Miracle-dz/UniFAR-FTUs huggingface dataset:
Care to share? Experimental evidence on code sharing behavior in the social sciences

Transparency and peer control are cornerstones of good scientific practice and entail the replication and reproduction of findings. The feasibility of replications, however, hinges on the premise that original researchers make their data and research code publicly available. This applies in particular to large-N observational studies, where analysis code is complex and may involve several ambiguous analytical decisions. To investigate which specific factors influence researchers’ code sharing behavior upon request, we emailed code requests to 1,206 authors who published research articles based on data from the European Social Survey between 2015 and 2020. In this preregistered multifactorial field experiment, we randomly varied three aspects of our code request’s wording in a 2x4x2 factorial design: the overall framing of our request (enhancement of social science research, response to replication crisis), the appeal why researchers should share their code (FAIR principles, academic altruism, prospect of citation, no information), and the perceived effort associated with code sharing (no code cleaning required, no information). Overall, 37.5% of successfully contacted authors supplied their analysis code. Of our experimental treatments, only framing affected researchers’ code sharing behavior, though in the opposite direction we expected: Scientists who received the negative wording alluding to the replication crisis were more likely to share their research code. Taken together, our results highlight that the availability of research code will hardly be enhanced by small-scale individual interventions but instead requires large-scale institutional norms.
Chinese medicine treatment of mastitis in COVID-19 patients

Abstract Background: Assessing the effectiveness and safety of Chinese medicine for the mastitis in COVID-19 patients is the main purpose of this systematic review protocol. Methods: The following electronic databases will be searched from inception to April 2020: MEDLINE, Ovid, EMBASE, the Cochrane Library, the Allied and Complementary Medicine Database (AMED), Chinese National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), VIP Database and Wanfang Database. In addition, Clinical trial registries, like the Chinese Clinical Trial Registry (ChiCTR), the Netherlands National Trial Register (NTR) and ClinicalTrials.gov, will be searched for ongoing trials with unpublished data. No language restrictions will be applied. The primary outcome will be the time of disappearance of main symptoms (including fever, asthenia, cough disappearance rate, and temperature recovery time), and serum cytokine levels. The secondary outcome will be the accompanying symptoms (such as myalgia, expectoration, stuffiness, runny nose, pharyngalgia, anhelation, chest distress, dyspnea, crackles, headache, nausea, vomiting, anorexia, diarrhea) disappear rate, negative COVID-19 results rate on 2 consecutive occasions (not on the same day), CT image improvement, average hospitalization time, occurrence rate of common type to severe form, clinical cure rate, and mortality. Two independent reviewers will conduct the study selection, data extraction and assessment. RevMan V.5. 3 will be used for the assessment of risk of bias and data synthesis. Results: The results will provide a high-quality synthesis of current evidence for researchers in this subject area. Conclusion: The conclusion of the study will provide an evidence to judge whether Chinese medicine is effective and safe for mastitis in COVID-19 patients. PROSPERO registration number: CRD42020189924.
Tourism, recreation and climate change.

