Miracle-dz/UniFAR-FTUs huggingface dataset:
Human brain trauma severity is associated with lectin complement pathway activation

We explored the involvement of the lectin pathway of complement in post-traumatic brain injury (TBI) pathophysiology in humans. Brain samples were obtained from 28 patients who had undergone therapeutic contusion removal, within 12 h (early) or from >12 h until five days (late) from injury, and from five non-TBI patients. Imaging analysis indicated that lectin pathway initiator molecules (MBL, ficolin-1, ficolin-2 and ficolin-3), the key enzymes MASP-2 and MASP-3, and the downstream complement components (C3 fragments and TCC) were present inside and outside brain vessels in all contusions. Only ficolin-1 was found in the parenchyma of non-TBI tissues. Immunoassays in brain homogenates showed that MBL, ficolin-2 and ficolin-3 increased in TBI compared to non-TBI (2.0, 2.2 and 6.0-times) samples. MASP-2 increased with subarachnoid hemorrhage and abnormal pupil reactivity, two indicators of structural and functional damage. C3 fragments and TCC increased, respectively, by 3.5 - and 4.0-fold in TBI compared to non-TBI tissue and significantly correlated with MBL, ficolin-2, ficolin-3, MASP-2 and MASP-3 levels in the homogenates. In conclusion, we show for the first time the direct presence of lectin pathway components in human cerebral contusions and their association with injury severity, suggesting a central role for the lectin pathway in the post-traumatic pathophysiology of human TBI.
Updating Dynamic Random Hyperbolic Graphs in Sublinear Time

Generative network models play an important role in algorithm development, scaling studies, network analysis, and realistic system benchmarks for graph data sets. A complex network model gaining considerable popularity builds random hyperbolic graphs, generated by distributing points within a disk in the hyperbolic plane and then adding edges between points with a probability depending on their hyperbolic distance. We present a dynamic extension to model gradual network change, while preserving at each step the point position probabilities. To process the dynamic changes efficiently, we formalize the concept of a probabilistic neighborhood: Let P be a set of n points in Euclidean or hyperbolic space, q a query point, dist a distance metric, and f : R+ → [0, 1] a monotonically decreasing function. Then, the probabilistic neighborhood N(q, f) of q with respect to f is a random subset of P and each point p ∈ P belongs to N(q, f) with probability f(dist(p, q)). We present a fast, sublinear-time query algorithm to sample probabilistic neighborhoods from planar point sets. For certain distributions of planar P, we prove that our algorithm answers a query in O((|N(q, f)| + √n) log n) time with high probability. This enables us to process a node movement in random hyperbolic graphs in sublinear time, resulting in a speedup of about one order of magnitude in practice compared to the fastest previous approach. Apart from that, our query algorithm is also applicable to Euclidean geometry, making it of independent interest for other sampling or probabilistic spreading scenarios.
Propagation of combustion waves in the shell–core energetic materials with external heat losses

In this paper, the properties and stability of combustion waves propagating in the composite solid energetic material of the shell–core type are numerically investigated within the one-dimensional diffusive-thermal model with heat losses to the surroundings. The flame speed is calculated as a function of the parameters of the model. The boundaries of stability are determined in the space of parameters by solving the linear stability problem and direct integration of the governing non-stationary equations. The results are compared with the characteristics of the combustion waves in pure solid fuel. It is demonstrated that a stable travelling combustion wave solution can exist for the parameters of the model for which the flame front propagation is unstable in pure solid fuel and it can propagate several times faster even in the presence of significant heat losses.
D2.4 Report on the final prototype of programming abstractions for energy-efficient inter-process communication

Work package 2 (WP2) aims to develop libraries for energy-efficient inter-process communication and data sharing on the EXCESS platforms. The Deliverable D2.4 reports on the final prototype of programming abstractions for energy-efficient inter- process communication. Section 1 is the updated overview of the prototype of programming abstraction and devised power/energy models. The Section 2-6 contain the latest results of the four studies: i) GreenBST, a energy-efficient and concurrent search tree (cf. Section 2) ii) Customization methodology for implementation of streaming aggregation in embedded systems (cf. Section 3) iii) Energy Model on CPU for Lock-free Data-structures in Dynamic Environments (cf. Section 4.10) iv) A General and Validated Energy Complexity Model for Multithreaded Algorithms (cf. Section 5)
Assessing the influence of time-since-death: Pilot scale kraft and thermomechanical pulping of beetle-killed lodgepole pine

