Miracle-dz/UniFAR-FTUs huggingface dataset:
Homogeneous vs. heterogeneous nucleation in water-dicarboxylic acid systems

Abstract. Binary heterogeneous nucleation of water-succinic/glutaric/malonic/adipic acid on nanometer-sized particles is investigated within the frame of classical heterogeneous nucleation theory. Homogeneous nucleation is also included for comparison. It is found that the nucleation probabilities depend on the contact angle and on the size of the seed particles. New thermodynamical properties, such as saturation vapor pressure, density and surface tension for all the dicarboxylic acid aqueous solutions are included in the calculations. While the new surface tension and density formulations do not bring any significant difference in the computed nucleation rate for homogeneous nucleation for succinic and glutaric acids, the use of the newly derived equations for the vapor pressure decrease the acid concentrations in gas phase by 3 orders of magnitude. According to our calculations, the binary heterogeneous nucleation of succinic acid-water and glutaric acid-water – although it requires a 3–4 orders of magnitude lower vapor concentrations than the homogeneous nucleation – cannot take place under atmospheric conditions. On the other hand binary homogeneous nucleation of adipic acid-water systems might be possible under conditions occuring in upper boundary layer. However, a more detailed characterization of the interaction between the surface and the molecules of the nucleating vapor should be considered in the future.
Altered synaptic marker abundance in the hippocampal stratum oriens of Ts65Dn mice is associated with exuberant expression of versican

DS (Down syndrome), resulting from trisomy of chromosome 21, is the most common cause of genetic mental retardation; however, the molecular mechanisms underlying the cognitive deficits are poorly understood. Growing data indicate that changes in abundance or type of CSPGs (chondroitin sulfate proteoglycans) in the ECM (extracellular matrix) can influence synaptic structure and plasticity. The purpose of this study was to identify changes in synaptic structure in the hippocampus in a model of DS, the Ts65Dn mouse, and to determine the relationship to proteoglycan abundance and/or cleavage and cognitive disability. We measured synaptic proteins by ELISA and changes in lectican expression and processing in the hippocampus of young and old Ts65Dn mice and LMCs (littermate controls). In young (5 months old) Ts65Dn hippocampal extracts, we found a significant increase in the postsynaptic protein PSD-95 (postsynaptic density 95) compared with LMCs. In aged (20 months old) Ts65Dn hippocampus, this increase was localized to hippocampal stratum oriens extracts compared with LMCs. Aged Ts65Dn mice exhibited impaired hippocampal-dependent spatial learning and memory in the RAWM (radial-arm water maze) and a marked increase in levels of the lectican versican V2 in stratum oriens that correlated with the number of errors made in the final RAWM block. Ts65Dn stratum oriens PNNs (perineuronal nets), an extension of the ECM enveloping mostly inhibitory interneurons, were dispersed over a larger area compared with LMC mice. Taken together, these data suggest a possible association with alterations in the ECM and inhibitory neurotransmission in the Ts65Dn hippocampus which could contribute to cognitive deficits.
Nanostructured Biomaterials for Regeneration

Biomaterials play a pivotal role in regenerative medicine, which aims to regenerate and replace lost/dysfunctional tissues or organs. Biomaterials (scaffolds) serve as temporary 3D substrates to guide neo tissue formation and organization. It is often beneficial for a scaffolding material to mimic the characteristics of extracellular matrix (ECM) at the nanometer scale and to induce certain natural developmental or/and wound healing processes for tissue regeneration applications. This article reviews the fabrication and modification technologies for nanofibrous, nanocomposite, and nanostructured drug‐delivering scaffolds. ECM‐mimicking nanostructured biomaterials have been shown to actively regulate cellular responses including attachment, proliferation, differentiation, and matrix deposition. Nanoscaled drug delivery systems can be successfully incorporated into a porous 3D scaffold to enhance the tissue regeneration capacity. In conclusion, nanostructured biomateials are a very exciting and rapidly expanding research area, and are providing new enabling technologies for regenerative medicine.
Energy-Efficient Power Allocation in Millimeter Wave Massive MIMO With Non-Orthogonal Multiple Access

