Miracle-dz/UniFAR-FTUs huggingface dataset:
PAX5 interacts with RIP2 to promote NF-κB activation and drug-resistance in B-lymphoproliferative disorders

ABSTRACT Paired box protein 5 (PAX5) plays a lineage determination role in B-cell development. However, high expression of PAX5 has been also found in various malignant diseases, including B-lymphoproliferative disorders (B-LPDs), but its functions and mechanisms in these diseases are still unclear. Here, we show that PAX5 induces drug resistance through association and activation of receptor-interacting serine/threonine-protein kinase 2 (RIP2; also known as RIPK2), and subsequent activation of NF-κB signaling and anti-apoptosis gene expression in B-lymphoproliferative cells. Furthermore, PAX5 is able to interact with RIP1 and RIP3, modulating both RIP1-mediated TNFR and RIP2-mediated NOD1 and NOD2 pathways. Our findings describe a new function of PAX5 in regulating RIP1 and RIP2 activation, which is at least involved in chemotherapeutic drug resistance in B-LPDs. Summary: PAX5 enhances RIP1- and RIP2-mediated NF-κB activation through protein interactions, indicating a new role for PAX5 in regulating cell signaling.
Cyanobacteria and BMAA exposure from desert dust: A possible link to sporadic ALS among Gulf War veterans

Abstract Veterans of the 1990–1991 Gulf War have been reported to have an increased incidence of amyotrophic lateral sclerosis (ALS) compared to personnel who were not deployed. An excess of ALS cases was diagnosed in Gulf War veterans younger than 45 years of age. Increased ALS among Gulf War veterans appears to be an outbreak time-limited to the decade following the Gulf War. Seeking to identify biologically plausible environmental exposures, we have focused on inhalation of cyanobacteria and cyanotoxins carried by dust in the Gulf region, particularly Qatar. Cyanobacterial crusts and mats are widespread in the deserts of Qatar, occupying up to 56% of the available area in some microhabitats. These cyanobacterial crusts, which help bind the desert sands, are dormant throughout most of the year, but during brief spring rains actively photosynthesize. When disturbed by vehicular traffic or other military activities, the dried crusts and mats can produce significant dust. Using HPLC/FD, an amino acid analyzer, UPLC/MS, and triple quadrupole LC/MS/MS we find that the dried crusts and mats contain neurotoxic cyanobacterial toxins, including β-N-methylamino-L-alanine (BMAA) and 2,4 diaminobutyric acid (DAB). If dust containing cyanobacteria is inhaled, significant exposure to BMAA and other cyanotoxins may occur. We suggest that inhalation of BMAA, DAB, and other aerosolized cyanotoxins may constitute a significant risk factor for the development of ALS and other neurodegenerative diseases.
Robotic Friction Stir Welding of AA5754 Aluminum Alloy Sheets at Different Initial Temper States

Robotic friction stir welding experiments were performed on AA5754 aluminium alloy sheets, 2.5 mm in thickness, in two different temper states (H111 and O-annealed). A six axes robot with a hybrid structure, characterised by an arm with parallel kinematics and a roll-pitch-roll wrist with serial kinematics, was used. The effect of the process parameters on the macro-and micro-mechanical properties and microstructure of joints was widely analysed. It was shown that, under the same process condition, the mechanical properties of the joints are strongly influenced by the initial temper state of the alloy. In particular, as AA5754-H111 is welded, the ultimate tensile strength is not significantly affected by the process parameters whilst the ultimate elongation significantly depends on the welding speed. In AA5754-O, both ultimate values of tensile strength and elongation are affected by the welding speed whilst a negligible effect of the rotational speed can be observed. Irrespective of the welding parameters, the H111 temper state leads to mechanical properties higher than those given by the O-annealed state. An investigation has been also carried out in order to evaluate the micro-hardness profiles and microstructure of the FSWed joints in order to understand the mechanisms operating during robotic friction stir welding.
The Textility of Emotion: A Study Relating Computational Textile Textural Expression to Emotion

Computational textiles are textiles that respond to computer programming commands through embedded electronics. The purpose of this study is to determine what still and shape-changing, textural expressions of computational textiles can communicate emotionally to people. The central hypothesis is that for both kinds of textiles, there will be differences depending on whether the study participants experience the textiles via vision alone or via both vision and touch. If designers could begin to understand the nature of what various textile expressions communicated, and what computational textiles communicated in transformation then it would be possible to more clearly understand the role that texture of a computational textile plays in communicating emotion through a computational object.
The Huygens-Hellas giant dike system on Mars: Implications for Late Noachian–Early Hesperian volcanic resurfacing and climatic evolution

