julilili42/papers huggingface dataset:
Occurrence and ecological risk assessment of heavy metals in agricultural soils of Lake Chilwa catchment in Malawi, Southern Africa
2020-10-28

Understanding the levels and associated ecological risk caused by heavy metals is important for the sustainable management and utilization of Lake Chilwa catchment, an important ecosystem in Malawi providing fertile lands for agriculture and a designated wetland ratified by the Ramsar convention in 1997. Concentrations of chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), zinc (Zn), arsenic (As), mercury (Hg) and cadmium (Cd) were analyzed from 22 soil sampling locations. Extraction and quantification were achieved by microwave digestion and Inductively Coupled Plasma Optical Emission Spectrometer, respectively. Mean values were detected in the following order; Zn > Cr > Ni > Cu > Pb > As. Strong correlations were observed between As and Pb (r = 0.85), Cr and Ni (r = 0.82), Cu and Ni (r = 0.81), Cr and Cu (r = 0.8), and Pb and Zn (r = 0.73) suggesting similar sources of input. Principal component analysis revealed that Cu, Pb, Zn and As originate from anthropogenic activities, while Cr and Ni were geogenic. The ecological risk caused by these metals, calculated by the Ecological Risk Index (RI) method, showed a low to moderate ecological risk. The wetland areas had higher overall concentrations and RI values compared to the rest of the catchment. It is therefore important to enforce measures to manage and control these levels to avoid their damaging effects.
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
2020-10-28

Abstract We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.
Adolescent boys with constitutional delay of growth and puberty grow faster than patients with organic growth hormone deficiency
2020-10-28

Abstract Objective Constitutional delay of growth and puberty (CDGP) is a tempo variant with a good prognosis. Healthy late‐maturing adolescents grow slower than postulated by age‐related references, and therefore, CDGP is frequently confused with growth hormone deficiency (GHD). For differential diagnosis, height velocity references for CDGP are needed. Design and Patients Here, we provide height velocity data for late‐maturing boys based on mixed longitudinal and cross‐sectional observations in a group of 38 German adolescents with proven CDGP and compare them with cross‐sectional observations in a group of 164 adolescents with organic GHD from the National Cooperative Growth Study registry. Results In the critical age interval from 13.4 to 14.9 years, the growth of prepubertal adolescents with CDGP was faster (mean/median height velocity, 5.2/5.4 cm/years; quartiles, 4.4‐6.2 cm/years) than that of prepubertal adolescents with organic GHD (3.5/3.2 cm/years; quartiles, 2.0‐4.4 cm/years) in the cross‐sectional analysis ( p &lt; .0001). Based on our mixed longitudinal and cross‐sectional analysis, the height velocity of adolescent boys with CDGP exceeded previous model calculations on average by 1.0 cm. Conclusions In conclusion, prepubertal adolescents with CDGP grow faster than patients with organic GHD. Previous model estimates underestimated height velocity of boys with CDGP.
Usos discursivos de la forma verbal doxásticacreoen la interacción oral en español
2020-10-28

Abstract The present paper describes the main discursive uses of creo , a performative form of doxastic verb creer , in oral Spanish interaction, specifically those in which the verbal form shows attenuation or intensification. To that end, this paper performs a thorough analysis of creo instances across conversational corpora ( COGILA, COJEM, Val.Es.Co., Val.Es.Co. 2.0 ) and parliamentary debates corpora ( Congreso de los Diputados, Les Corts Valencianes ), with a combined 700 000 words collated as the sample. A preliminary qualitative and quantitative investigation was carried out in which the goals were twofold: First, to isolate the features of each Concrete Interactive Context ( CIC , Briz y Albelda, 2013) of creo in wich the doxastic verbal form appears and to identify which features favor its use (namely, register, level of dialogicity, and specific genre traits, Soler, 2019). Second, to determine what argumentative, face, or discursive factors influence the development of frequent pragmatic functions (Soler, 2018). This work finds that creo , although defined as a polyfunctional form (Simon-Vandenbergen, 2000; Gachet, 2009: Mullan, 2010), exhibits a set of three pragmatic values that affects, in different ways, the interactants’ face: affiliation or reinforcement of relations with other/-s - neutrality - de-responsibility.
When the Going Gets Tough, the Tough Get Going: Improving the Disaster Preparedness of Health Care Providers: A Single Center’s 4-Year Experience
2020-10-28

