Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulations of Glycolytic Activities on Macrophages Functions in Tumor and Infectious Inflammation

Macrophages differentiated into a classically activated (M1) or alternatively activated phenotype (M2) in infection and tumor, but the precise effects of glycolysis and oxidative phosphorylation (OXPHOS) metabolic pathway remain unclear. Herein, the effects of glycolysis or OXPHOS on macrophage polarizations were investigated using a pharmacological approach in mice. 2-Deoxy-D-glucose (2-DG) treatments, which blocks the key enzyme hexokinase of glycolysis, efficiently inhibits a specific switch to M1 lineage, decreasing the secretion of pro-inflammatory cytokines and expressions of co-stimulatory molecules associated with relieving infectious inflammation in vitro and in vivo. Glycolytic activation through the hypoxia-inducible factor-1α (HIF-1α) pathway was required for differentiation to the M1 phenotype, which conferred protection against infection. Dimethyl malonate (DMM) treatment, which blocks the key element succinate of OXPHOS, efficiently inhibits a specific switch to M2 lineage when macrophages receiving M2 stimulation, decreasing the secretion of anti-inflammatory cytokine and CD206 expressions. Mitochondrial dynamic alterations including mitochondrial mass, mitochondrial membrane potential (Dym) and ROS productions were critically for differentiation to the M2 phenotype, which conferred protection against anti-tumor immunity. Glycolysis is also required for macrophage M2 differentiation. Thus, these data provide a basis for a comprehensively understanding the role of glycolysis and OXPHOS in macrophage differentiation during anti-infection and anti-tumor inflammation.
A Typology of Community Forestry Approaches in Indonesia: Implications for External Support to Forest Communities

SUMMARY Community-based management is an increasingly important form of governance and control of forests and other natural resources. In Indonesia, government policy aims to expand the role of communities in controlling and managing forests. Since the 1970s, many different forms of community forestry (CF) have been implemented in Indonesia but there has been little systematic analysis of these different approaches. This paper presents a typology of CF in Indonesia to present academic knowledge of CF in a form that is useful for practice. The typology acknowledges the networked nature of communities and was developed through qualitative analysis of 311 documents representing 112 cases of CF. Two dimensions emerged that illustrate the evolution of CF: a ‘formality' dimension and a ‘support’ dimension. The former indicated the degree of government authorisation and the latter indicated the degree and type of support provided to communities from governments, businesses, NGOs or other external actors. Nine types of CF were identified, six formal, two partially formalised and one informal. An analysis of these types revealed there are mixed benefits for communities in formalising their access to forests and that the challenges, and therefore needs for support, differ markedly between communities. This study provides a systematic basis for researchers aiming to understand the processes of transition to CF, and for policy makers and practitioners aiming to implement CF in Indonesia and elsewhere.
Modelling seed dispersal by wind in herbaceous species

Wind can be regarded as the most important vector for seed dispersal in open grassland vegetation. Experimental estimates of seed dispersal distances in this environment are complex because of low arrival probabilities at large distances. Therefore, a proper mathematical generalization would be essential to give insight in dispersal probability distributions. Hence a promising individual-based model for seed dispersal presented by Andersen was tested for different wind velocities and seeds. Simulation results from the seed dispersal model were compared with observations in a horizontal wind tunnel. Considering the large variation in seed morphology and mass, the simulation results fitted wind tunnel results reasonably well, indicating the general applicability of the tested model for herbaceous species. Model sensitivity was evaluated with respect to wind speed and vegetation height. Differences in wind speed had a larger impact on the tail of the seed shadow than on median dispersal. However, vegetation height had little impact on the tail of the seed shadow compared to the median. Terminal velocity (V,) is the crucial species specific parameter in wind dispersal models. There are two frequently used methods to determine V,: a dropping method and a method to float seeds in an upward air stream. However, these methods have never been compared directly. This paper presents V, values determined with both methods. In general results were in the same order. Only for high values of V, the results of the floating method were found to be lower than the results of the dropping method. Simulation results showed that the intraspecific differences in V, values were an important factor in determining the seed shadow.
The effects of soil amendments and mulch on emergence, pod development and yield of bambara groundnut (Vigna subterranea L.) in a hard-setting soil

