Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping the discursive dimensions of the reproducibility crisis: A mixed methods analysis

To those involved in discussions about rigor, reproducibility, and replication in science, conversation about the “reproducibility crisis” appear ill-structured. Seemingly very different issues concerning the purity of reagents, accessibility of computational code, or misaligned incentives in academic research writ large are all collected up under this label. Prior work has attempted to address this problem by creating analytical definitions of reproducibility. We take a novel empirical, mixed methods approach to understanding variation in reproducibility discussions, using a combination of grounded theory and correspondence analysis to examine how a variety of authors narrate the story of the reproducibility crisis. Contrary to expectations, this analysis demonstrates that there is a clear thematic core to reproducibility discussions, centered on the incentive structure of science, the transparency of methods and data, and the need to reform academic publishing. However, we also identify three clusters of discussion that are distinct from the main body of articles: one focused on reagents, another on statistical methods, and a final cluster focused on the heterogeneity of the natural world. Although there are discursive differences between scientific and popular articles, we find no strong differences in how scientists and journalists write about the reproducibility crisis. Our findings demonstrate the value of using qualitative methods to identify the bounds and features of reproducibility discourse, and identify distinct vocabularies and constituencies that reformers should engage with to promote change.
Looking down: a model for visual route following in flying insects

Insect visual navigation is often assumed to depend on panoramic views of the horizon, and how these change as the animal moves. However, it is known that honey bees can visually navigate in flat, open meadows where visual information at the horizon is minimal, or would remain relatively constant across a wide range of positions. In this paper we hypothesise that these animals can navigate using view memories of the ground. We find that in natural scenes, low resolution views from an aerial perspective of ostensibly self-similar terrain (e.g. within a field of grass) provide surprisingly robust descriptors of precise spatial locations. We propose a new visual route following approach that makes use of transverse oscillations to centre a flight path along a sequence of learned views of the ground. We deploy this model on an autonomous quadcopter and demonstrate that it provides robust performance in the real world on journeys of up to 30 m. The success of our method is contingent on a robust view matching process which can evaluate the familiarity of a view with a degree of translational invariance. We show that a previously developed wavelet based bandpass orientated filter approach fits these requirements well, exhibiting double the catchment area of standard approaches. Using a realistic simulation package, we evaluate the robustness of our approach to variations in heading direction and aircraft height between inbound and outbound journeys. We also demonstrate that our approach can operate using a vision system with a biologically relevant visual acuity and viewing direction.
Balanced carbohydrate ratios are associated with improved diet quality in Australia: A nationally representative cross-sectional study

Background Carbohydrate quality influences major health outcomes; however, the best criteria to assess carbohydrate quality remain unknown. Objective The objectives were to: i) evaluate whether a diet that meets a carbohydrate ratio (simple, modified or dual ratio) is associated with higher nutrient intakes and diet quality, and ii) model the impact of substituting carbohydrate foods that meet the proposed ratios in place of foods that do not, on nutrient intakes. Design A secondary analysis of cross-sectional data from the 2011–12 Australian National Nutrition and Physical Activity Survey. Participants/Setting National data from participants aged 2 years and older (n = 12,153). Main outcome measures Ratios were defined as (i) simple ratio, 10:1 (10g carbohydrate:≥1g dietary fiber); (ii) modified ratio, 10:1:2 (10g carbohydrate:≥1g dietary fiber:≤2g free sugars); and (iii) dual ratio, 10:1 & 1:2 (10g carbohydrate:≥1g dietary fiber & ≤2g free sugars per 1g dietary fiber). Ratios were compared to nutrient intakes obtained via automated multiple-pass 24-hour dietary recall and diet quality calculated using the Australian Healthy Eating Index. Statistical analyses performed Substitution dietary modelling was performed. Data were analyzed using paired and independent sample t-tests. Results Ratio adherence was highest for simple (50.2% adults; 28.6% children), followed by dual (40.6% adults; 21.7% children), then modified (32.7% adults; 18.6% children) ratios. Participants who met any ratio reported higher nutrient intake and diet quality compared to those who failed to meet the respective ratio (P < .001 for all), with the greatest nutrient intakes found for those who met modified or dual ratios. Dietary modelling improved nutrient intakes for all ratios, with the greatest improvement found for the dual ratio. Conclusions All carbohydrate ratios were associated with higher diet quality, with a free sugars constraint in the dual ratio providing the greatest improvements.
LAPNet: Non-Rigid Registration Derived in k-Space for Magnetic Resonance Imaging