Abstract Objective: Operation based exercises represent simulation activities, which are of great importance for emergency preparedness, as they simulate real experiences in a guided manner. Whereas their primary purpose is to address the organizational emergency preparedness, little is known about the personal benefits of involved participants and whether these positive changes endure over time. Methods: Immediate and medium term assessment of the effectiveness on individual preparedness and benefits of participants, based on self-perception, after participating in a set of 4 interdisciplinary field exercises organized as part of the MSc in Global Health-Disaster Medicine of the Medical School of the National and Kapodistrian University of Athens, Greece. The field exercises were carried out yearly, from 2016 to 2019. Data were collected via questionnaires pre- and post-exercise (1 week and 10 months after participation). The sample size was 228 trainees, with a response rate of 88%. Results: The majority (95%) stated that Mass Casualty Incident (MCI) exercises are appropriate for disaster management training in terms of comprehending theory, and for team-building training. In the case of a real MCI, 22% of the participants declared themselves to be ready to respond prior to MCI exercises. Upon completion, the overall perception of readiness among the participants increased to 77%. Trainee feedback indicated enhancement of both technical and non-technical skills (87%), which were persistent over time, and revealed a high level of satisfaction with the training. Conclusion: This study shows a positive immediate and medium-term impact of operation-based exercises on technical, non-technical skills, and self-perception of participants.
Novel Adapter CAR-T cell Technology for precisely controllable Multiplex Cancer Targeting
2020-10-28

<title>Abstract</title> Chimeric antigen receptor (CAR)-T therapy holds great promise to sustainably improve cancer treatment. However, currently, a broad applicability of CAR-T cell therapies is hampered by limited CAR-T cell versatility and tractability and the lack of exclusive target antigens to discriminate cancerous from healthy tissues. To achieve temporal and qualitative control on CAR-T function, we engineered the Adapter CAR (AdCAR) system. AdCAR-T are redirected to surface antigens via biotin-labeled adapter molecules in the context of a specific linker structure, referred to as Linker-Label-Epitope. AdCAR-T execute highly specific and controllable effector function against a multiplicity of target antigens. In mice, AdCAR-T durably eliminate aggressive lymphoma. Importantly, AdCAR-T might prevent antigen evasion by combinatorial simultaneous or sequential targeting of multiple antigens and are capable to identify and differentially lyse cancer cells by integration of adapter molecule mediated signals based on multiplex antigen expression profiles.
Sinusoidal Obstruction Syndrome Following Myeloablative Therapy and Tranexamic Acid Treatment for Hemorrhage in Two Patients with Neuroblastoma
2020-10-28

Adverse thromboembolic events following administration of the anti-fibrinolytic agent tranexamic acid (TA), used to prevent/treat excessive blood loss, are rare. We present the clinical course of two young patients (22 and 56 months) receiving busulfan/melphalan (Bu/Mel) high-dose chemotherapy with autologous hematopoietic stem cell transplantation (HSCT) to treat high-risk neuroblastoma, who developed hepatic sinusoidal obstruction syndrome (SOS) within 48 h after systemic TA treatment for a hemodynamically relevant hemorrhage. Defibrotide treatment resolved hepatic SOS, but the short time between TA administration and SOS onset suggests a causal association.
Is a derived Caton-Deschamps index for arthroplasty a reliable and valid measure of patella height?
2020-10-28

Measuring patella height has been a hot topic for decades. Multiple radiological indices exist for native knees and arthroplasty. A concise concept of patella height analysis is needed for daily practice and scientific research.
Long-term safety and effectiveness of etanercept in JIA: an 18-year experience from the BiKeR registry
2020-10-29