1. Introduction C. Michael Hall & James Higham 2. The Climate-Tourism Relationship and its Relevance to Climate Change Impact Assessment, C. R. de Freitas 3. Tracing the Development of the Climate Change Issue in the Tourism Sector, Daniel Scott, Geoff Wall & Geoff McBoyle SECTION II THE EFFECTS OF CLIMATE CHANGE ON TOURIST FLOWS AND RECREATION PATTERNS 4. Climate and Policy Changes: Their Implications for International Tourism Flows, Sue Mather, David Viner & Graham Todd 5. The Mediterranean: How Can the Worlds Most Popular Tourist Destination Adjust to a Changing Climate? Allen Perry 6. Why Should French Tourism Pay Attention to Climate Change? Jean-Paul Ceron & Ghislain Dubois 7. Climate Change and Tourism and Recreation in North America, Daniel Scott, Geoff McBoyle, & Geoff Wall 8. Tourism and Climatic Change in Southern Africa, R.A. Preston-Whyte & H. Watson 9. Changing Snow-cover and Winter Tourism in the Scottish Highlands, S.J. Harrison, S.J. Winterbottom & R.C. Johnson 10. Climate Change and Tourism in the Swiss Alps, Rolf Burki, Hans Elsasser, Bruno Abegg, & Urs Koenig 11. Effects of Climate Change on Tourism Demand and Benefits in Alpine Areas, Robert B. Richardson & John B. Loomis 12. Implications of Climate Change on Tourism in Oceania, Stephen Craig-Smith & Lisa Ruhanen 13. Tourism, Fossil Fuels and the Resulting Impacts on Climate Change, Susanne Becken & David Simmons SECTION III ADAPTATION AND RESPONSE 14. Tourism and Climate Change Adaptation, Carlo Aall & Karl G Hoyer 15. Tourism and the Ozone Hole: Industry and Tourist Perceptions, L. Michael Trapasso 16. Doing Something About the Weather, Keith Dewar 17. Climate Change and Transport for Tourism, Paul Peeters 18. Sustainable Mobility and Sustainable Tourism, Karl G. Hoyer & Carlo Aall 19. Tourism as victim, problem or solution: Story lines of a complex industry-environment relation, Lotta Frandberg 20. Tourism's Contribution to Global Environmental Change, Stefan Gossling 21. Making Tourism Sustainable: The Real Challenge of Climate Change? , James Higham & C. Michael Hall
Viruses - a major cause of amyloid deposition in the brain

ABSTRACT Introduction Clinically, Alzheimer’s disease (AD) is a syndrome with a spectrum of various cognitive disorders. There is a complete dissociation between the pathology and the clinical presentation. Therefore, we need a disruptive new approach to be able to prevent and treat AD. Areas Covered In this review, the authors extensively discuss the evidence why the amyloid beta is not the pathological cause of AD which makes therefore the amyloid hypothesis not sustainable anymore. They review the experimental evidence underlying the role of microbes, especially that of viruses, as a trigger/cause for the production of amyloid beta leading to the establishment of a chronic neuroinflammation as the mediator manifesting decades later by AD as a clinical spectrum. In this context, the emergence and consequences of the infection/antimicrobial protection hypothesis are described. The epidemiological and clinical data supporting this hypothesis are also analyzed. Expert opinion For decades, we have known that viruses are involved in the pathogenesis of AD. This discovery was ignored and discarded for a long time. Now we should accept this fact, which is not a hypothesis anymore, and stimulate the research community to come up with new ideas, new treatments, and new concepts.
A Self-Adaptive Dual-ILRO Clock-Recovery Technique for Two-Tone Battery-Free Crystal-Free Neural-Recording SoC

Wireless implantable devices are widely used in medical treatment, which should meet clinical constraints such as longevity, miniaturization, and reliable communication. Wireless power transfer (WPT) can eliminate the battery to reduce system size and prolong device life, while it's challenging to generate a reliable clock without a crystal. In this work, we propose a self-adaptive dual-injection-locked-ring-oscillator (dual-ILRO) clock-recovery technique based on two-tone WPT and integrate it into a battery-free neural-recording SoC. The 2<inline-formula><tex-math notation="LaTeX">$\text{nd}$</tex-math></inline-formula>-order inter-modulation (IM2) component of the two WPT tones is extracted as a low-frequency reference for battery-free SoC, and the proposed self-adaptive dual-ILRO technique extends the lock range to ensure an anti-interference PVT-robust clock generation. The neural-recording SoC includes a low-noise signal acquisition unit, a power management unit, and a backscatter circuit to perform neural signal recording, wireless power harvesting, and neural data transmission. Benefiting from the 6.4 <inline-formula><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula>W low power of the clock recovery circuit, the overall SoC power is cut down to 49.8 <inline-formula><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula>W. In addition, the proposed clock-recovery technique enables both signal acquisition and uplink communication to perform as well as that synchronized by an ideal clock, i.e., an effective number of 9.6 bits and a bit error rate (BER) less than 4.8 <inline-formula><tex-math notation="LaTeX">$\times\, 10^{-7}$</tex-math></inline-formula> in chip measurement. The SoC takes a die area of 2.05 mm<inline-formula><tex-math notation="LaTeX">$^{2}$</tex-math></inline-formula>, and an animal test is conducted in a Sprague-Dawley rat to validate the wireless neural-recording performance, compared to a crystal-synchronized commercial chip.
Cyclin-dependent kinase-9 in B-cell malignancies: pathogenic role and therapeutic implications