Pilot plant kraft and mechanical pulping trials were carried out for a well controlled sample set to determine the influence of TSD of mountain pine beetle (MPB)-killed lodgepole pine on pulping and pulp quality. Samples included trees of red, grey and late grey attack stages as well as unattacked trees and sample sites were established in three different biogeoclimatic subzones in British Columbia, thus accounting for natural variability. Prior to pulping, samples were tested for wood and fibre properties as well as chip quality. Kraft and thermomechanical (TMP) pulping parameters were monitored, pulp quality was determined, and sheet structure was evaluated by scanning electron microscopy. Wood and fibre quality showed little measurable influence from TSD other than a significant drop in moisture. Kraft pulping and pulp quality was also independent of TSD, although some influence on kink index was seen which could suggest a greater susceptibility to mechanical damage for fibres from MPB-killed wood. For TMP pulp, MPB-killed wood showed lower sheet density and possibly higher sheet roughness when compared to unattacked wood. Preliminary calendering and linting tests also resulted in some differences, suggesting that runnability and printing quality of TMP paper may be affected. The results of this study suggest that MPB-killed wood is an acceptable source of fibre for kraft pulping even at grey and late grey stages. However there are operational issues, including impacts on chemical recovery, that are being addressed in other projects. For TMP, such wood can be used with little penalty regarding pulping and strength parameters, however some effect on sheet structure and surface structure may exist which would be important in the printing paper sector. Thus, TMP results should be followed up with a more detailed study of printing behaviour of MPB-killed wood.
A model for characterising the collective dynamic behaviour of evolutionary algorithms

Exploration and exploitation are considered essential notions in evolutionary algorithms. However, a precise interpretation of what constitutes exploration or exploitation is clearly lacking and so are specific measures for characterising such notions. In this paper, we start addressing this issue by presenting new measures that can be used as indicators of the exploitation behaviour of an algorithm. These work by characterising the extent to which available information guides the search. More precisely, they quantify the dependency of a population's activity on the observed fitness values and genetic material, utilising an empirical model that uses a coarse-grained representation of population dynamics and records information about it. The model uses the k-means clustering algorithm to identify the population's "basins of activity". The exploitation behaviour is then captured by an entropy-based measure based on the model that quantifies the strength of the association between a population's activity distribution and the observed fitness landscape information. In experiments, we analysed the effects of the search operators and their parameter settings on the collective dynamic behaviour of populations. We also analysed the effect of using different problems on algorithm behaviours.We define a behavioural landscape for each problem to identify the appropriate behaviour to achieve good results and point out possible applications for the proposed model.
Proposal for Protocol on a Quorum Blockchain with Zero Knowledge

In this paper, we present an implementation scheme of an RTGS1 on Quorum using the Solidity language. It is heavily inspired by the Schnorr signature protocol to verify the identity of the participants. We have implemented a distributed ledger solution for Delivery vs Payment that promises to offer increased efficiency and resilience. Our architecture mimics current market structure. For such needs, we added an extra layer of security that allows our solution to comply with the requirements of the regulator while enabling competitive actors to collaborate using the shared registry. It also leaves room for regulation, while still running in a decentralised way with coordinating agents. We use non-interactive zero-knowledge algorithms, which are cryptographic protocols with numerous applications in the fields of cryptocurrencies. They allow an agent to verify that another agent holds a specific information, while the latter never discloses this information. For the sake of our experimentations, we had to use very small integers in our protocols. These integers are too small to comply with current security standards in finance, although the architectural principles can be easily transposed with better performing protocols. We present suggestions to improve our proof of concept and our architecture in the last part.
Ethanol Consumption in Mice Lacking CD14, TLR2, TLR4, or MyD88