Physiological motion, such as cardiac and respiratory motion, during Magnetic Resonance (MR) image acquisition can cause image artifacts. Motion correction techniques have been proposed to compensate for these types of motion during thoracic scans, relying on accurate motion estimation from undersampled motion-resolved reconstruction. A particular interest and challenge lie in the derivation of reliable non-rigid motion fields from the undersampled motion-resolved data. Motion estimation is usually formulated in image space via diffusion, parametric-spline, or optical flow methods. However, image-based registration can be impaired by remaining aliasing artifacts due to the undersampled motion-resolved reconstruction. In this work, we describe a formalism to perform non-rigid registration directly in the sampled Fourier space, i.e. k-space. We propose a deep-learning based approach to perform fast and accurate non-rigid registration from the undersampled k-space data. The basic working principle originates from the Local All-Pass (LAP) technique, a recently introduced optical flow-based registration. The proposed LAPNet is compared against traditional and deep learning image-based registrations and tested on fully-sampled and highly-accelerated (with two undersampling strategies) 3D respiratory motion-resolved MR images in a cohort of 40 patients with suspected liver or lung metastases and 25 healthy subjects. The proposed LAPNet provided consistent and superior performance to image-based approaches throughout different sampling trajectories and acceleration factors.
Functionality of Prosopis juliflora gum in the preparation of mango (Mangifera indica L.) nectar of low calorie content

Prosopis juliflora “cuji”, species widely disseminated in Venezuela, produces seed gum. The behavior of this hydrocolloid in preparation of fruit nectars of low caloric content was studied. Six treatments, using different gum concentrations (0.10; 0.15; 0.20; 0.25 and 0.30%) and a control treatment (without gum), were carry out. The physicochemical characteristics (pH, °Brix, viscosity, turbidity), sensory (appearance, flavor, texture) of the elaborated product, were determinate. An experimental totally randomized design was applied. The comparison of the averages was made using Tukey’s method, with a significance level of (p
Dissolution of Metals from Biosolid-Treated Soils by Organic Acid Mixtures

Results for the solubilization of metals from biosolid- (BSL-) treated soils by simulated organic acid-based synthetic root exudates (OA mixtures) of differing composition and concentrations are presented. This study used two BSL-treated Romona soils and a BSL-free Romona soil control that were collected from experimental plots of a long-term BSL land application experiment. Results indicate that the solubility of metals in a BSL-treated soil with 0.01 and 0.1 M OA mixtures was significantly higher than that of 0.001 M concentrations. Differences in composition of OAs caused by BSL treatment and the length of growing periods did not affect the solubility of metals. There were no significant differences in organic composition and metals extracted for plants grown at 2, 4, 8, 12, and 16 weeks. The amount of metals extracted tended to decrease with the increase of the pH. Results of metal dissolution kinetics indicate two-stage metal dissolution. A rapid dissolution of metals occurred in the first 15 minutes. For Cd, Cu, Ni, and Zn, approximately 60–70% of the metals were released in the first 15 minutes while the initial releases for Cr and Pb were approximately 30% of the total. It was then followed by a slow but steady release of additional metals over 48 hours.
CsrA enters Hfq's territory: Regulation of a base‐pairing small RNA

Post‐transcriptional regulatory networks in Gammaproteobacteria are to a large extent built around the two globally acting RNA‐binding proteins (RBPs) CsrA and Hfq. Both RBPs interact with small regulatory RNAs (sRNAs), but the functional outcomes of these interactions are generally distinct. Whereas Hfq both stabilizes sRNAs and promotes their base‐pairing to target mRNAs, the sRNAs bound by CsrA act as sequestering molecules that titrate the RBP away from its mRNA targets. In this issue of Molecular Microbiology, Lai et al. reveal that CsrA interacts with the Hfq‐associated and base‐pairing sRNA Spot 42. In this case, CsrA increases Spot 42 stability by masking a cleavage site for endoribonuclease RNase E, thereby promoting Spot 42‐dependent regulation of srlA mRNA. Interestingly, the effect of CsrA on srlA expression is two‐fold. In addition to affecting Spot 42‐dependent regulation, CsrA directly inhibits translation of SrlM, an activator of srlA transcription. Together, this study reveals a new function for CsrA and indicates more intricate connections between the CsrA and Hfq networks than previously anticipated. Several recent studies have identified additional RBPs that interact with sRNAs. With new RBP identification methods at hand, it will be intriguing to see how many more sRNA‐binding proteins will be uncovered.
The nature of ICT in technology convergence: A knowledge-based network analysis

This study aims to understand the nature of information and communication technology in technology convergence. We form a knowledge network by applying social network theories to Korean patent data collected from the European Patent Organization. A knowledge network consists of nodes representing technology sectors identified by their International Patent Classification codes and edges that link International Patent Classification codes when they appear concurrently in a patent. We test the proposed hypotheses using four indices (degree centrality, E-I index, entropy index, and clustering coefficient). The results show that information and communication technology is easily attached but tends to converge with similar technology and has the greatest influence on technology convergence over other technologies. This study is expected to help practitioners and policymakers understand the structure and interaction mechanisms of technology from a systematic perspective and improve national-level technology policies.
Selüloz ve Selüloz Türevi Diyet Liflerin Özellikleri ve Fırın Ürünlerinde Kullanım İmkanları