Abstract Cyclin-dependent kinases (CDK) regulate cell cycle and transcriptional activity. Pan-CDK inhibitors demonstrated early efficacy in lymphoid malignancies, but also have been associated with narrow therapeutic index. Among transcriptional CDKs, CDK7 and CDK9 emerged as promising targets. CDK9 serves as a component of P-TEFb elongation complex and thus is indispensable in mRNA transcription. Selective CDK9 inhibitors demonstrated pre-clinical efficacy in in vitro and in vivo models of B-cell non-Hodgkin lymphoma. CDK9 inhibition results in transcriptional pausing with rapid downmodulation of short-lived oncogenic proteins, e.g. Myc and Mcl-1, followed by cell apoptosis. Early phase clinical trials established safety of CDK9 inhibitors, with manageable neutropenia, infections and gastrointestinal toxicities. In this review, we summarize the rationale of targeting CDK9 in lymphoid malignancies, as well as pre-clinical and early clinical data with pan-CDK and selective CDK9 inhibitors.
Lie symmetry analysis of (2+1)-dimensional KdV equations with variable coefficients

ABSTRACT In this paper, symmetry groups are used to obtain symmetry reductions of (2+1)-dimensional KdV equations with variable coefficients. Despite the fact that these equations emerge in a nonlocal form, by using suitable transformations, they can be written as systems of partial differential equations, and in potential form, as fourth-order partial differential equations. We show that the point symmetries of the potential equation involve a large number of arbitrary functions. Moreover, these symmetries are used to transform the fourth-order partial differential equations into (1+1)-dimensional fourth-order differential equations. Furthermore, we have determined all two-dimensional solvable symmetry subalgebras, under certain restrictions, which the potential equation admits. Finally, by way of example, taking into account a two-dimensional abelian subalgebra, we obtain a direct reduction of the potential equation to an ordinary differential equation.
Evaluation of real‐time polymerase chain reaction for the diagnosis of protozoal myeloencephalitis in horses using cerebrospinal fluid

Abstract Background Equine protozoal myeloencephalitis (EPM) caused by Sarcocystis neurona remains an antemortem diagnostic challenge in some horses. Recent work suggested the use of real‐time PCR (rtPCR) on cerebrospinal fluid (CSF) as a promising diagnostic tool. Objective To evaluate the sensitivity and specificity of S. neurona rtPCR on CSF for EPM diagnosis using horses with EPM and S. neurona‐seropositive horses with other neurologic conditions. Animals Ninety‐nine horses with neurologic disease that underwent complete neurologic examination, CSF collection, and, if euthanized, necropsy including the central nervous system (CNS). Methods Retrospective case‐control study using banked CSF samples. Samples from horses with neurologic abnormalities and necropsy‐confirmed EPM diagnosis, presumptive EPM diagnosis using strict criteria (SnSAG2/4/3 ELISA serum:CSF titer ratios <50) and horses diagnosed with other neurologic diseases were used. Results Fifty‐two horses had EPM; 23 were confirmed on necropsy, and 29 were presumptive clinical diagnoses. The other 47 horses all had necropsy‐confirmed diagnoses. Four of the 47 horses had normal neurologic findings on necropsy and the remaining 43 horses had neurologic diseases including equine degenerative myeloencephalopathy (EDM), cervical vertebral stenotic myelopathy, trauma, and other miscellaneous conditions. One CSF sample was weakly positive for S. neurona by rtPCR, this sample was obtained from a horse with confirmed EDM. Samples from the other 98 horses were negative for S. neurona by rtPCR. Conclusions and Clinical Importance Our study contradicts previous conclusions that S. neurona rtPCR is potentially useful for EPM diagnosis, because our results indicate that the assay has a low sensitivity (0%) for EPM.
Application of digital pathology‐based advanced analytics of tumour microenvironment organisation to predict prognosis and therapeutic response