Two narrow, broadly arcuate, low ridges extend for 600–700 km in western Terra Tyrrhena, Mars, crosscut ancient Noachian terrain, and are associated with Early Hesperian plains, which cover ∼30% of Mars. Geological relationships suggest that the ridges represent near-surface erosional remnants of subsurface dikes, solidified magma-filled cracks that were responsible for the volcanic emplacement of the plains. Ridge width and geometry are consistent with very high-effusion-rate flood basalt eruptions, emplacement events that would form smooth featureless plains and input significant volcanic gas into the atmosphere. Geological relationships suggest that the ridges were exposed by erosion (fluvial, sublimation, eolian) and partial removal of a regional volatile-rich dust layer.
Comparison of Accumulation, Subcellular Location, and Sonodynamic Cytotoxicity between Hematoporphyrin and Protoporphyrin IX in L1210 Cells

Background: Sonodynamic therapy (SDT) is a promising modality for cancer treatment which requires the synergistic effect of ultrasound and tumor-localized sonosensitizers. Sonodynamic efficacy can be improved through a better understanding of the accumulation and subcellular location of sonosensitizers. Here, a comparison of the accumulation, sublocation, and sonodynamic effect of hematoporphyrin (Hp) and protoporphyrin IX (PpIX) was studied in L1210 cells. Methods: The kinetics of intracellular Hp and PpIX accumulation were detected using a fluorescence spectrophotometer. The subcellular distributions of Hp and PpIX were monitored by laser scanning confocal microscopy. The cytotoxic effects of Hp-mediated SDT (Hp-SDT) and PpIX-mediated SDT (PpIX-SDT) were evaluated by MTT assay. Results: The accumulation of Hp and PpIX presented different kinetic changes depending on the time, and was also concentration- and temperature-dependent. The intracellular PpIX content was much higher than that of Hp under the same conditions; however, there were no obvious differences in terms of their subcellular locations, and both of them mainly accumulated on the mitochondria and the plasma membrane in L1210 cells. PpIX exhibited more potential cytotoxicity than did Hp when they were irradiated with ultrasound under the same experimental conditions. Conclusion: Our results indicate that there were significant differences regarding the intracellular accumulation features between Hp and PpIX. PpIX-SDT produced a more serious cytotoxic effect than did Hp-SDT, which may be due to the higher PpIX uptake in L1210 cells compared to that of Hp at the same concentrations. Additionally, the absorption of Hp and PpIX in L1210 cells might be energy dependent.
IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms

As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as “isomiRs”) might exhibit different biological properties, such as a different target repertoire, or enhanced/reduced stability. Nonetheless, this layer of information has remained largely unexplored due to the scarcity of small RNA NGS-datasets and the absence of proper analytical tools. Here, we present a workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRs can originate from an alternative dicing event (“templated” forms) or from the addition of nucleotides through an enzymatic activity or target-dependent mechanisms (“non-templated” forms). Our pipeline allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3′-, 5′-, and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g., uridylation, adenylation, trimming …) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3′-end adenylation and uridylation as the most frequent events, suggesting that miRNA post-transcriptional modification frequently occurs. In conclusion, our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms.
Increased binding of calcitonin to renal receptors in parathyroidectomized rats.

Salmon calcitonin (sCT) binding was studied in isolated renal membrane preparations from control and parathyroidectomized (PTX) rats. PTX rats showed increased binding of sCT with an increased number of receptor sites: 247 and 376 femtomole (fmole)'mg of receptor protein in control and PTX rats respectively, but no change in affinity: Km equal to 12.5 × 10−10 and 9.9 × 10−10M in control and PTX rats respectively. The concentrations of both high affinity-low capacity and low affinity-high capacity receptors were increased. Time course studies, competitive binding experiments and the effects of changing pH confirmed increased binding of sCT to membranes from PTX rats but inactivation of sCT was similar in the two preparations. (Endocrinology 95: 632, 1974)
Variability of Aspergillus nidulans antigens with media and time and temperature of growth