BACKGROUND Molecular and behavioral studies support a role for innate immune proinflammatory pathways in mediating the effects of alcohol. Increased levels of Toll-like receptors (TLRs) have been observed in animal models of alcohol consumption and in human alcoholics, and many of these TLRs signal via the MyD88-dependent pathway. We hypothesized that this pathway is involved in alcohol drinking and examined some of its key signaling components. METHODS Different ethanol (EtOH)-drinking paradigms were studied in male and female control C57BL/6J mice versus mice lacking CD14, TLR2, TLR4 (C57BL/10ScN), or MyD88. We studied continuous and intermittent access 2-bottle choice (2BC) and 1-bottle and 2BC drinking-in-the-dark (DID) tests as well as preference for saccharin, quinine, and NaCl. RESULTS In the 2BC continuous access test, EtOH intake decreased in male TLR2 knockout (KO) mice, and we previously reported reduced 2BC drinking in male and female CD14 KO mice. In the intermittent access 2BC test, EtOH intake decreased in CD14 KO male and female mice, whereas drinking increased in MyD88 KO male mice. In the 2BC-DID test, EtOH drinking decreased in male and female mice lacking TLR2, whereas drinking increased in MyD88 KO male mice. In the 1-bottle DID test, EtOH intake decreased in female TLR2 KO mice. TLR2 KO and CD14 KO mice did not differ in saccharin preference but showed reduced preference for NaCl. MyD88 KO mice showed a slight reduction in preference for saccharin. CONCLUSIONS Deletion of key components of the MyD88-dependent pathway produced differential effects on EtOH intake by decreasing (TLR2 KO and CD14 KO) or increasing (MyD88 KO) drinking, while deletion of TLR4 had no effect. Some of the drinking effects depended on the sex of the mice and/or the EtOH-drinking model.
Photovoltaic properties and size-pH phase stability of iron disulfide from density-functional theory

Despite its exceptional optical absorptivity, suitable band gap, and earth abundance, the low open-circuit voltage of pyrite FeS₂ has remained the biggest challenge preventing its use in photovoltaic devices. Two widely-accepted causes are: (i) Fermi level pinning caused by intrinsic surface states that appear as gap states; (ii) presence of the polymorph marcasite. Based on density-functional theory (DFT) calculations, (i) the intrinsic (100) surface states are not gap states but located at the conduction band edge; (ii) epitaxial growth of marcasite on pyrite is thermodynamically favorable, but its band gap (from Kohn-Sham [delta]-sol method) is not less than pyrite. It is unlikely that the photovoltaic performance of pyrite is undermined by intrinsic surface states or marcasite. The stoichiometry and the ubiquitous observation of unintentional p-type conductivity of pyrite thin films are investigated via DFT defect computations. Native defects occur in low concentrations due to high formation energies, implying that pyrite is intrinsically stoichiometric. The p-type conductivity can be caused by OS defects under oxidizing conditions. Band gap engineering of pyrite is studied by alloying with non-rare-earth isovalent elements via DFT computations. We identify six MS₂ candidates that have larger band gaps than pyrite. Band gap enhancement of pyrite is observed only in the Ru and Os alloyed systems, but their incorporation into pyrite may be severely limited. All other candidate alloys exhibit large gap bowing effects due to size and/or electronegativity mismatch. The effects of particle size and pH on the relative phase stability of pyrite and marcasite polymorphs are explored. The size effect is incorporated through volume scaling of Wulff shapes. The pH effect is modeled by generalized, charged surface energies as a result of ion adsorption from the aqueous environment. Based on joint density-functional theory calculations, pyrite is unstable in highly acidic conditions due to a negative H+-adsorbed (110) surface energy, but stabilized for pH >/~ 2. Directions for future work are briefly discussed.
Effective cytotoxic activity of OSW-1 on colon cancer by inducing apoptosis in vitro and in vivo.