Poor crop establishment is a common problem in the soils of semi-arid areas of South Africa and is often one of the main factors limiting crop yields. Hard-setting Hutton soils (Chromic Luvisol) expose shoots of emerging crop seedlings to high soil strength, which is detrimental to growth and. early establishment. The effects of surface application of 3.0 t ha−1 gypsum, 1.0 t ha−1 polymer gel, 3.0 t ha−1 grass mulch, 5.0 t ha−1 cattle manure and an untreated control on the establishment and yield of bambara groundnut were investigated in a hard- setting soil at Mafikeng in the North West Province. Soil amendments and mulch significantly improved (P<0.05) seedling emergence (75.2, 87.9 vs 64.8%), pegging (71.3, 78.9 vs 58.7%), podding (70.2, 78.6 vs 60.0%), pod yield (1440.0, 1846.1 vs 807.3 kg ha−1) and grain yield (896.3, 1115.0 vs 603 kg ha−1) of bambara groundnuts over the control. The improvements in amended soils were associated with increased moisture contents and reduced penetrometer resistance compared with un-amended soils. Differences within the amendments were consistently in the order mulch>manure>gypsum=polymer gel>control. The results indicate that the application of amendments to hard-setting soil can significantly improve the establishment and yield of bambara groundnut under local conditions. Further testing of mulches and other locally available materials for use as soil amendments is recommended, especially for smallholder farmers.
Snow Samples Combined With Long-Range Transport Modeling to Reveal the Origin and Temporal Variability of Black Carbon in Seasonal Snow in Sodankylä (67°N)

In the Arctic areas, the influence of global climate change is enhanced. Enabling a better understanding of the changes in the Arctic environment is of the utmost importance. The deposition of local and long-range transported air pollutants includes light-absorbing aerosols, such as black carbon (BC), which darken bright surfaces and induce snow melt. In 2009–2013, surface snow was sampled on a weekly basis during autumn, winter and spring at the Arctic Space Center of the Finnish Meteorological Institute in Sodankylä, which is located north of the Arctic Circle (67.37° N, 26.63° E). Snow samples were analyzed for BC with an Organic/Elemental Carbon Aerosol (OCEC) analyzer. These data were combined with SILAM modeling (System for Integrated modeLing of Atmospheric coMposition) to reveal the origin and temporal (weekly, monthly, and seasonal) variability of black carbon in seasonal snow. Quantitative footprint calculations for the BC observations were performed with the SILAM-model considering emission sources at all heights and including also the sensitivity to the local and near-surface sources. The median BC concentration in snow was 25 μg/kg (number of samples n = 107, skewness γ1 = 0.12, 75th percentile Q3 = 42 μg/kg), determined as [μg-EC/L-H2O]. During snow accumulation season, the median surface snow black carbon concentration was 21 μg/kg (n = 78, γ1 = 1.5, Q3 = 33 μg/kg), and during melt season, it was 57 μg/kg (n = 29, γ1 = 2.2, Q3 = 85 μg/kg). The melt period was identified using snow depth data from the Sodankylä station. The highest values in spring represented the enrichment of BC to the snow surface due to seasonal snow melt. The spring melt BC enrichment ratio was 2.7 (calculated as the ratio of median spring melt season concentration to median accumulation season snow concentration). The results showed that increased surface snow BC concentrations (>30 μg/kg) were due to air masses originating from the Murmansk region in Russia, where smelting and mining industries are located. The temporal variability of BC in snow was high and depended on atmospheric and cryospheric processes, mostly the origin of BC due to atmospheric transport and dry and wet deposition processes, as well as post-depositional snow processes.
A workflow for the rapid assessment of the landslide-tsunami hazard in peri-alpine lakes