In this letter, we investigate the energy efficiency (EE) problem in a millimeter wave massive MIMO system with non-orthogonal multiple access (NOMA). Multiple two-user clusters are formulated according to their channel correlation and gain difference. Following this, we propose a hybrid analog/digital precoding scheme for the low radio frequency chains structure at the base station. On this basis, we formulate a power allocation problem aiming to maximize the EE under users’ quality of service requirements and per-cluster power constraint. An iterative algorithm is proposed to obtain the optimal power allocation. Simulation results show that the proposed NOMA scheme achieves superior EE performance than conventional OMA scheme.
Mining Library Migration Graphs

Software systems intensively depend on external libraries, chosen at conception time. However, relevance of any library irremediably changes during projects and/or library life cycle. As a consequence, projects developers must periodically reconsider the libraries they depend on, and must think about library migration. When they want to migrate their libraries, they then have to identify candidate libraries that offer similar facilities and thus can substitute to each other. They also have to compare candidates to choose the one that best fits their needs. Finding a relevant library replacement is a well known tedious and time-consuming task. In this paper, we propose an approach that identifies sets of similar libraries and that produces what we call library migration graphs that show how existing projects have performed migrations among them. These graphs, constructed from the observation of a large number of software projects, ease the discovery and selection of library replacements.
SNIF-ACT: A Cognitive Model of User Navigation on the World Wide Web

ABSTRACT We describe the development of a computational cognitive model that explains navigation behavior on the World Wide Web. The model, called SNIF-ACT (Scent-based Navigation and Information Foraging in the ACT cognitive architecture), is motivated by Information Foraging Theory (IFT), which quantifies the perceived relevance of a Web link to a user's goal by a spreading activation mechanism. The model assumes that users evaluate links on a Web page sequentially and decide to click on a link or to go back to the previous page by a Bayesian satisficing model (BSM) that adaptively evaluates and selects actions based on a combination of previous and current assessments of the relevance of link texts to information goals. SNIF-ACT 1.0 utilizes the measure of utility, called information scent, derived from IFT to predict rankings of links on different Web pages. The model was tested against a detailed set of protocol data collected from 8 participants as they engaged in two information-seeking tasks using the World Wide Web. The model provided a good match to participants' link selections. In SNIF-ACT 2.0, we included the adaptive link selection mechanism from the BSM that sequentially evaluates links on a Web page. The mechanism allowed the model to dynamically build up the aspiration levels of actions in a satisficing process (e.g., to follow a link or leave a Web site) as it sequential assessed link texts on a Web page. The dynamic mechanism provides an integrated account of how and when users decide to click on a link or leave a page based on the sequential, ongoing experiences with the link context on current and previous Web pages. SNIF-ACT 2.0 was validated on a data set obtained from 74 subjects. Monte Carlo simulations of the model showed that SNIF-ACT 2.0 provided better fits to human data than SNIF-ACT 1.0 and a Position model that used position of links on a Web page to decide which link to select. We conclude that the combination of the IFT and the BSM provides a good description of user-Web interaction. Practical implications of the model are discussed.
Perspective training to treat anger problems after brain injury: Two case studies.

BACKGROUND People with acquired brain injury (ABI) often show increased anger and aggression. Anger has been linked to attributions of hostile intent. The more intentional and hostile the judgments of other's behaviours are, the angrier the responses tend to be. Some people with ABI tend to make harsher attributions than healthy controls (negative attribution bias). Poor perspective-taking may distort assessment of others' intentions, thereby contributing to this bias and subsequent anger responses. OBJECTIVE Examine changes in anger and perspective-taking after a Perspectives Group in two participants with ABI. METHODS This study is a case report exploring observational changes in anger, hostility, verbal and physical aggression and perspective-taking in two males with ABI and severe emotion dysregulation. Participants and their spouses also provided qualitative feedback through a semi-structured interview following perspectives training. The six-week "Perspectives Group" used hypothetical and real-life situations to teach participants to consider the perspectives of others when determining their intentions. RESULTS Both participants showed post-treatment declines in aggression. Although only minimal changes occurred on the perspective-taking measure, spouses described important behavioural changes in their partners that indicated both decreased aggression and better perspective taking. CONCLUSIONS These preliminary findings support further investigation of perspectives training for reducing anger after ABI.
A unique population of bone marrow cells migrates to skeletal muscle via hepatocyte growth factor/c-met axis

