, and then regains its mature phase in January. During austral summer, the Indian Ocean ITCZ exists over maximum surface moist static energy (MSE), consistent with convective quasi-equilibrium theory. This relationship breaks up during boreal summer when the surface MSE maximizes in the northern monsoon region. The position and orientation of the Indian Ocean ITCZ can be simulated well in both a linear dynamical model and the state-of-the-art Community Atmosphere Model version 6 (CAM6) when driven by observed sea surface temperature (SST). To quantify the contributions of the planetary boundary layer (PBL) and free-atmosphere processes to this ITCZ, we homogenize the free-atmosphere diabatic heating over the Indian Ocean in CAM6. In response, the ITCZ weakens significantly, owing to a weakened circulation and deep convection. Therefore, in CAM6, the SST drives the Indian Ocean ITCZ directly through PBL processes and indirectly via free-atmosphere diabatic heating. Their contributions are comparable during most seasons, except during the austral summer when the free-atmosphere diabatic heating dominates the mature-phase ITCZ.

Significance Statement
The intertropical convergence zone (ITCZ) is the globe-encircling band where trade winds converge and strong rainfall occurs in the tropics. Its rains provide life-supporting water to billions of people. Its associated latent heating invigorates the tropical atmospheric circulation and influences climate and weather across the planet. The ITCZ is located north of the equator in most tropical oceans, except in the Indian Ocean where it sits south of the equator year-around. In contrast to the well-known northern ITCZs, the origin of the southern ITCZ in the Indian Ocean remains unknown. This work provides the first explanation for how ocean surface temperature works together with processes in the lower and upper atmosphere to shape the unique ITCZ in the Indian Ocean.
The contribution of rare copy number variants in FAS toward pathogenesis of autoimmune lymphoproliferative syndrome
Authors: Jevtich Kathleen , Price Susan , Similuk Morgan , Kulm Elaine , Yan Jia , Setzer Michael , Jamal Leila , Franco Luis M. , Ghosh Rajarshi , Walkiewicz Magdalena , Rao V. Koneti 
Published: April 2022

Abstract
Autoimmune lymphoproliferative syndrome (ALPS) is characterized by chronic nonmalignant lymphadenopathy, splenomegaly, cytopenias, and other autoimmune manifestations. ALPS is caused by lymphocyte accumulation from defects in FAS-mediated apoptosis. Heterozygous germline or somatic pathogenic single nucleotide variants in FAS are the most common molecular etiology of ALPS. Through the Centralized Sequencing Program at the National Institute of Allergy and Infectious Diseases, we performed exome sequencing on subjects with a clinical diagnosis of ALPS, with a subset receiving copy number variant (CNV) analysis. In this cohort, we identified 3 subjects from unrelated families with CNVs at the FAS locus. One subject had a de novo ∼0.828 Mb copy number loss encompassing all of FAS. The second subject had a maternally inherited ∼1.004 Mb copy number loss encompassing all of FAS. The third subject had a paternally inherited ∼0.044 Mb copy number loss encompassing exons 7 through 9 of FAS. Subjects with deletions in FAS had clinical presentations and biomarker profiles similar to those with ALPS and with germline and somatic FAS variants. We demonstrate that CNV analysis should be pursued if there is clinical and biomarker evidence of ALPS because it can lead to a molecular diagnosis and appropriate treatment when FAS sequencing is inconclusive.
CD47 overexpression is common in intestinal non-GCB type diffuse large B-cell lymphoma and associated with 18q21 gain
Authors: Cho Junhun , Yoon Sang Eun , Kim Seok Jin , Ko Young Hyeh , Kim Won Seog 
Published: April 2022