The influence of culture medium and time and temperature of growth on the appearance of Aspergillus nidulans antigens was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, followed by silver staining or Western blot (immunoblot), of the proteins present in total cellular extracts or culture supernatants. Samples in the exponential, deceleration, and stationary growth phases were selected by biochemical, morphological, and ultrastructural criteria. Protein and antigen patterns (detected with rabbit antibodies) from total extracts were very similar in all cases, and the major differences observed seemed to depend on the age of the cultures. Culture supernatant patterns were highly dependent on the type of medium (complex or defined) and the age of the culture. Temperature did not significantly influence these results. The reproducible reactivity of selected human sera from aspergilloma-affected individuals was strictly associated with the use of defined media, especially Czapek Dox-AOAC, in both total extracts and culture supernatants. Extended growth times were necessary in the case of metabolic antigens (those obtained from culture supernatants). Screening of a battery of 10 selected human serum samples from patients with aspergilloma or invasive aspergillosis demonstrated that two of the antigens (96 to 98 and 45 kDa) from stationary-phase culture supernatants in Czapek Dox-AOAC medium were consistently reactive. When considered together as one unit, both antigens reacted with more than 50% of the sera, and at least one or the other of the antigens reacted with more than 90% of the sera. Less consistent results were obtained for two somatic antigens (from total cell extracts) of 45 to 50 and 20 to 22 kDa.
Explaining interindividual differences in toddlers' collaboration with unfamiliar peers: individual, dyadic, and social factors

During their third year of life, toddlers become increasingly skillful at coordinating their actions with peer partners and they form joint commitments in collaborative situations. However, little effort has been made to explain interindividual differences in collaboration among toddlers. Therefore, we examined the relative influence of distinct individual, dyadic, and social factors on toddlers' collaborative activities (i.e., level of coordination and preference for joint activity) in joint problem-solving situations with unfamiliar peer partners (n = 23 dyads aged M = 35.7 months). We analyzed the dyadic nonindependent data with mixed models. Results indicated that mothers' expectations regarding their children's social behaviors significantly predicted toddlers' level of coordination. Furthermore, the models revealed that toddlers' positive mutual experiences with the unfamiliar partner assessed during an initial free play period (Phase 1) and their level of coordination in an obligatory collaboration task (Phase 2) promoted toddlers' preference for joint activity in a subsequent optional collaboration task (Phase 3). In contrast, children's mastery motivation and shyness conflicted with their collaborative efforts. We discuss the role of parents' socialization goals in toddlers' development toward becoming active collaborators and discuss possible mechanisms underlying the differences in toddlers' commitment to joint activities, namely social preferences and the trust in reliable cooperation partners.
Treatment of atrophic scars with fractional photothermolysis: Short-term follow-up

Abstract Background: Various modalities have been used to treat scars, but limited efficacy and problematic side effects have restricted their application. Objective: To determine the effectiveness and safety of fractional photothermolysis treatment of various atrophic scars in Korean patients. Methods: Fifty-nine patients with atrophic scars (caused by acne, trauma, herpes zoster, and burns) were treated with fractional photothermolysis using either Fraxel™ SR 750 or Fraxel™ SR 1500 instruments. Each patient underwent one to three treatment sessions 3–4 weeks apart. The assessment of treatment response was conducted by three dermatologists, who independently evaluated a series of photographs using a quartile grading scale. Skin biopsies were taken before treatment and 4 weeks after the final treatment, and were examined for procollagen-1, matrix metalloproteinase-1 (MMP-1), and elastin by immunofluorescence staining. Results: Four weeks after the final treatment, the mean overall improvement in objective grade was 2.0 when the Fraxel SR 750 was employed and 2.9 when the Fraxel SR 1500 was used. Confocal microscopy revealed an increase in procollagen-1 in dermis, with no difference or a slight increase in the levels of elastin and MMP-1. Side effects were minimal. Conclusions: After short-term follow-up, fractional photothermolysis appeared to be a safe and effective option for atrophic scar treatment of Asian skin.
Characterizing Task Usage Shapes in Google Compute Clusters

The increase in scale and complexity of large compute clusters motivates a need for representative workload benchmarks to evaluate the performance impact of system changes, so as to assist in designing better scheduling algorithms and in carrying out management activities. To achieve this goal, it is necessary to construct workload characterizations from which realistic performance benchmarks can be created. In this paper, we focus on characterizing run-time task resource usage for CPU, memory and disk. The goal is to find an accurate characterization that can faithfully reproduce the performance of historical workload traces in terms of key performance metrics, such as task wait time and machine resource utilization. Through experiments using workload traces from Google production clusters, we find that simply using the mean of task usage can generate synthetic workload traces that accurately reproduce resource utilizations and task waiting time. This seemingly surprising result can be justified by the fact that resource usage for CPU, memory and disk are relatively stable over time for the majority of the tasks. Our work not only presents a simple technique for constructing realistic workload benchmarks, but also provides insights into understanding workload performance in production compute clusters.
Chapter 7 Exploring Civic Engagement on Public Displays

