julilili42/papers huggingface dataset:
SCAPA: Development of a Questionnaire Assessing Self-Concept and Attitudes Toward Programming
2020-06-03

There is a constantly growing number of initiatives asserting the relevance of programming already in primary education and offering respective interventions with the goal to foster interest in and positive attitudes toward programming. To evaluate to what extent this goal is achieved, assessing students' attitudes toward programming reliably is indispensable. However, there still is a need for validated instruments for assessing this in elementary school students. This seems particularly relevant as self-concept and attitudes toward a school subject were repeatedly observed to be significant predictors of learning motivation and achievement. The newly developed Self-Concept and Attitude toward Programming Assessment (SCAPA) is based on existing instruments for assessing students' self-concept and attitude toward mathematics. SCAPA measures aspects of students' self-concept and attitudes toward programming on seven scales: i) self-reported previous programming experience and understanding, ii) self-concept, iii) intrinsic value belief, iv) attainment value belief, v) utility value belief, vi) cost belief, and vii) compliance and persistence. We administered SCAPA to 197 elementary school students between seven and ten years of age in the context of an evaluation of a computational thinking intervention. Data were analyzed for reliability (i.e., internal consistency on item and scale level) and construct validity (by means of confirmatory factor analysis). Results indicated good reliability for all scales except for the self-reported previous programming experience and understanding scale. Overall, these results reflect SCAPA's suitability for assessing different aspects of elementary school students' self-concept and attitudes toward programming.
Sleep and circadian phenotype in people without cone-mediated vision
2020-06-03

Abstract Background Light exposure entrains the circadian clock through the intrinsically photosensitive retinal ganglion cells, which sense light in addition to the cones and rods. In congenital achromatopsia (ACHM; prevalence 1:30-50,000), the cone system is non-functional, resulting in severe light avoidance and photophobia at daytime light levels. How this condition affects circadian and neuroendocrine responses to light is not known. Methods In genetically confirmed ACHM patients (n=7; age 30-72 years; 6 women, 1 male), we examined survey-assessed sleep/circadian phenotype (PSQI, ESS, MEQ, MCTQ), self-reported visual function (NEI-VFQ-25), sensitivity to light (VLSQ-8) and use of spectral filters that modify chronic light exposure. In all but one patient, we measured rest-activity cycles using actigraphy over 3 weeks and measured the melatonin phase angle of entrainment using the dim-light melatonin onset (DLMO). Results ACHM patients experience a severely attenuated light-dark cycle due to severe light sensitivity and habitual use of filters to reduce retinal illumination. In aggregate, both MEQ and MCTQ indicated a tendency to late chronotype. We found regular rest-activity patterns in all patients and normal phase angles of entrainment in participants with a measurable DLMO. Conclusions Our results reveal that a functional cone system and exposure to daytime light intensities are not necessary for regular behavioural and hormonal entrainment, even when survey-assessed sleep and circadian phenotype indicated a tendency for a late chronotype and sleep problems in our ACHM cohort. Our results can be explained by an adaptation mechanism in circadian photoreception which adjusts to the range of habitual light exposures.
Tropical Geometry: new directions
2020-06-03

The workshop "Tropical Geometry: New Directions" was devoted to a wide discussion and exchange of ideas between the leading experts representing various points of view on the subject, notably, to new phenomena that have opened themselves in the course of the last 4 years. This includes, in particular, refined enumerative geometry (using positive integer q -numbers instead of positive integer numbers), unexpected appearance of tropical curves in scaling limits of Abelian sandpile models, as well as a significant progress in more traditional areas of tropical research, such as tropical moduli spaces, tropical homology and tropical correspondence theorems.
How Efficient Can Non-Professional Masks Suppress COVID-19 Pandemic?
2020-06-03

Abstract The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be transmitted via respiratory secretions. Since there are currently no specific therapeutics or vaccines available against the SARS-CoV-2, the commen non-pharmaceutical interventions (NPIs) are still the main measures to curb the COVID-19 epidemic. Face mask wearing is one important measure to suppress the pandemic. In order to know how efficient is face mask wearing in reducing the pandemic even with low efficiency non-professional face masks, we exploit physical abstraction to model the non-professional face masks made from cotton woven fabrics and characterize them by a parameter virus penetration rate (VPR) γ . Monte Carlo simulations exhibit that the effective reproduction number R of COVID-19 or similar pandemics can be approximately reduced by factor γ 4 with respect to the basic reproduction number R 0 , if the face masks with 70% &lt; γ &lt; 90% are universally applied for the entire network. Furthermore, thought experiments and practical exploitation examples in country-level and city-level are enumerated and discussed to support our discovery in this study and indicate that the outbreak of a COVID-19 like pandemic can be even suppressed by the low efficiency non-professional face masks.
Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance
2020-06-03