In recent years, the application of advanced analytics, especially artificial intelligence (AI), to digital H&E images, and other histological image types, has begun to radically change how histological images are used in the clinic. Alongside the recognition that the tumour microenvironment (TME) has a profound impact on tumour phenotype, the technical development of highly multiplexed immunofluorescence platforms has enhanced the biological complexity that can be captured in the TME with high precision. AI has an increasingly powerful role in the recognition and quantitation of image features and the association of such features with clinically important outcomes, as occurs in distinct stages in conventional machine learning. Deep‐learning algorithms are able to elucidate TME patterns inherent in the input data with minimum levels of human intelligence and, hence, have the potential to achieve clinically relevant predictions and discovery of important TME features. Furthermore, the diverse repertoire of deep‐learning algorithms able to interrogate TME patterns extends beyond convolutional neural networks to include attention‐based models, graph neural networks, and multimodal models. To date, AI models have largely been evaluated retrospectively, outside the well‐established rigour of prospective clinical trials, in part because traditional clinical trial methodology may not always be suitable for the assessment of AI technology. However, to enable digital pathology‐based advanced analytics to meaningfully impact clinical care, specific measures of ‘added benefit’ to the current standard of care and validation in a prospective setting are important. This will need to be accompanied by adequate measures of explainability and interpretability. Despite such challenges, the combination of expanding datasets, increased computational power, and the possibility of integration of pre‐clinical experimental insights into model development means there is exciting potential for the future progress of these AI applications. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Sex Differences in Poststroke Cognitive Impairment: A Multicenter Study in 2343 Patients With Acute Ischemic Stroke

BACKGROUND: Poststroke cognitive impairment (PSCI) occurs in about half of stroke survivors. Cumulative evidence indicates that functional outcomes of stroke are worse in women than men. Yet it is unknown whether the occurrence and characteristics of PSCI differ between men and women. METHODS: Individual patient data from 9 cohorts of patients with ischemic stroke were harmonized and pooled through the Meta-VCI-Map consortium (n=2343, 38% women). We included patients with visible symptomatic infarcts on computed tomography/magnetic resonance imaging and cognitive assessment within 15 months after stroke. PSCI was defined as impairment in ≥1 cognitive domains on neuropsychological assessment. Logistic regression analyses were performed to compare men to women, adjusted for study cohort, to obtain odds ratios for PSCI and individual cognitive domains. We also explored sensitivity and specificity of cognitive screening tools for detecting PSCI, according to sex (Mini-Mental State Examination, 4 cohorts, n=1814; Montreal Cognitive Assessment, 3 cohorts, n=278). RESULTS: PSCI was found in 51% of both women and men. Men had a lower risk of impairment of attention and executive functioning (men: odds ratio, 0.76 [95% CI, 0.61–0.96]), and language (men: odds ratio, 0.67 [95% CI, 0.45–0.85]), but a higher risk of verbal memory impairment (men: odds ratio, 1.43 [95% CI, 1.17–1.75]). The sensitivity of Mini-Mental State Examination (<25) for PSCI was higher for women (0.53) than for men (0.27; P=0.02), with a lower specificity for women (0.80) than men (0.96; P=0.01). Sensitivity and specificity of Montreal Cognitive Assessment (<26.) for PSCI was comparable between women and men (0.91 versus 0.86; P=0.62 and 0.29 versus 0.28; P=0.86, respectively). CONCLUSIONS: Sex was not associated with PSCI occurrence but affected domains differed between men and women. The latter may explain why sensitivity of the Mini-Mental State Examination for detecting PSCI was higher in women with a lower specificity compared with men. These sex differences need to be considered when screening for and diagnosing PSCI in clinical practice.
Learned Tensor Low-CP-Rank and Bloch Response Manifold Priors for Non-Cartesian MRF Reconstruction

Magnetic resonance fingerprinting (MRF) can rapidly perform simultaneous imaging of multiple tissue parameters. However, the rapid acquisition schemes used in MRF inevitably introduce aliasing artifacts in the recovered tissue fingerprints, reducing the reconstruction parameter accuracy. Current regularized reconstruction methods are based on iterative procedures which are time-consuming. In addition, most deep learning-based methods lack interpretability and are inapplicable to non-Cartesian scenarios. In this paper, we propose a joint reconstruction model incorporating MRF-physics prior and the data correlation constraint for non-Cartesian MRF reconstruction. To avoid time-consuming iterative procedures, we unroll the reconstruction model into a deep neural network. Specifically, we propose a learned CANDECOMP/PARAFAC (CP) decomposition module to exploit the tensor low-rank priors of high-dimensional MRF data, which avoids computationally burdensome singular value decomposition. Inspired by the MRF-physics, we also propose a Bloch response manifold module to learn the mapping between reconstructed MRF data and the multiple parameter maps. Preliminary numerical experiments show that the proposed network can reconstruct high-quality MRF data and multiple parameter maps within significantly reduced computational time.
Accuracy of Orbital Shape Reconstruction—Comparative Analysis of Errors in Implant Shape Versus Implant Positioning: A Cadaveric Study