As a natural compound, Ornithogalum caudatum Ait is primarily used as an anti-inflammatory and antitumor agent in Chinese folk medicine. In 1992, OSW-1 was isolated from this compound, which is a new member of cholestane saponin family. In numerous recent studies, OSW-1 has been shown to have powerful cytotoxic anticancer effects against various malignant cells. However, the therapeutic efficacy of OSW-1 on colon cancer and the underlying mechanism are not understood. To explore the mechanism underlying OSW-1 in antitumor therapy, a therapeutic function analysis of OSW-1 on colon cancer was performed in vitro and in vivo. It was shown that with low toxicity on normal colonic cells, OSW-1 suppresses colon cancer cells in vitro and this inhibition was via the intrinsic apoptotic pathway, which increased cellular calcium, changed mitochondrial membrane potential, disrupted mitochondrial morphology, and led to the release of cytochrome c and the activation of caspase-3. Furthermore, in a nude mouse model, OSW-1 had a powerful effect on suppressing colon tumor proliferation without significant side effects through the apoptosis pathway. Taken together, these results demonstrate that OSW-1 is a potential drug for colon cancer treatment.
Estrogen‐dependent control and cell‐to‐cell variability of transcriptional bursting

Cellular decision‐making and environmental adaptation are dependent upon a heterogeneous response of gene expression to external cues. Heterogeneity arises in transcription from random switching between transcriptionally active and inactive states, resulting in bursts of RNA synthesis. Furthermore, the cellular state influences the competency of transcription, thereby globally affecting gene expression in a cell‐specific manner. We determined how external stimuli interplay with cellular state to modulate the kinetics of bursting. To this end, single‐cell dynamics of nascent transcripts were monitored at the endogenous estrogen‐responsive GREB1 locus. Stochastic modeling of gene expression implicated a two‐state promoter model in which the estrogen stimulus modulates the frequency of transcriptional bursting. The cellular state affects transcriptional dynamics by altering initiation and elongation kinetics and acts globally, as GREB1 alleles in the same cell correlate in their transcriptional output. Our results suggest that cellular state strongly affects the first step of the central dogma of gene expression, to promote heterogeneity in the transcriptional output of isogenic cells.
Multi-species Identification of Polymorphic Peptide Variants via Propagation in Spectral Networks

Peptide and protein identification remains challenging in organisms with poorly annotated or rapidly evolving genomes, as are commonly encountered in environmental or biofuels research. Such limitations render tandem mass spectrometry (MS/MS) database search algorithms ineffective as they lack corresponding sequences required for peptide-spectrum matching. We address this challenge with the spectral networks approach to (1) match spectra of orthologous peptides across multiple related species and then (2) propagate peptide annotations from identified to unidentified spectra. We here present algorithms to assess the statistical significance of spectral alignments (Align-GF), reduce the impurity in spectral networks, and accurately estimate the error rate in propagated identifications. Analyzing three related Cyanothece species, a model organism for biohydrogen production, spectral networks identified peptides from highly divergent sequences from networks with dozens of variant peptides, including thousands of peptides in species lacking a sequenced genome. Our analysis further detected the presence of many novel putative peptides even in genomically characterized species, thus suggesting the possibility of gaps in our understanding of their proteomic and genomic expression. A web-based pipeline for spectral networks analysis is available at http://proteomics.ucsd. edu/software.
Association between PD-L1 expression and driver gene status in non-small-cell lung cancer: a meta-analysis

Objective To assess the association between PD-L1 expression and driver gene mutations in patients with non-small-cell lung cancer (NSCLC). Method We performed a meta-analysis of 26 studies (7541 patients) which were published from 2015 to 2017. Pooled odds ratios (ORs) with 95% confidence intervals (CI) were calculated to describe the correlation. Subgroup analysis was performed based on population characteristics, types of PD-L1 antibodies and quality of individual studies. Results A lower frequency of PD-L1 positivity was observed in NSCLCs harboring EGFR mutation (OR: 0.64, 95% CI, 0.45–0.91, p = 0.014). A negative correlation was also found at 1% (OR: 0.35, 95% CI, 0.22–0.55, p = 0.000) and 50% (OR: 0.33, 95% CI, 0.14–0.81, p = 0.015) cutoff for PD-L1 positive, elderly age group (OR: 0.56, 95% CI, 0.35–0.89, p = 0.013), female dominant group (OR: 0.55, 95% CI, 0.29–0.94, p = 0.030) and smoker dominant group (OR: 0.52, 95% CI, 0.29–0.96, p = 0.035). No significant differences in PD-L1 expression were observed among patients with different ALK, BRAF, HER2, PIK3CA status and MET expression level. Higher level of PD-L1 was found in tumors with KRAS mutation (OR: 1.45, 95% CI, 1.18–1.80, p = 0.001). PD-L1 expression level was not significantly different between triple (EGFR/ALK/KRAS) wild type NSCLCs and those with EGFR/ALK/KRAS mutation. Conclusions PD-L1 expression in EGFR mutated NSCLCs were lower than those in EGFR wild type NSCLCs, while tumors with KRAS mutation showed higher levels of PD-L1.
Prostate Cancer Molecular Imaging Standardized Evaluation (PROMISE): Proposed miTNM Classification for the Interpretation of PSMA-Ligand PET/CT