Abstract Background At present, etanercept represents the most commonly prescribed biologic agent for juvenile idiopathic arthritis (JIA) treatment. Children and adolescents with JIA are often treated with etanercept over long periods, sometimes even into adulthood. The objectives of this analysis were to determine the long-term safety of etanercept compared to a biologic-naïve cohort and to assess the long-term treatment response upon continuous etanercept exposure using data from the German biologics registry (BiKeR). Methods JIA patients newly exposed to etanercept were documented in the BiKeR registry from January 2001 to March 2019, and baseline characteristics, effectiveness, and safety parameters were analysed. Response to treatment was assessed according to 10-joint Juvenile Arthritis Disease Activity Score (JADAS10), JADAS-defined minimal disease activity and remission, JIA-American College of Rheumatology (ACR) improvement criteria, and ACR-inactive disease definition. Safety assessments were based on adverse event (AE) reports. Results A total of 2725 new etanercept users with a diagnosis of JIA were registered. Of these, etanercept was received as a first-line biologic by 95.8% and as monotherapy without concomitant methotrexate by 31.5%. After nine years on continuous treatment, 68.1% of patients presented minimal disease activity, 43.1% JADAS-defined remission on drug, and 36.6% ACR-inactive disease. JIA-ACR30/50/70/90 response rates were still 82/79/71/54% after nine years of treatment. Overall, 2053 AEs (34.3/100PY), including 226 serious AEs (SAE, 3.8/100PY), were observed upon etanercept, compared to 1345 AEs [35.6/100PY; p = 0.3] and 52 SAEs (1.4/100PY; p = 0.0001) in the biologic-naïve cohort. Respective exposure-adjusted rates for etanercept and biologic-naïve patients were 0.9/100PY and 0.2/100PY ( p = 0.0001) for serious infections, 0.4/100PY and 0.1/100PY ( p = 0.01) for zoster reactivation, 0.3/100PY and 0.03/100PY ( p = 0.015) for inflammatory bowel disease, and 1.9/100PY and 1.4/100PY ( p = 0.09) for uveitis. Three and two malignancies were documented in the etanercept and biologic-naïve groups, as well as three and one deaths, respectively. Conclusions No new safety signal was observed, especially no increased risk for malignancies or autoimmune disorders other than inflammatory bowel disease. However, SAEs and serious infections, though infrequent, were more often reported on etanercept than in biologic-naïve patients. In addition, etanercept demonstrated a long-term maintenance of clinical benefits up to nine years of continuous treatment.
CellRank for directed single-cell fate mapping
2020-10-29

<title>Abstract</title> Computational trajectory inference enables the reconstruction of cell-state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank (https://cellrank.org) for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. Our approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors. On data from pancreas development, we show that it automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. CellRank also predicts a novel dedifferentiation trajectory during regeneration after lung injury, which we follow up experimentally by confirming the existence of previously unknown intermediate cell states.
Metaphyseal anchoring short stem hip arthroplasty provides a more physiological load transfer: a comparative finite element analysis study
2020-10-29

Abstract Background Short stem total hip arthroplasty (SHA) preserves femoral bone stock and is supposed to provide a more natural load transfer compared to standard stem total hip arthroplasty (THA). As comparative biomechanical reference data are rare we used a finite element analysis (FEA) approach to compare cortical load transfer after implantations of a metaphyseal anchoring short and standard stem in native biomechanical femora. Methods The subject specific finite element models of biomechanical femora, one native and two with implanted metaphyseal anchoring SHA (Metha, B. Braun Aesculap) and standard THA (CLS, Zimmer-Biomet), were generated from computed tomography datasets. The loading configuration was performed with an axial force of 1400 N. Von Mises stress was used to investigate the change of cortical stress distribution. Results Compared to the native femur, a considerable reduction of cortical stress was recorded after implantation of SHA and standard THA. The SHA showed less reduction proximally with a significant higher metaphyseal cortical stress compared to standard THA. Moreover, the highest peak stresses were observed metaphyseal for the SHA stem while for the standard THA high stress pattern was observed more distally. Conclusions Both, short and standard THA, cause unloading of the proximal femur. However, the metaphyseal anchoring SHA features a clearly favorable pattern in terms of a lower reduction proximally and improved metaphyseal loading, while standard THA shows a higher proximal unloading and more distal load transfer. These load patterns implicate a reduced stress shielding proximally for metaphyseal anchoring SHA stems and might be able to translate in a better bone preservation.
Eosinophilia/Hypereosinophilia in the Setting of Reactive and Idiopathic Causes, Well-Defined Myeloid or Lymphoid Leukemias, or Germline Disorders
2020-10-29