Cells expressing the CD45-associated hematopoietic marker are predominantly present in the mammalian bone marrow (BM), but have recently been shown to also reside in the skeletal muscle and potentially participate in muscle repair. Despite the consistent observations, the specific relationship and potential migration of CD45+ cells in the BM versus CD45+ cells residing in the muscle remain unclear, in addition to any understanding of the factors that may regulate the trafficking of CD45+-derived BM cells to skeletal muscle upon i.v. transplantation. Here, transplantation of BM-derived cells fully replaced the CD45+ fraction of skeletal muscle, but gave rise to progenitor cells with distinct hematopoietic lineage capacity from CD45+ cells residing in the BM. Using transwell migration assays, a subset of BM cells was shown to migrate exclusively to mature skeletal muscle cells and not BM-derived stromal cells. Unlike migration of BM cells to stroma, myofiber induced migration of BM-derived cells was not affected by stromal-derived factor-1 (SDF-1) neutralization or CXCR4-blocking antibody, but could be reduced by addition of c-met-blocking antibody and augmented by hepatocyte growth factor (HGF), the putative ligand for c-met. We suggest that the BM compartment consists of a functionally complex population of CD45+ progenitors that includes a subset of HGF/c-met responsive cells capable of migration to skeletal muscle. This previously unappreciated basis for cellular tracking now aids in defining regulatory networks that distinguish the stem cell niche of the BM versus skeletal muscle microenvironments.
Bcl-2 Undergoes Phosphorylation by c-Jun N-terminal Kinase/Stress-activated Protein Kinases in the Presence of the Constitutively Active GTP-binding Protein Rac1*

We have studied the phosphorylation of the Bcl-2 family of proteins by different mitogen-activated protein (MAP) kinases. Purified Bcl-2 was found to be phosphorylated by the c-Jun N-terminal kinase/stress-activated protein kinase (JNK/SAPK) p54-SAPKβ, and this is specific insofar as the extracellular signal-regulated kinase 1 (ERK1) and p38/RK/CSBP (p38) catalyzed only weak modification. Bcl-2 undergoes similar phosphorylation in COS-7 when coexpressed together with p54-SAPKβ and the constitutive Rac1 mutant G12V. This is seen by both 32PO4labeling and the appearance of five discrete Bcl-2 bands with reduced gel mobility. As anticipated, both intracellular p54-SAPKβ activation and Bcl-2 phosphorylation are blocked by co-transfection with the MAP kinase specific phosphatase MKP3/PYST1. MAP kinase specificity is also seen in COS-7 cells as Bcl-2 undergoes only weak phosphorylation when co-expressed with enzymatically activated ERK1 or p38. Four critical residues undergoing phosphorylation in COS-7 cells were identified by expression of the quadruple Bcl-2 point mutant T56A,S70A,T74A,S87A. Sequencing phosphopeptides derived from tryptic digests of Bcl-2 indicates that purified GST-p54-SAPKβ phosphorylates identical sitesin vitro. This is the first report of Bcl-2 phosphorylation by the JNK/SAPK class of MAP kinases and could indicate a key modification allowing control of Bcl-2 function by cell surface receptors, Rho family GTPases, and/or cellular stresses.
MOLECULAR SIGNATURES OF SELECTION ON REPRODUCTIVE CHARACTER DISPLACEMENT OF FLOWER COLOR IN PHLOX DRUMMONDII

Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower‐color variation in the native Texas wildflower Phlox drummondii. Here, we use population genetic analyses to investigate molecular signatures of selection on flower‐color variation in this species. First, we quantify patterns of neutral genetic variation across the range of P. drummondii to demonstrate that restricted gene flow and genetic drift cannot explain the pattern of flower‐color divergence in this species. There is evidence of extensive gene flow across populations with different flower colors, suggesting selection caused flower‐color divergence. Second, analysis of sequence variation in the genes underlying this divergence reveals a signature of a selective sweep in one of the two genes, further indicating selection is responsible for divergence in sympatry. The lack of a signature of selection at the second locus does not necessarily indicate a lack of selection on this locus but instead brings attention to the uncertainty in depending on molecular signatures to identify selection.
Tumor Spheroids as an In Vitro Model for Determining the Therapeutic Response to Proton Beam Radiotherapy and Thermally Sensitive Nanocarriers

Multicellular Tumor Spheroids (MCTS) strongly resemble tumor tissues, which makes them useful tools for radiation biology studies and screening of various chemotherapeutics. The goal of this pilot study was to use MCTS as an in vitro model to determine the response of cells to low temperature-sensitive liposomes (LTSLs) encapsulating doxorubicin (Dox) and proton beam radiotherapy (PBRT). Prior to treatment, MCTS were characterized for morphology and LTSLs were characterized for size, encapsulation efficiency, and ability to thermally release Dox (a model anticancer agent). Two groups of MCTS were treated with LTSL in combination with mild hyperthermia (40-42 °C) or PBRT alone in the presence of appropriate controls. Cytotoxic response was assessed after 48-72 h using an acid phosphatase assay. At 72 h, LTSL in combination with heat significantly reduced the viability of MCTS (15-30%) compared to the control (P < 0.05). A similar cytotoxic response was observed with PBRT treatment. The data suggest that like a monolayer cell culture, MCTS can be used to determine cytotoxic outcomes of thermal and proton therapy.
Disruption of the principal, progesterone-activated sperm Ca2+ channel in a CatSper2-deficient infertile patient

The female steroid hormone progesterone regulates ovulation and supports pregnancy, but also controls human sperm function within the female reproductive tract. Progesterone causes elevation of sperm intracellular Ca2+ leading to sperm hyperactivation, acrosome reaction, and perhaps chemotaxis toward the egg. Although it has been suggested that progesterone-dependent Ca2+ influx into human spermatozoa is primarily mediated by cationic channel of sperm (CatSper), the principal flagellar Ca2+ channel of sperm, conclusive loss-of-function genetic evidence for activation of CatSper by progesterone has yet to be provided. Moreover, it is not clear whether the responsiveness of CatSper to progesterone is an innate property of human spermatozoa or is acquired as the result of exposure to the seminal plasma. Here, by recording ionic currents from spermatozoa of an infertile CatSper-deficient patient, we demonstrate that CatSper is indeed the principal Ca2+ channel of human spermatozoa, and that it is strongly potentiated by progesterone. In addition, by recording CatSper currents from human epididymal and testicular spermatozoa, we show that CatSper sensitivity to progesterone arises early in sperm development and increases gradually to a peak when spermatozoa are ejaculated. These results unambiguously establish an important role of CatSper channel in human sperm nongenomic progesterone signaling and demonstrate that the molecular mechanism responsible for activation of CatSper by progesterone arises early in sperm development concurrently with the CatSper channel itself.
Imaginary interfaces: touchscreen-like interaction without the screen

Screenless mobile devices achieve maximum mobility, but at the expense of the visual feedback that is generally assumed to be necessary for spatial interaction. With Imaginary Interfaces we re-enable spatial interaction on screenless devices. Users point and draw in the empty space in front of them or on the palm of their hands. While they cannot see the results of their interaction, they do obtain some visual feedback by watching their hands move. Our user studies show that Imaginary Interfaces allow users to create simple drawings, to annotate with them and to operate interfaces, as long as their layout mimics a physical device they have used before. We demonstrate how this allows an imaginary interface to serve as a shortcut for a physical device and we believe that ultimately Imaginary Interfaces will lead to the development of standalone ultra-mobile devices.
Platelet ultrastructural abnormalities in three patients with type 2B von Willebrand disease