Abstract Background :West African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction. The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi , an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu ( Bos indicus indicus ) breeds: Ngaoundere Gudali, White Fulani and Red Fulani. Results: Approximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~100 million (M) SNPs were identified and 7.7 M of those were breed-specific. Approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic traits and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome. Conclusions: The findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.
COVID-19 pandemic and troponin: indirect myocardial injury, myocardial inflammation or myocarditis?
2020-06-04

The initial mechanism for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the binding of the virus to the membrane-bound form of ACE2, which is mainly expressed in the lung. Since the heart and the vessels also express ACE2, they both could become targets of the virus. However, at present the extent and importance of this potential involvement are unknown. Cardiac troponin levels are significantly higher in patients with more severe infections, patients admitted to intensive care units or in those who have died. In the setting of COVID-19, myocardial injury, defined by an increased troponin level, occurs especially due to non-ischaemic myocardial processes, including severe respiratory infection with hypoxia, sepsis, systemic inflammation, pulmonary thrombosis and embolism, cardiac adrenergic hyperstimulation during cytokine storm syndrome, and myocarditis. At present, there are limited reports on definite diagnosis of myocarditis caused by SARS-CoV-2 in humans and limited demonstration of the virus in the myocardium. In conclusion, although the heart and the vessels are potential targets in COVID-19, there is currently limited evidence on the direct infection of the myocardium by SARS-CoV-2. Additional pathological studies and autopsy series will be very helpful to clarify the potentiality of COVID-19 to directly infect the myocardium and cause myocarditis.
Genomic insights into the early peopling of the Caribbean
2020-06-04

A complex dispersal into the Caribbean The settlement of the Caribbean and genetic relationships among pre-European Caribbean people remain a mystery. After examining 93 ancient genomes dating to a range from about 3200 to 400 years ago, Nägele et al. suggest that at least three separate colonization events, including a previously unknown wave, were connected to radiation events in North America. The two more ancient lineages coexisted in Cuba but were fully separate genetically, with later movement into the region from a third group from South America. The study not only informs on the settlement of the Caribbean but also lends insights into the broader-scale intercontinental radiation of humans across the American landscape, including across substantial water boundaries. Science , this issue p. 456
Allogeneic hematopoietic cell transplantation with non-myeloablative conditioning for patients with hematologic malignancies: Improved outcomes over two decades
2020-06-04

We have used a non-myeloablative conditioning regimen for allogeneic hematopoietic cell transplantation for the past twenty years. During that period, changes in clinical practice have been aimed at reducing morbidity and mortality from infections, organ toxicity, and graft-versus-host disease. We hypothesized that improvements in clinical practice led to better transplantation outcomes over time. From 1997-2017, 1,720 patients with hematologic malignancies received low-dose total body irradiation +/- fludarabine or clofarabine before transplantation from HLA-matched sibling or unrelated donors, followed by mycophenolate mofetil and a calcineurin inhibitor ± sirolimus. We compared outcomes in three cohorts by year of transplantation: 1997 +/- 2003 (n=562), 2004 +/- 2009 (n=594), and 2010 +/- 2017 (n=564). The proportion of patients ≥60 years old increased from 27% in 1997 +/- 2003 to 56% in 2010–2017, and with scores from the Hematopoietic Cell Transplantation Comborbidity Index of ≥3 increased from 25% in 1997 +/- 2003 to 45% in 2010 +/- 2017. Use of unrelated donors increased from 34% in 1997 +/- 2003 to 65% in 2010–2017. When outcomes from 2004 +/- 2009 and 2010–2017 were compared to 1997 +/- 2003, improvements were noted in overall survival (P=.0001 for 2004–2009 and P &lt;.0001 for 2010–2017), profression-free survival (P=.002 for 2004–2009 and P &lt;.0001 for 2010 +/- 2017), non-relapse mortality (P&lt;.0001 for 2004 +/- 2009 and P &lt;.0001 for 2010 +/- 2017), and in rates of grades 2 +/- 4 acute and chronic graft-vs.-host disease. For patients with hematologic malignancies who underwent transplantation with non-myeloablative conditioning, outcomes have improved during the past two decades. Trials reported are registered under ClinicalTrials.gov identifiers: NCT00003145, NCT00003196, NCT00003954, NCT00005799, NCT00005801, NCT00005803, NCT00006251, NCT00014235, NCT00027820, NCT00031655, NCT00036738, NCT00045435, NCT00052546, NCT00060424, NCT00075478, NCT00078858, NCT00089011, NCT00104858, NCT00105001, NCT00110058, NCT00397813, NCT00793572, NCT01231412, NCT01252667, NCT01527045.
HIV-1 induced changes in HLA-C∗03 : 04-presented peptide repertoires lead to reduced engagement of inhibitory natural killer cell receptors
2020-06-04