Abstract Objectives To report the findings of the 2019 Society for Hematopathology/European Association for Haematopathology Workshop within the categories of reactive eosinophilia, hypereosinophilic syndrome (HES), germline disorders with eosinophilia (GDE), and myeloid and lymphoid neoplasms associated with eosinophilia (excluding entities covered by other studies in this series). Methods The workshop panel reviewed 109 cases, assigned consensus diagnosis, and created diagnosis-specific sessions. Results The most frequent diagnosis was reactive eosinophilia (35), followed by acute leukemia (24). Myeloproliferative neoplasms (MPNs) received 17 submissions, including chronic eosinophilic leukemia, not otherwise specified (CEL, NOS). Myelodysplastic syndrome (MDS), MDS/MPN, and therapy-related myeloid neoplasms received 11, while GDE and HES received 12 and 11 submissions, respectively. Conclusions Hypereosinophilia and HES are defined by specific clinical and laboratory criteria. Eosinophilia is commonly reactive. An acute leukemic onset with eosinophilia may suggest core-binding factor acute myeloid leukemia, blast phase of chronic myeloid leukemia, BCR-ABL1–positive leukemia, or t(5;14) B-lymphoblastic leukemia. Eosinophilia is rare in MDS but common in MDS/MPN. CEL, NOS is a clinically aggressive MPN with eosinophilia as the dominant feature. Bone marrow morphology and cytogenetic and/or molecular clonality may distinguish CEL from HES. Molecular testing helps to better subclassify myeloid neoplasms with eosinophilia and to identify patients for targeted treatments.
Numbers and phenotype of non-classical CD14dimCD16+ monocytes are predictors of adverse clinical outcome in patients with coronary artery disease and severe SARS-CoV-2 infection
2020-10-29

Abstract Aims To elucidate the prognostic role of monocytes in the immune response of patients with coronary artery disease (CAD) at risk for life-threatening heart and lung injury as major complications of SARS-CoV-2 infection. Methods and results From February to April 2020, we prospectively studied a cohort of 96 participants comprising 47 consecutive patients with CAD and acute SARS-CoV-2 infection (CAD + SARS-CoV-2), 19 CAD patients without infections, and 30 healthy controls. Clinical assessment included blood sampling, echocardiography, and electrocardiography within 12 h of admission. Respiratory failure was stratified by the Horovitz Index (HI) as moderately/severely impaired when HI ≤200 mmHg. The clinical endpoint (EP) was defined as HI ≤200 mmHg with subsequent mechanical ventilation within a follow-up of 30 days. The numbers of CD14dimCD16+ non-classical monocytes in peripheral blood were remarkably low in CAD + SARS-CoV-2 compared with CAD patients without infection and healthy controls (P &amp;lt; 0.0001). Moreover, these CD14dimCD16 monocytes showed decreased expression of established markers of adhesion, migration, and T-cell activation (CD54, CD62L, CX3CR1, CD80, and HLA-DR). Decreased numbers of CD14dimCD16+ monocytes were associated with the occurrence of EP. Kaplan–Meier curves illustrate that CAD + SARS-CoV-2 patients with numbers below the median of CD14dimCD16+ monocytes (median 1443 cells/mL) reached EP significantly more often compared to patients with numbers above the median (log-rank 5.03, P = 0.025). Conclusion Decreased numbers of CD14dimCD16+ monocytes are associated with rapidly progressive respiratory failure in CAD + SARS-CoV-2 patients. Intensified risk assessments comprising monocyte sub- and phenotypes may help to identify patients at risk for respiratory failure.
Numeral classifiers and number marking in Indo-Iranian
2020-10-29