Research and deployment of public interactive displays is moving from laboratory environments into urban spaces and public areas (Müller et al. 2010 ). Public displays augment the activities in the space around them by facilitating different use cases, such as public statements (Ananny and Strohecker 2009 ; Dalsgaard and Halskov 2010 ), play and performance (O’Hara et al. 2008 ; Hosio et al. 2012 ), or information foraging (Kukka et al. 2012 ). It is even envisioned that such public display installations will fuel the next big wave of social change (Kuikkaniemi et al. 2011 ). In our research we seek to augment urban space with public displays to promote civic engagement by addressing local and temporally and spatially relevant issues. Civic engagement lacks a unifi ed defi nition in literature, but in general it is perceived as an instrument for local governance and a foundation to empower people, often by informing citizens and utilizing feedback channels towards authorities (Mohammadi et al. 2011 ). Over a 2-year period, we incrementally evaluated applications that disseminate information about a long-term renovation project in Oulu, Finland. We used these applications to disseminate information about the construction work being done and by enabling users to provide in situ comments and feedback to the local Technical Centre (later TC). The TC is responsible for the execution of the renovation project, and while information provisioning has been of principal interest to them, our focus has also been on studying the characteristics of different situated feedback mechanisms in authentic city settings. Chapter 7 Exploring Civic Engagement on Public Displays
Infrared Spectroscopic Analyses on the Nature of Water in Montmorillonite

Interlayer cations and moisture content greatly influence the molecular vibrations of H2O in montmorillonite as shown through reflectance spectroscopy in the infrared. The absorptions due to H2O have been studied in montmorillonites exchanged with H, Na, Ca, Mg and Fe3+ interlayer cations under variable moisture environments. Band assignments have been made for absorptions in the 3 µm region due to structural OH vibrations, symmetric and asymmetric H2O stretching vibrations and the H2O bending overtone. Changes in the energies of the absorptions due to H2O stretching vibrations were observed as the samples were dehydrated by reducing the atmospheric pressure. Absorptions near 3620 cm−1 and 3550 cm−1 have been assigned to water bound directly to cations (inner sphere) and surface-bonded H2O and absorptions near 3450 cm−1 and 3350 cm−1 have been assigned to additional adsorbed water molecules. Band assignments have been made for combination bands in the near-infrared as well. Absorptions near 1.41 μm and 1.91 /an are assigned to bound H2O combination bands, while the shoulders near 1. 46μm and 1.97 μm are assigned to combinations of additional H2O molecules adsorbed in the interlayer regions and along grain surfaces.
Correlation of frequency of induced mutation and metastatic potential in tumor cell lines from a single mouse mammary tumor.

Spontaneous mutation rates were determined in mouse mammary tumor subpopulation lines that differ in metastatic phenotype. Although there was almost a 9-fold difference in spontaneous rates to ouabain resistance among the three lines tested, the difference did not correlate with ability to metastasize. Similarly a 10-fold difference in spontaneous rates to 6-thioguanine resistance did not correlate with metastatic ability. In contrast, the frequency of ethyl methanesulfonate-induced mutations was associated with metastatic potential. Thus, ethyl methanesulfonate only induced significant numbers of 6-thioguanine resistant colonies in 66 and 410.4 cells, the only 2 of 5 lines tested that spontaneously metastasize at high frequency, and of ouabain resistant colonies in 66, 410.4, and 168 cells, the only lines tested that produce experimental lung metastases after i.v. injection. Differential sensitivity to induced mutation was not correlated with differences in plating efficiency, wild type sensitivity to ethyl methanesulfonate, 6-thioguanine, or ouabain toxicity, ploidy, cell shape, cell size, or ability to engage in metabolic cooperation.
Collective dynamics of dislocations

We derive the grand-canonical partition function of straight and parallel dislocation lines without making a priori assumptions on the temperature regime. Such a systematic derivation for dislocations has, to our knowledge, not been carried out before, and several conflicting assumptions on the free energy of dislocations have been made in the literature. Dislocations have gained interest as they are the carriers of plastic deformation in crystalline materials and solid polymers, and they constitute a prototype system for two-dimensional Coulomb particles. Our microscopic starting level is the description of dislocations as used in the Discrete Dislocation Dynamics (DDD) framework. The macroscopic level of interest is characterized by the temperature, the boundary deformation and the dislocation density profile. By integrating over state space, we obtain a field theoretic partition function, which is a functional integral of the Boltzmann weight over an auxiliary field. The Hamiltonian consists of a term quadratic in the field and an exponential of this field. The partition function is strongly non-local, and reduces in special cases to the sineGordon model. Moreover, we determine implicit expressions for the response functions and the dominant scaling regime for metals, namely the low temperature regime. Collective behaviour of dislocations in a finite medium 9