Dietary fibers are commonly added in foods due to its decreasing effect of health risks. Cellulose and cellulose derivatives are accepted as dietary fiber because they resist in food process and are not digested in human gastrointestinal system. Cellulose and cellulose derivatives are prevalently used in bakery products with technological properties besides their health beneficial effects. These compounds interact with other macromolecules, which is in structure, during process of bakery product and they increase water absorption, volume and stability of dough by this way. So this polymers improve textural properties of final product thereby they extend the shelf life. Additionally, they are added in bakery products with aim of decreasing calorific value and protection of community health care. It was reviewed in this paper that dietary fiber properties, health improve effects and using possibilities of cellulose and cellulose derivatives in bakery products.
Thrombectomy in special populations: report of the Society of NeuroInterventional Surgery Standards and Guidelines Committee

Background The purpose of this guideline is to summarize the data available for performing mechanical thrombectomy (MT) for emergent large vessel occlusion (ELVO) stroke in special populations not typically included in large randomized controlled clinical trials, including children, the elderly, pregnant women, patients who have recently undergone surgery, and patients with thrombocytopenia, collagen vascular disorders, and endocarditis. Methods We performed a literature review for studies examining the indications, efficacy, and outcomes for patients undergoing MT for ischemic stroke aged <18 years and >80 years, pregnant patients, patients who have recently undergone surgery, and those with thrombocytopenia, collagen vascular diseases, or endocarditis. We graded the quality of the evidence. Results MT can be effective for the treatment of ELVO in ischemic stroke for patients over age 80 years and under age 18 years, thrombocytopenic patients, pregnant patients, and patients with endocarditis. While outcomes are worse compared to younger patients and those with normal platelet counts (respectively), there is still a benefit in the elderly (in both mRS and mortality). Data are very limited for patients with collagen vascular diseases; although diagnostic cerebral angiography carries increased risks, MT may be appropriate in carefully selected patients in whom untreated ELVO would likely result in disabling or fatal outcome.
High‐Throughput Computational Analysis of Biofilm Formation from Time‐Lapse Microscopy

Candida albicans biofilm formation in the presence of drugs can be examined through time‐lapse microscopy. In many cases, the images are used qualitatively, which limits their utility for hypothesis testing. We employed a machine‐learning algorithm implemented in the Orbit Image Analysis program to detect the percent area covered by cells from each image. This is combined with custom R scripts to determine the growth rate, growth asymptote, and time to reach the asymptote as quantitative proxies for biofilm formation. We describe step‐by‐step protocols that go from sample preparation for time‐lapse microscopy through image analysis parameterization and visualization of the model fit. © 2021 Wiley Periodicals LLC.
The journey is just as important as the destination—Digital neuropsychological assessment provides performance stability measures in patients with acquired brain injury

Background Cognitive performances on neuropsychological paper-and-pencil tests are generally evaluated quantitatively by examining a final score (e.g., total duration). Digital tests allow for a quantitative evaluation of “how” a patient attained a final score, which opens the possibility to assess more subtle cognitive impairment even when final scores are evaluated as normal. We assessed performance stability (i.e., the number of fluctuations in test performance) to investigate (1) differences in performance stability between patients with acquired brain injury (ABI) and healthy controls; (2) the added value of performance stability measures in patients with ABI; and (3) the relation between performance stability and cognitive complaints in daily life in patients with ABI. Methods We administered three digital neuropsychological tests (Rey Auditory Verbal Learning Test, Trail Making Test, Stroop Colour and Word Test) and the Cognitive Complaints—Participation (CoCo-P) inventory in patients with ABI (n = 161) and healthy controls (n = 91). Results Patients with ABI fluctuated more in their performance on all tests, when compared to healthy controls. Furthermore, 4–15% of patients who performed inside normal range on the conventional final scores were outside normal range on the performance stability measures. The performance stability measures, nor the conventional final scores, were associated with cognitive complaints in daily life. Conclusions Stability in test performance of patients was clearly dissociable from healthy controls, and may assess additional cognitive weaknesses which might not be observed or objectified with paper-and-pencil tests. More research is needed for developing measures better associated with cognitive complaints.
Inter-Carbon Nanotube Contact and Thermal Resistances in Heat Transport of Three-Phase Composites