Abstract This paper investigates the origins of sortal numeral classifiers in the Indo-Iranian languages. While these are often assumed to result from contact with non-Indo-European languages, an alternative possibility is that classifiers developed as a response to the rise of optional plural marking. This alternative is in line with the so-called Greenberg-Sanches-Slobin (henceforth GSS ) generalization. The GSS generalization holds that the presence of sortal numeral classifiers across languages is negatively correlated with obligatory plural marking on nouns. We assess the extent to which Indo-Iranian classifier development is influenced by loosening of restrictions on plural marking using a sample of 65 languages and a Bayesian phylogenetic model, inferring posterior distributions over evolutionary transition rates between typological states and using these rates to reconstruct the history of classifiers and number marking throughout Indo-Iranian, constrained by historically attested states. We find broad support for a diachronically oriented construal of the GSS generalization, but find no evidence for a strong bias against the synchronic co-occurrence of classifiers and obligatory plural marking. Inspection of the most likely diachronic trajectories in individual lineages in the tree shows a stronger effect of the GSS among Iranian languages than Indo-Aryan languages. Taken as a whole, these findings suggest that the association of classifiers and optional number marking in Indo-Iranian is neither solely the effect of universal mechanisms nor of the contingency of local contact histories.
Magnetoencephalographic Signatures of Conscious Processing Before Birth
2020-10-29

Abstract The concept of fetal consciousness is a widely discussed topic. In this study, we applied a hierarchical rule learning paradigm to investigate the possibility of fetal conscious processing during the last trimester of pregnancy. We used fetal magnetoencephalography, to assess fetal brain activity in 56 healthy fetuses between gestational week 25 and 40, during an auditory oddball paradigm containing first- and second-order regularities. The comparison of fetal brain responses towards standard and deviant tones revealed that the investigated fetuses show signs of hierarchical rule learning, and thus the formation of a memory trace for the second-order regularity. This ability develops over the course of the last trimester of gestation, in accordance with processes in physiological brain development and was only reliably present in fetuses older than week 35 of gestation. Analysis of fetal autonomic nervous system activity replicates findings in newborns, showing importance of activity state for cognitive processes. On the whole, our results support the assumption that fetuses in the last weeks of gestation are capable of consciously processing stimuli that reach them from outside the womb.
A new lepto-hadronic model applied to the first simultaneous multiwavelength data set for Cygnus X–1
2020-10-29

&lt;p&gt;This is a basic reproduction package for the paper &quot;A new lepto-hadronic model applied to the first simultaneous multiwavelength data set for Cygnus X-1&quot; by [Kantzas et al. (2020)](&lt;a href="https://doi.org/10.1093/mnras/staa3349"&gt;https://doi.org/10.1093/mnras/staa3349&lt;/a&gt;).&lt;/p&gt;
Pharmacological Inhibition of Acid Sphingomyelinase Prevents Uptake of SARS-CoV-2 by Epithelial Cells
2020-10-30

The acid sphingomyelinase/ceramide system plays an important role in bacterial and viral infections. Here, we report that either pharmacological inhibition of acid sphingomyelinase with amitriptyline, imipramine, fluoxetine, sertraline, escitalopram, or maprotiline or genetic downregulation of the enzyme prevents infection of cultured cells or freshy isolated human nasal epithelial cells with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or vesicular stomatitis virus (VSV) pseudoviral particles (pp-VSV) presenting SARS-CoV-2 spike protein (pp-VSV-SARS-CoV-2 spike), a bona fide system mimicking SARS-CoV-2 infection. Infection activates acid sphingomyelinase and triggers a release of ceramide on the cell surface. Neutralization or consumption of surface ceramide reduces infection with pp-VSV-SARS-CoV-2 spike. Treating volunteers with a low dose of amitriptyline prevents infection of freshly isolated nasal epithelial cells with pp-VSV-SARS-CoV-2 spike. The data justify clinical studies investigating whether amitriptyline, a safe drug used clinically for almost 60 years, or other antidepressants that functionally block acid sphingomyelinase prevent SARS-CoV-2 infection.