Abstract Although lake tsunamis constitute a rare peril, they have repeatedly occurred in peri-alpine lakes in the past. There are several documented historical examples of landslide-triggered tsunamis in Swiss lakes. However, fundamental information and workflows to rapidly quantify the lacustrine tsunami hazard for multiple lakes are missing so far. The fact that the shorelines of major peri-alpine lakes are densely populated underlines the need for a hazard assessment. Detailed assessments require high-resolution geophysical, geotechnical and sedimentological data, and considerable computation time. Due to the involved data acquisition and calculation efforts, such assessments are mainly conducted as detailed case studies for single lakes. We present a workflow for a rapid first-order estimation of the landslide-triggered tsunami hazard along the shores of peri-alpine lakes. A crucial step is the identification of potential tsunami sources. Unstable slopes are mapped automatically, based on parameters that are derived from past studies. Such parameters include the bathymetry and derived parameters, and type, characteristics and thickness of the sediments. Wave amplitudes are estimated with existing predictive equations, based on the constructed maps of potentially unstable slopes. The results may be used for focusing more detailed, lake-specific tsunami-hazard assessments in respective areas.
P2X7 Receptor Antagonism as a Potential Therapy in Amyotrophic Lateral Sclerosis

This review focuses on the purinergic ionotropic receptor P2X7 (P2X7R) as a potential target for developing drugs that delay the onset and/or disease progression in patients with amyotrophic lateral sclerosis (ALS). Description of clinical and genetic ALS features is followed by an analysis of advantages and drawbacks of transgenic mouse models of disease based on mutations in a bunch of proteins, particularly Cu/Zn superoxide dismutase (SOD1), TAR-DNA binding protein-43 (TDP-43), Fused in Sarcoma/Translocated in Sarcoma (FUS), and Chromosome 9 open reading frame 72 (C9orf72). Though of limited value, these models are however critical to study the proof of concept of new compounds, before reaching clinical trials. The authors also provide a description of ALS pathogenesis including protein aggregation, calcium-dependent excitotoxicity, dysfunction of calcium-binding proteins, ultrastructural mitochondrial alterations, disruption of mitochondrial calcium handling, and overproduction of reactive oxygen species (ROS). Understanding disease pathogenic pathways may ease the identification of new drug targets. Subsequently, neuroinflammation linked with P2X7Rs in ALS pathogenesis is described in order to understand the rationale of placing the use of P2X7R antagonists as a new therapeutic pharmacological approach to ALS. This is the basis for the hypothesis that a P2X7R blocker could mitigate the neuroinflammatory state, indirectly leading to neuroprotection and higher motoneuron survival in ALS patients.
Functional Assessment of the Thyrotropin Receptor-β Subunit

Posttranslational processing of the TSH receptor (TSHR) involves proteolysis of a single chain holoreceptor into TSHR-α (or A) and TSHR-β (or B) subunits, which remain associated via disulfide bonds and which may then form oligomers. As both uncleaved and cleavage-derived forms of this receptor have been reported to bind TSH and transduce signals, reasons for this cleavage into α- and β-subunits have remained enigmatic. Recently we suggested that TSHR cleavage was related to receptor oligomerization and now we have asked if cleavage influenced the binding of G proteins to this receptor. Furthermore, as TSHR-α subunits are subject to shedding from the cell surface membrane, we have examined whether the remaining TSHR-β subunits could mediate signaling themselves, either constitutively and /or ligand-induced. We found that only the cleaved form of the TSHR in transfected Chinese hamster ovary cells was able to bind Gsα protein, suggesting that cleavage of the native TSH receptor was associated with receptor.
NAMPT and BMAL1 Are Independently Involved in the Palmitate-Mediated Induction of Neuroinflammation in Hypothalamic Neurons