Single-walled carbon nanotubes (SWNTs) tend to aggregate into bundles due to van der Waals forces during the fabrication of the composite. A computational model using an off-lattice Monte Carlo method is developed to systematically investigate the effects of SWNT bundles, the number of SWNTs per bundle and the thermal boundary resistance (TBR) at the SWNT–SWNT interfaces on the effective thermal conductivity (Keff) of three-phase composites. It is found that the aggregation of the SWNTs in bundles can reduce significantly the Keff of the composites with SWNTs oriented parallel or randomly to the heat flux direction, but it enhances slightly the Keff of those with SWNTs perpendicular to the heat flux direction. The Keff of the composites also decreases when more individual SWNTs aggregate in each bundle and with larger SWNT–SWNT TBR values. The thermal transport mechanism within the composites is dominated by a critical SWNT–SWNT TBR of 0.155 × 10–8 m2K/W.
AVALIAÇÃO DA CAPACIDADE DE ADSORÇÃO DE FLÚOR EM CARVÃO ATIVADO DE ORIGEM ANIMAL

Neste trabalho foi avaliado o potencial de adsorção do carvão ativado de osso bovino na remoção de íons fluoreto. Para tanto, inicialmente, determinou-se o ponto de carga zero do adsorvente (pHPCZ). Em seguida, avaliou-se a cinética de adsorção, os efeitos do pH da solução (2 – 12) e da temperatura do sistema (20, 30, 40 e 50°C) e, finalmente, o equilíbrio de adsorção. Todos os testes foram realizados em sistema fechado e batelada sob agitação constante (130 rpm). Os resultados obtidos mostram que o pHPCZ do adsorvente é igual a 6,63. A cinética de adsorção indica que o equilíbrio do sistema foi alcançado em, aproximadamente, 6 horas de operação. Os dois modelos cinéticos ajustados aos dados experimentais (pseudoprimeira e pseudossegunda ordens) descreveram de forma satisfatória a cinética de adsorção do flúor, com coeficiente de determinação superiores a 0,98. As avaliações dos efeitos do pH e temperatura apontam que as melhores condições de remoção de flúor foram obtidas em pH 2 e temperaturas de 40 e 50 °C para baixas concentrações e 30°C para concentrações acima de 4 mg L -1 . No estudo do equilíbrio, verificou-se que o modelo de Langmuir foi o que melhor se ajustou aos dados experimentais, apresentando capacidade máxima de adsorção de 2,03 mg g -1 em 30°C. Os resultados obtidos demonstraram que o adsorvente estudado apresenta grande potencial para a remoção de flúor, quando comparado a outros materiais adsorventes.
Spatial heterogeneity in forest carbon storage affects priorities for reforestation

Reforestation is an important strategy for nature-based climate solutions and identifying carbon storage potential of different locations is critical to its success. Applying average carbon values from forest inventories ignores the spatial heterogeneity in forest carbon and the effects of forest edges on carbon storage degradation. Here we show how spatially-explicit, predictive carbon modeling, that leverages satellite, social and biogeophysical datasets, can be used to identify more efficient restoration opportunities for climate mitigation than area-based carbon stock averages. Accounting for regeneration of forest edges, in addition to reforestation, boosts estimates of potential carbon gains by more than 20%. The total potential carbon gain that could be achieved through reforestation at the level indicated by the Bonn Challenge (350Mha) is 51 Gt CO2-eq, but the “missing carbon” in our current forests accounts for 64.6 Gt CO2-eq globally; the greatest potential carbon gains are found in areas of high fragmentation.
Nicotine dependence and functional connectivity of insular cortex subregions

The insular cortex has been identified as a promising target in brain-based therapies for Tobacco Use Disorder, and has three major sub-regions (ventral anterior, dorsal anterior, and posterior) that serve distinct functional networks. How these subregions and associated networks contribute to nicotine dependence has not been well understood, and therefore was the subject of this study. Forty-seven individuals (24 women; 18-45 years old) who smoked cigarettes daily rated their dependence using the Fagerström Test for Nicotine Dependence (FTND), abstained from smoking overnight (~12 h), and underwent resting-state functional MRI. Correlations between dependence and resting-state functional connectivity (RSFC) of the major insular sub-regions were evaluated using whole-brain-corrected voxel-wise analyses and post-hoc region-of-interest (ROI) analyses. Dependence was analyzed both as a unitary (FTND total score) and bivariate construct – two FTND factors (“morning smoking” and “daytime smoking”). Dependence was negatively correlated with connectivity of both the right dorsal and left ventral anterior insula with the left precuneus, and with connectivity of the left posterior insula to the left putamen. In post-hoc analyses, dependence correlated negatively with connectivity between all anterior insula subregions and the left precuneus, and with bilateral posterior insula connectivity with the left posterior putamen. The latter finding was driven by “daytime smoking”. These results suggest an anterior-posterior distinction in functional insular networks associated with different dimensions of nicotine dependence, with greater dependence linked to weaker connectivity. They may inform therapeutic approaches involving brain stimulation that may elicit differential clinical outcomes depending on the insular subnetwork targeted.