Abstract
The CD47/signal regulatory protein α pathway is an emerging immune checkpoint that is a new therapeutic target. We investigated CD47 expression in diffuse large B-cell lymphoma (DLBCL) of various subtypes and organs. Moreover, the relationship between CD47 expression and genetic alterations was analyzed using panel-based massively parallel sequencing (next-generation sequencing [NGS]). CD8, CD68, and CD47 immunohistochemical staining were performed on 238 patients with DLBCL. CD47 was scored according to intensity on a 5-level scale, and CD8 and CD68 were quantitatively evaluated using QuPath software. Panel-based NGS was performed in 37 patients. In CD8 and CD68 quantitative analyses by organs, intestinal DLBCL showed significantly lower cytotoxic T-cell infiltration than that in others (P &lt; .001). The CD47-high group comprised 24 of 58 (41.4%) patients in the group with DLBCL from intestine and 15 of 180 (8.3%) patients in the group with DLBCL from other organs (P &lt; .001). The 18q21 gain/amplification was found in 10 of 37 patients, and all of them were CD47-high. Intestinal CD47-high DLBCL occurred in terminal ileum to ascending colon and was restricted to nongerminal center B-cell type. In the survival analyses, the prognosis of nonintestinal CD47-high DLBCL was poorer than that of intestinal CD47-high DLBCL (P = .025). CD47-high DLBCL was closely associated with 18q21 gain/amplification and showed a high prevalence in intestine. We propose to classify CD47-high DLBCL into intestinal and nonintestinal types. Further studies are necessary to assess whether the constellation of features seen here is reproducible and sufficient to consider primary intestinal DLBCL as a distinct biological entity.
Interleukin-15 augments NK cell–mediated ADCC of alemtuzumab in patients with CD52+ T-cell malignancies
Authors: Miljkovic Milos D. , Dubois Sigrid P. , Müller Jürgen R. , Bryant Bonita , Ma Elaine , Conlon Kevin C. , Waldmann Thomas A. 
Published: April 2022

AbstractInterleukin-15 (IL-15) monotherapy substantially increases the number and activity of natural killer (NK) cells and CD8+ T cells but has not produced clinical responses. In a xenograft mouse model, IL-15 enhanced the NK cell–mediated antibody-dependent cell cytotoxicity (ADCC) of the anti-CD52 antibody alemtuzumab and led to significantly more durable responses than alemtuzumab alone. To evaluate whether IL-15 potentiates ADCC in humans, we conducted a phase 1 single-center study of recombinant human IL-15 and alemtuzumab in patients with CD52-positive mature T-cell malignances. We gave IL-15 subcutaneously 5 days per week for 2 weeks in a 3 + 3 dose escalation scheme (at 0.5, 1, and 2 μg/kg), followed by standard 3 times weekly alemtuzumab IV for 4 weeks. There were no dose-limiting toxicities or severe adverse events attributable to IL-15 in the 11 patients treated. The most common adverse events were lymphopenia (100%), alemtuzumab-related infusion reactions (90%), anemia (90%), and neutropenia (72%). There were 3 partial and 2 complete responses, with an overall response rate of 45% and median duration of response 6 months. Immediately after 10 days of IL-15, there was a median 7.2-fold increase in NK cells and 2.5-fold increase in circulating CD8+ T cells, whereas the number of circulating leukemic cells decreased by a median 38% across all dose levels. Treatment with IL-15 was associated with increased expression of NKp46 and NKG2D, markers of NK-cell activation, and increased ex vivo ADCC activity of NK cells, whereas inhibitory receptors PD1 and Tim3 were decreased. This trial was registered at www.clinicaltrials.gov as #NCT02689453.
Functional interaction between compound heterozygous TERT mutations causes severe telomere biology disorder
Authors: Niaz Aram , Truong Jia , Manoleras Annabel , Fox Lucy C. , Blombery Piers , Vasireddy Raja S. , Pickett Hilda A. , Curtin Julie A. , Barbaro Pasquale M. , Rodgers Jonathan , Roy John , Riley Lisa G. , Holien Jessica K. , Cohen Scott B. , Bryan Tracy M. 
Published: April 2022