Obesity is a prominent metabolic disease that predisposes individuals to multiple comorbidities, including type 2 diabetes mellitus, cardiovascular diseases, and cancer. Elevated circulating levels of fatty acids contribute to the development of obesity, in part, by targeting the hypothalamus. Palmitate, the most abundant circulating saturated fatty acid, has been demonstrated to dysregulate NAMPT and circadian clock proteins, as well as induce neuroinflammation. These effects ultimately result in hypothalamic dysregulation of feeding behavior and energy homeostasis. NAMPT is the rate-limiting enzyme of the NAD+ salvage pathway and its expression is under the control of the circadian clock. NAD+ produced from NAMPT can modulate the circadian clock, demonstrating bidirectional interactions between circadian and metabolic pathways. Using NPY/AgRP-expressing mHypoE-46 neurons as well as the novel mHypoA-BMAL1-WT/F and mHypoA-BMAL1-KO/F cell lines, we studied whether there were any interactions between NAMPT and the core circadian clock protein BMAL1 in the palmitate-mediated induction of neuroinflammation. We report that palmitate altered Nampt, Bmal1, Per2 and the inflammatory genes Nf-κb, IκBα, Il-6, and Tlr4. Contrary to studies performed with peripheral tissues, the palmitate-mediated induction in Nampt was independent of BMAL1, and basal Nampt levels did not appear to exhibit rhythmic expression. Palmitate-induced downregulation of Bmal1 and Per2 was independent of NAMPT. However, NAMPT and BMAL1 were both involved in the regulation of Nf-κb, IκBα, Il-6, and Tlr4, as NAMPT inhibition resulted in the repression of basal Nf-κb and IκBα and normalized palmitate-mediated increases in Il-6, and Tlr4. On the other hand, BMAL1 deletion repressed basal Nf-κb, but increased basal Il-6. We conclude that NAMPT and BMAL1 do not interact at the transcriptional level in hypothalamic neurons, but are independently involved in the expression of inflammatory genes.
Comparing Deep-Sea Larval Dispersal Models: A Cautionary Tale for Ecology and Conservation

Larval dispersal data are increasingly sought after in ecology and marine conservation, the latter often requiring information under time limited circumstances. Basic estimates of dispersal [based on average current speeds and planktonic larval duration (PLD)] are often used in these situations, usually acknowledging their oversimplified nature, but rarely with an understanding of how oversimplified those assumptions are. Larval dispersal models (LDMs) are becoming more accessible and may produce “better” dispersal predictions than estimates, but the uncertainty introduced by choosing one underlying hydrodynamic model over another is rarely discussed. This case study uses theoretical and simplified deep-sea LDMs to compare the passive predictions of dispersal as driven by two different hydrodynamic models (HYCOM and POLCOMS) and a range of informed basic estimates (based on average current speeds of 0.05, 0.1, and 0.2 m/s). The aim is to provide generalizable insight into the predictive variability introduced by (a) choosing a model over an estimate, and (b) one hydrodynamic over another. LDMs were found to be up to an order of magnitude more conservative in dispersal distance predictions than even the slowest tested estimate (0.05 m/s). The difference increased with PLD which may result in a bigger disparity for deep-sea species predictions. Although the LDMs were more spatially targeted than the estimates, the two LDM predictions were also significantly different from each other. This means that choosing one hydrodynamic model over another could result in contrasting ecological interpretations or advice for marine conservation. These results show a greater potential for hydrodynamic model variability than previously appreciated by larval dispersal ecologists and strongly advocates groundtruthing predictions before use in management. Advice is offered for improved model selection and interpretation of predictions.
Things That Go Bump in the Literature: An Environmental Appraisal of “Haunted Houses”

This paper contains a narrative overview of the past 20-years of environmental research on anomalous experiences attributed to “haunted house. ” This exercise served as a much-needed update to an anthology of noteworthy overviews on ghosts, haunts, and poltergeists (Houran and Lange, 2001b). We also considered whether new studies had incorporated certain recommendations made in this anthology. Our search revealed a relative paucity of studies (n = 66) on environmental factors that ostensibly stimulate haunt-type experiences. This literature was diverse and often lacked methodological consistency and adherence to the prior suggestions. However, critical consideration of the content revealed a recurring focus on six ambient variables: embedded (static) cues, lighting levels, air quality, temperature, infrasound, and electromagnetic fields. Their relation to the onset or structure of witness reports showed mostly null, though sometimes inconsistent or weak outcomes. However, such research as related to haunts is arguably in its infancy and new designs are needed to account better for environmental and architectural phenomenology. Future studies should therefore address four areas: (i) more consistent and precise measurements of discrete ambient variables; (ii) the potential role of “Gestalt influences” that involve holistic environment-person interactions; (iii) individual differences in attentional or perceptual sensitivities of percipients to environmental variables; and (iv) the role of attitudinal and normative influences in the interpretation of environmental stimuli. Focused scrutiny on these issues should clarify the explanatory power of evolutionary-environmental models for these and related anomalous experiences.
Neural Mechanisms of Memory Enhancement and Impairment Induced by Visual Statistical Learning