Prostate-specific membrane antigen (PSMA)–ligand PET imaging provides unprecedented accuracy for whole-body staging of prostate cancer. As PSMA-ligand PET/CT is increasingly adopted in clinical trials and routine practice worldwide, a unified language for image reporting is urgently needed. We propose a molecular imaging TNM system (miTNM, version 1.0) as a standardized reporting framework for PSMA-ligand PET/CT or PET/MRI. miTNM is designed to organize findings in comprehensible categories to promote the exchange of information among physicians and institutions. Additionally, flowcharts integrating findings of PSMA-ligand PET and morphologic imaging have been designed to guide image interpretation. Specific applications, such as assessment of prognosis or impact on management, should be evaluated in future trials. miTNM is a living framework that evolves with clinical experience and scientific data.
Anticonvulsant activity of the antidepressant drug, tianeptine, against pentylenetetrazole-induced seizures mitigates cognitive impairment in rats

Treatment of depression, a common comorbidity in patients with epilepsy, is restricted as certain antidepressants are considered to be proconvulsants. In contrast, anticonvulsant effects have been reported with some antidepressants. In the present study, the effect of tianeptine, an antidepressant, was evaluated against pentylenetetrazole (PTZ)-induced seizures, cognitive impairment and oxidative stress in rats. Tianeptine was administered in three doses (20, 40 and 80 mg/kg) 30 min before PTZ (60 mg/kg, intraperitoneally). MK801, an N-methyl-D-aspartate antagonist, and naloxone, an opioid receptor antagonist, were administered with tianeptine to evaluate the involvement of N-methyl-D-aspartate and opioid receptors, respectively. Morris water maze, elevated plus maze and passive avoidance tests were performed for behavioural assessment. Brain malondialdehyde and reduced glutathione levels were estimated as markers of oxidative stress. Tianeptine showed dose-dependent protection against PTZ seizures. Coadministration of tianeptine with MK801 potentiated the anticonvulsant effect of tianeptine. The protective effect of tianeptine against PTZ seizures was mitigated when tianeptine was administered with naloxone. Impairment of learning and memory by PTZ was prevented by tianeptine. Tianeptine also attenuated the seizure-induced increased oxidative stress. Thus, tianeptine showed an anticonvulsant effect along with amelioration of seizure-induced cognitive impairment and oxidative stress. Hence, tianeptine could be a useful drug in epileptic patients with depression, with the advantage of having both antidepressant and antiepileptic effects.
Decomposition of leg movements during overground walking in individuals with traumatic brain injury

ABSTRACT Objective: Walking requires precise coordination of bilateral lower extremity motions at all joints. This ability can be affected by traumatic brain injury (TBI). The study investigated inter-joint coordination of lower extremities during overground walking after TBI. Methods: Ten individuals with post-injury ataxia, postural stability and gait abnormalities, as well as 10 sex- and age-matched control subjects were involved in the study. Participants walked at self-selected speed in three experimental conditions: normal walking without any additional task; walking with a narrow base of support, and walking while holding a cup full of water. Inter-joint coordination was analysed as the percentage of gait cycle during which the leg movement was decomposed with 0% indicating simultaneous motion of the two joints (i.e. hip-knee, knee-ankle, and hip-ankle) through the entire gait cycle or 100% indicating motion of only one joint. Decomposition was calculated for each pair of joints and for the left and right leg separately. Results: Participants with TBI showed greater decomposition indices and poorer inter-joint coordination respectively than control individuals for all joint pairs (p < 0.01). Walking with the narrower base of support or with a cup, increased movement decomposition in the TBI group, but not in the control group. Conclusion: The results revealed post-injury gait impairment that manifests as decomposition of multi-joint motions of the lower extremities during overground walking.