Abstract
Telomere biology disorders (TBDs) are a spectrum of multisystem inherited disorders characterized by bone marrow failure, resulting from mutations in the genes encoding telomerase or other proteins involved in maintaining telomere length and integrity. Pathogenicity of variants in these genes can be hard to evaluate, because TBD mutations show highly variable penetrance and genetic anticipation related to inheritance of shorter telomeres with each generation. Thus, detailed functional analysis of newly identified variants is often essential. Herein, we describe a patient with compound heterozygous variants in the TERT gene, which encodes the catalytic subunit of telomerase, hTERT. This patient had the extremely severe Hoyeraal-Hreidarsson form of TBD, although his heterozygous parents were clinically unaffected. Molecular dynamic modeling and detailed biochemical analyses demonstrate that one allele (L557P) affects association of hTERT with its cognate RNA component hTR, whereas the other (K1050E) affects the binding of telomerase to its DNA substrate and enzyme processivity. Unexpectedly, the data demonstrate a functional interaction between the proteins encoded by the two alleles, with wild-type hTERT rescuing the effect of K1050E on processivity, whereas L557P hTERT does not. These data contribute to the mechanistic understanding of telomerase, indicating that RNA binding in one hTERT molecule affects the processivity of telomere addition by the other molecule. This work emphasizes the importance of functional characterization of TERT variants to reach a definitive molecular diagnosis for patients with TBD, and, in particular, it illustrates the importance of analyzing the effects of compound heterozygous variants in combination, to reveal interallelic effects.
Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
Authors: Zhang Mengjia , Chen Nansheng 
Published: April 2022

AbstractThe cosmopolitanThalassionemaspecies are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation onThalassionemabiodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of sevenThalassionemastrains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of theseThalassionemacpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed thatThalassionemacpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among differentThalassionemaspecies but also among strains of a same speciesT. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position ofThalassionemaspecies, this study also estimated their emergence time at approximately 38 Mya. The availability of theThalassionemaspecies cpDNAs not only helps understand theThalassionemaspecies, but also facilitates phylogenetic analysis of diatoms.
Prevalence of potentially inappropriate medications based on the STOPPFrail criteria in frail older patients with limited life expectancy: a cross-sectional study
Authors: Chae Hyun-Woo , Kim Yoonhee , Suh Yewon , Lee Junghwa , Lee Eunsook , Lee Euni , Choi Jung-Yeon , Kim Kwang-il , Lee Ju-Yeun 
Published: April 2022

Abstract
Background
The recently developed Screening Tool of Older Persons' Prescriptions in Frail adults with a limited life expectancy (STOPPFrail) criteria can be helpful for screening medications (PIMs), but it is yet to be widely used in clinical practice. Herein, we aimed to investigate the prevalence of PIMs based on the STOPPFrail criteria (STOPPFrail-PIM) among frail older adults with limited life expectancy admitted to the geriatric center.

Methods
This was a retrospective cross-sectional study conducted in the geriatric center at an academic tertiary care hospital in Korea. We evaluated frail older adults with limited life expectancy who received comprehensive geriatric assessment (CGA) admitted between 1 January, 2019 and 30 June, 2020. Frail older adults with limited life expectancy were identified by geriatricians with retrospective records and the prevalence of STOPPFrail-PIMs was analysed by trained pharmacists. Descriptive analysis, t-test, and chi-square test were conducted using IBM SPSS software version 25.0.

Results
Among 504 older adults who underwent CGA after admission, 171 frail older adults with limited life expectancy were identified by geriatricians and included in the study. An average of 11.3 ± 4.7 medications were administered regularly to each patient before admission. Overall, 97.1% (166/171) had at least one STOPPFrail-PIM, and the mean number of STOPPFrail-PIM was 4.2 ± 2.8. Drugs without clear clinical indication (A2) were the most frequent pre-admission STOPPFrail-PIM, followed by lipid-lowering therapies (B1) and neuroleptic antipsychotics (D1). The number of STOPPFrail-PIM was significantly lower at discharge than that at admission, with the decrease being the highest for A2 at 94.7%.

Conclusions
Most frail older adults with limited life expectancy had at least one STOPPFrail-PIM at admission, and the rate of STOPPFrail-PIM decreased significantly at discharge after the geriatric multidisciplinary team care. Further studies are needed to investigate the association between the use of STOPPFrail-PIM and adverse consequences in frail older adults.