Several reports have described the presence of giant platelets in patients with type 2B von Willebrand disease (VWD). We have now characterized the ultrastructural changes in platelets from three unrelated patients with type 2B VWD and different mutations within exon 28 of the von Willebrand factor (VWF) gene. Electron microscopy showed that each of these subjects had an increased proportion of large platelets when compared with those of a patient with type 2A VWD or control subjects. Immunogold labelling for VWF was performed. Large masses detected by anti‐VWF antibody were seen not only on the platelet surface, but also inside the platelet surface‐connected canalicular system (SCCS) when ultrathin sections were labelled. This suggested translocation of the abnormally bound VWF from the platelet surface. Labelling of the α‐granules was eccentric as for normal platelets. Labelling for glycoprotein (GP) Ib was seen on the surface and within the SCCS, suggesting co‐localization with the bound VWF. However, there was no evidence for VWF in endosomes or other endocytic vesicles. The presence of platelet‐bound VWF was not accompanied by high levels of platelet activation, as detected by electron microscopy, or by using monoclonal antibodies against P‐selectin or activation‐dependent determinants on GP IIb‐IIIa in flow cytometry. Intriguingly, platelet ultrastructure often resembled that seen in patients with congenital thrombocytopathies characteristic of giant platelet syndromes.
Clinical and genomic responses to ultra-short course chemotherapy in spinal tuberculosis

Traditional treatments for spinal tuberculosis (TB) involve chemotherapy and surgery. In the present study, it has been identified that chemotherapy lasting <6 months [ultra-short course chemotherapy (UCCT)], rather than the 6–18 months of the traditional regimen, is effective in sustaining TB clearance following complete surgical debridement. This current study aims to compare the changes in peripheral blood gene expression prior to and following UCCT, subsequent to complete debridement of spinal TB lesions. The study includes 5 patients without TB and 27 patients with spinal, divided into three groups: Group 1 (untreated group, n=8); group 2 (UCCT treatment group, n=9); and group 3 (UCCT treatment 1 year follow-up group, n=10). Gene changes were detected using DNA microarray analysis, confirmed through reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and the results were examined using the DAVID Knowledgebase to identify the pathways and functions of differentially expressed genes. TB lesions were active in group 1, while groups 2 and 3 showed no signs of active TB, as indicated by clinical manifestations and imaging. Comparison of the transcription profiles of the control and study groups showed that treatment of spinal TB resulted in upregulation of genes that are associated with immune response pathways; RT-qPCR produced similar findings. In conclusion, these results indicate that UCCT is an effective treatment against TB following complete surgical debridement. Furthermore, DNA microarray analysis proved a useful tool to evaluate the effects of spinal TB treatment on the expression of genes associated with immune response pathways.
SARS-CoV heptad repeat 2 is a trimer of parallel helices

In severe acute respiratory syndrome coronavirus, the envelope heptad repeat 2 (HR2) plays a critical role in viral entry. Moreover, HR2 is both the target for novel antiviral therapies and, as an isolated peptide, presents a potential antiviral therapeutic. The structure of HR2, as determined by NMR spectroscopy in the presence of the co‐solvent trifluoroethanol (TFE), is a trimer of parallel helices, whereas the structure of HR2, as determined by X‐ray crystallography, is a tetramer of anti‐parallel helices. In this work, we added a nitroxide spin label to the N‐terminal region of HR2 and used paramagnetic relaxation enhancement to assess the orientation of the HR2 helices under different solution conditions. We find that the relaxation effects are consistent with an orientation corresponding to a trimer of parallel helices in both the presence and absence of TFE. This work suggests that the different orientation and oligomerization states observed by NMR and X‐ray are due to the 11 additional residues present at the N‐terminus of the NMR construct.
Determination of Pentapeptide Repeat Units in Qnr Proteins by the Structure-Based Alignment Approach

ABSTRACT The Qnr proteins belong to the pentapeptide repeat protein family. Despite each pentapeptide repeat unit being an important structural determinant, accurately determining pentapeptide repeat units in the Qnr proteins through sequence-based alignments has been challenging. In the present study, the pentapeptide repeat units of the nine representative Qnr proteins have been precisely determined via the structure-based alignment approach using homology modeling and superposition of their best models.