Objective: Viral infections influence intracellular peptide repertoires available for presentation by HLA-I. Alterations in HLA-I/peptide complexes can modulate binding of killer immunoglobuline-like receptors (KIRs) and thereby the function of natural killer (NK) cells. Although multiple studies have provided evidence that HLA-I/KIR interactions play a role in HIV-1 disease progression, the consequence of HIV-1 infection for HLA-I/KIR interactions remain largely unknown. Design: We determined changes in HLA-I presented peptides resulting from HIV-1-infection of primary human CD4 + T cells and assessed the impact of changes in peptide repertoires on HLA-I/KIR interactions. Methods: Liquid chromatography-coupled tandem mass spectrometry to identify HLA-I presented peptides, cell-based in-vitro assays to evaluate functional consequences of alterations in immunopeptidome and atomistic molecular dynamics simulations to confirm experimental data. Results: A total of 583 peptides exclusively presented on HIV-1-infected cells were identified, of which only 0.2% represented HIV-1 derived peptides. Focusing on HLA-C∗03 : 04/KIR2DL3 interactions, we observed that HLA-C∗03 : 04-presented peptides derived from noninfected CD4 + T cells mediated stronger binding of inhibitory KIR2DL3 than peptides derived from HIV-1-infected cells. Furthermore, the most abundant peptide presented by HLA-C∗03 : 04 on noninfected CD4 + T cells (VIYPARISL) mediated the strongest KIR2DL3-binding, while the most abundant peptide presented on HIV-1-infected cells (YAIQATETL) did not mediate KIR2DL3-binding. Molecular dynamics simulations of HLA-C∗03 : 04/KIR2DL3 interactions in the context of these two peptides revealed that VIYPARISL significantly enhanced the HLA-C∗03 : 04/peptide contact area to KIR2DL3 compared with YAIQATETL. Conclusion: These data demonstrate that HIV-1 infection-induced changes in HLA-I-presented peptides can reduce engagement of inhibitory KIRs, providing a mechanism for enhanced activation of NK cells by virus-infected cells.
Short-scale variations in high-resolution crystal-preferred orientation data in an alpine ice core - do we need a new statistical approach?
2020-06-04

We analysed crystal-preferred orientation of c-axis and microstructure data from the Alpine ice core KCC at an unprecedented resolution and coverage of any Alpine ice core. We find that an anisotropic single-maximum fabric develops as early as 25 m depth in firn under vertical compression and strengthens under simple shear conditions towards the bedrock at 72 m depth. The analysis of continuously measured intervals with subsequent thin section samples from several depths of the ice core reveals a high spatial variability in the crystal orientation and crystal size on the 10 cm-scale as well as within a few centimeters. We quantify the variability and investigate the possible causes and links to other microstructural properties. Our findings support the hypothesis that the observed variability is a consequence of strain localisation on small spatial scales with influence on fabric and microstructure. From a methodological perspective, the results of this study lead us to challenge whether single thin sections from ice cores provide representative parameters for their depth to be used to infer the fabric development in a glacier on the large scale. Previously proposed uncertainty estimates for fabric and grain size parameters do not capture the observed variability. This might therefore demand a new scale-sensitive statistical approach.
20 years of African Neuroscience: Waking a sleeping giant
2020-06-04