Abstract Prior research has reported that the medial temporal, parietal, and frontal brain regions are associated with visual statistical learning (VSL). However, the neural mechanisms involved in both memory enhancement and impairment induced by VSL remain unknown. In this study, we examined this issue using event-related fMRI. fMRI data from the familiarization scan showed a difference in the activation level of the superior frontal gyrus (SFG) between structured triplets, where three objects appeared in the same order, and pseudorandom triplets. More importantly, the precentral gyrus and paracentral lobule responded more strongly to Old Turkic letters inserted into the structured triplets than to those inserted into the random triplets, at the end of the familiarization scan. Furthermore, fMRI data from the recognition memory test scan, where participants were asked to decide whether the objects or letters shown were old (presented during familiarization scan) or new, indicated that the middle frontal gyrus and SFG responded more strongly to objects from the structured triplets than to those from the random triplets, which overlapped with the brain regions associated with VSL. In contrast, the response of the lingual gyrus, superior temporal gyrus, and cuneus was weaker to letters inserted into the structured triplets than to those inserted into the random triplets, which did not overlap with the brain regions associated with observing the letters during the familiarization scan. These findings suggest that different brain regions are involved in memory enhancement and impairment induced by VSL.
Platelet and Plasma Phosphatidylcholines as Biomarkers to Diagnose Cerebral Amyloid Angiopathy

Alzheimer's disease is a severe neurodegenerative brain disorder and characterized by deposition of extracellular toxic β-amyloid (42) plaques and the formation of intracellular tau neurofibrillary tangles. In addition, β-amyloid peptide deposits are found in the walls of small to medium blood vessels termed cerebral amyloid angiopathy (CAA). However, the pathogenesis of CAA appears to differ from that of senile plaques in several aspects. The aim of the present study was to analyze different lipids [phosphatidylcholines (PCs) and lysoPCs] in platelets and plasma of a novel mouse model of sporadic CAA (1). Our data show that lipids are significantly altered in plasma of the CAA mice. Levels of eight diacyl PCs, two acyl-alkyl PCs, and five lysoPCs were significantly increased. In extracts of mouse blood platelets, four diacyl and two acyl-alkyl PCs (but not lysoPCs) were significantly altered. Our data show that lipids are changed in CAA with a specific pattern, and we provide for the first time evidence that selected platelet and plasma PCs may help to characterize CAA.
Antibacterial activity of leaf extracts of Gymnema sylvestre (R. Br.)

In vitro antibacterial studies were carried out with the aqueous extract of Gymnema sylvestre leaf powder (1:5) and gymnemagenin (1:10) on six human pathogenic bacterial strains using agar disc diffusion method at 50 µl, 150 µl and 200µl concentrations. Results revealed that the extracts showed good inhibitory activity against all the tested pathogens. Leaf powder extract was better in activity than gymnemagenin extract at the tested concentrations. The inhibitory activities were found to be dose dependent. The ranges of activity were in the order of Shigella dysenteriae (7.86, 10.20, 11.9 mm) >Klebsiella pneumoniae > Escherichia coli >Pseudomonas aeruginosa >Staphylococcus aureus > Proteus vulgaris for leaf powder extract and K. pneumoniae (5.00, 6.54, 11.54 mm) followed by Shi. dysenteriae, Pro. vulgaris, E. coli, Staph. aureus and Pseudo. aeruginosa for gymnemagenin extract. This study confirms significant antibacterial activity of G. sylvestre and the results suggest that G. sylvestre can be used as a potential antibacterial agent.