Introduction: Orbital blowout fractures are commonly reconstructed with implants shaped to repair orbital cavity defects, restore ocular position and projection, and correct diplopia. Orbital implant shaping has traditionally been performed manually by surgeons, with more recent use of computer-assisted design (CAD). Accuracy of implant placement is also key to reconstruction. This study compares the placement accuracy of orbital implants, testing the hypothesis that CAD-shaped implants indexed to patient anatomy will better restore orbit geometry compared with manually shaped implants and manually placed implants. Methods: The placement accuracy of orbital implants was assessed within a cadaveric blowout fracture model (3 skulls, 6 orbits) via 3-dimensional CT analysis. Defects were repaired with 4 different techniques: manually placed-manually shaped composite (titanium-reinforced porous polyethylene), manually placed CAD composite, indexed placed CAD composite, and indexed placed CAD titanium mesh. Results: Implant placement accuracy differed significantly with the implant preparation method (P=0.01). Indexing significantly improved the placement accuracy (P=0.002). Indexed placed titanium mesh CAD implants (1.42±0.33 mm) were positioned significantly closer to the intact surface versus manually placed-manually shaped composite implants (2.12±0.39 mm). Discussion: Computer-assisted design implants indexed to patient geometry yielded average errors below the acceptable threshold (2 mm) for enophthalmos and diplopia. This study highlights the importance of adequately indexing CAD-designed implants to patient geometry to ensure accurate orbital reconstructions.
Characterisation of ChE in Solea solea and exposure of isoflavones in juveniles of commercial flatfish (Solea solea and Solea senegalensis)

The isoflavones genistein and daidzein are flavonoid compounds mainly found in legumes, especially in soybeans and their derived products. These flavonoids can be present in agricultural, domestic and industrial wastewater effluents as a result of anthropogenic activities and may be discharged in the environment. Due to the large growth of the aquaculture sector in recent decades, new and cost‐effective fish feeds are being sought, but there is also a particular need to determine the effects of exposed flavonoids on fish in the aquatic environment, as this is the main route of exposure of organisms to endocrine disruptors. This study evaluated the possible effects of these isoflavones on juveniles of Solea senegalensis and Solea solea. After 48–96 h of exposure, the acetylcholinesterase activity in the sole head tissues was measured, and the cholinesterase activity in juveniles of common sole (S. solea) was determined. Experiments were carried out to determine the optimal pH, investigate the specificity of three substrates (acetylthiocholine, butyrylthiocholine, propionylthiocholine) on cholinesterase activity and determine the kinetic parameters (Vmax and Km). The results obtained showed that neither genistein nor daidzein exposure to S. senegalensis and S. solea inhibited the activity of acetylcholinesterase at the tested concentrations (genistein: 1.25, 2.5, 5, 10 and 20 mg/L; daidzein: 0.625, 1.25, 2.5, 5 and 10 mg/L).
Language Impairment in Vascular Dementia: A Clinical Review

Vascular cognitive impairment (VCI) encompasses a wide range of conditions, including cognitive impairment associated with stroke or vascular brain injury, mild vascular cognitive impairment, and vascular dementia (VD). Knowledge of language impairment associated with VD is far less extensive than that of Alzheimer's disease. Although not prevalent in VD, impairment in language skills has been reported. A better understanding of the neurolinguistic features associated with the different presentations of VD could facilitate medical diagnosis. In this article, we report data on language impairment in VD, with particular attention to their primary or secondary functional origin. To better appreciate this functional origin, we also outline the main characteristics of impairment in other cognitive functions. Key elements that should be considered in the speech-language assessment of individuals with possible or proven VD are also highlighted.