Understanding the function and dysfunction of the brain remains one of the key challenges of our time. However, an overwhelming majority of brain research is carried out in the Global North, by a minority of well-funded and intimately interconnected labs. In contrast, with an estimated one neuroscientist per million people in Africa, news about neuroscience research from the Global South remains sparse. Clearly, devising new policies to boost Africa’s neuroscience landscape is imperative. However, the policy must be based on accurate data, which is largely lacking. Such data must reflect the extreme heterogeneity of research outputs across the continent’s 54 countries distributed over an area larger than USA, Europe and China combined. Here, we analysed all of Africa’s Neuroscience output over the past 21 years. Uniquely, we individually verified in each of 12,326 publications that the work was indeed performed in Africa and led by African-based researchers. This step is critical: previous estimates grossly inflated figures, because many of Africa’s high-visibility publications are in fact the result of internationally led collaborations, with most work done outside of Africa. The remaining number of African-led Neuroscience publications was 5,219, on average only ~5 per country and year. From here, we extracted metrics such as the journal and citations, as well as detailed information on funding, international collaborations and the techniques and model systems used. We link these metrics to demographic data and indicators of mobility and economy. For reference, we also extracted the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our unique dataset allows us to gain accurate and in-depth information on the current state of African Neuroscience research, and to put it into a global context. This in turn allows us to make actionable recommendations on how African research might best be supported in the future.
White matter abnormalities across different epilepsy syndromes in adults: an ENIGMA-Epilepsy study
2020-06-05

Abstract The epilepsies are commonly accompanied by widespread abnormalities in cerebral white matter. ENIGMA-Epilepsy is a large quantitative brain imaging consortium, aggregating data to investigate patterns of neuroimaging abnormalities in common epilepsy syndromes, including temporal lobe epilepsy, extratemporal epilepsy, and genetic generalized epilepsy. Our goal was to rank the most robust white matter microstructural differences across and within syndromes in a multicentre sample of adult epilepsy patients. Diffusion-weighted MRI data were analysed from 1069 healthy controls and 1249 patients: temporal lobe epilepsy with hippocampal sclerosis (n = 599), temporal lobe epilepsy with normal MRI (n = 275), genetic generalized epilepsy (n = 182) and non-lesional extratemporal epilepsy (n = 193). A harmonized protocol using tract-based spatial statistics was used to derive skeletonized maps of fractional anisotropy and mean diffusivity for each participant, and fibre tracts were segmented using a diffusion MRI atlas. Data were harmonized to correct for scanner-specific variations in diffusion measures using a batch-effect correction tool (ComBat). Analyses of covariance, adjusting for age and sex, examined differences between each epilepsy syndrome and controls for each white matter tract (Bonferroni corrected at P &amp;lt; 0.001). Across ‘all epilepsies’ lower fractional anisotropy was observed in most fibre tracts with small to medium effect sizes, especially in the corpus callosum, cingulum and external capsule. There were also less robust increases in mean diffusivity. Syndrome-specific fractional anisotropy and mean diffusivity differences were most pronounced in patients with hippocampal sclerosis in the ipsilateral parahippocampal cingulum and external capsule, with smaller effects across most other tracts. Individuals with temporal lobe epilepsy and normal MRI showed a similar pattern of greater ipsilateral than contralateral abnormalities, but less marked than those in patients with hippocampal sclerosis. Patients with generalized and extratemporal epilepsies had pronounced reductions in fractional anisotropy in the corpus callosum, corona radiata and external capsule, and increased mean diffusivity of the anterior corona radiata. Earlier age of seizure onset and longer disease duration were associated with a greater extent of diffusion abnormalities in patients with hippocampal sclerosis. We demonstrate microstructural abnormalities across major association, commissural, and projection fibres in a large multicentre study of epilepsy. Overall, patients with epilepsy showed white matter abnormalities in the corpus callosum, cingulum and external capsule, with differing severity across epilepsy syndromes. These data further define the spectrum of white matter abnormalities in common epilepsy syndromes, yielding more detailed insights into pathological substrates that may explain cognitive and psychiatric co-morbidities and be used to guide biomarker studies of treatment outcomes and/or genetic research.
Diagnostic Techniques of Soil-Transmitted Helminths: Impact on Control Measures
2020-06-05

Soil-transmitted helminth (STH) infections are common in the tropical and subtropical countries. The burden of disease is highest in endemic areas with limited access to good quality water supply and poor sanitary conditions. Major approaches to control and reduce morbidity caused by worm infections include the periodic deworming of pre-school and school-aged children with anthelminthic drugs. Population-based studies and individual patient management including interventional studies can only be successful when accurate diagnostic techniques are used. The lack of appropriate diagnostic tools providing accurate results concerning both infectious status and intensity of infection—as these two factors vary in regions of low infection intensities—is a major challenge. Currently, available techniques show limited sensitivity and specificity and as such, a combination of several techniques is usually used to diagnose the large variety of parasite species. The objective of this review was to describe the advantages and disadvantages of the different available techniques for the diagnosis of STH infections and to highlight their use in control programs.