Miracle-dz/UniFAR-FTUs huggingface dataset:
Recursive Least Squares for an Entropy Regularized MSE Cost Function

Minimum MSE plays an indispensable role in learning and adaptation of neural systems. Nevertheless, the instantaneous value of the modeling error alone does not convey sufficient information about the accuracy of the estimated model in representing the underlying structure of the data. In this paper, we propose an extension to the traditional MSE cost function, a regularization term based on the incremental errors in model output. We demonstrate the stochastic equivalence between the proposed regularization term and the error entropy. Finally, we derive an RLS-type algorithm for the proposed cost function, which we call recursive least squares with entropy regularization (RLSER) algorithm. The performance of RLSER is shown to be better than RLS in supervised training with noisy data.
Tasks and newest trends in geodetic deformation analysis: A tutorial

Within the last years a fundamental change took place in the methodology of geodetic deformation analysis. High sensitive sensor networks enable the installation of area-wide monitoring systems and require new methods for modelling of measuring errors. The classical stochastic view is extended to fuzzified approaches quantifying remaining uncertainties in the error budget. In addition the geometrical deformation analysis dealing with kinematic displacement fields has changed to cause-response models which also quantify monitored trigger events like temperature, wind etc. One challenge is to find deformation transfer functions for complex structures. In this context also AI-methods are trained and used. The paper will give a brief overview over the current state of the art and newest developments in geodetic deformation analysis.
SLOAVx: Scalable LOgarithmic AlltoallV Algorithm for Hierarchical Multicore Systems

Scientific applications use collective communication operations in Message Passing Interface (MPI) for global synchronization and data exchanges. Alltoall and AlltoallV are two important collective operations. They are used by MPI jobs to exchange messages among all of MPI processes. AlltoallV is a generalization of Alltoall, supporting messages of varying sizes. However, the existing MPI AlltoallV implementation has linear complexity, i.e., each process has to send messages to all other processes in the job. Such linear complexity can result in sub optimal scalability of MPI applications when they are deployed on millions of cores. To address above challenge, in this paper, we introduce a new Scalable LOgarithmic AlltoallV algorithm, named SLOAV, for MPI AlltoallV collective operation. SLOAV aims to achieve global exchange of small messages of different sizes in a logarithmic number of rounds. Furthermore, given the prevalence of multicore systems with shared memory, we design a hierarchical AlltoallV algorithm based on SLOAV by leveraging the advantages of shared memory, which is referred to as SLOAVx. Compared to SLOAV, SLOAVx significantly reduces the inter-node communication, thus improving the entire system performance and mitigating the impact of message latency. We have implemented and embedded both algorithms in Open MPI. Our evaluation on large-scale computer systems shows that for the 8-byte and 1024-process MPI Alltoallv operation, the SLOAV can reduce the latency by as much as 86.4%, when compared to the state-of-the-art, and SLOAVx can further optimize the SLOAV by up to 83.1% in terms of message latency on multicore systems. In addition, experiments with NAS Parallel Benchmark (NPB) demonstrate that our algorithms are very effective for real-world applications.
Circular forms of Uukuniemi virion RNA: an electron microscopic study

Because the ribonucleoprotein forms of the segments of the Uukuniemi virus genome have previously been characterized as circular, we examined the isolated RNAs by electron microscopy under conditions of increasing denaturation. After spreading under moderately denaturing conditions (50 or 60% formamide), 50 to 70% of the molecules were circular. Increasing the formamide concentration to 70 and 85% decreased the number of circular forms, and only linear forms were observed after incubation of the RNA at 60 degrees C for 15 min in 99% formamide. When spread from 4 M urea-80% formamide--another condition known to denature RNA--only 5 to 30% circular molecules were observed. Pretreatment of the RNA with 0.5 M glyoxal at 37 degrees C for 15 min prior to spreading from 50% formamide gave less than 5% cirucular forms. Length measurement of the molecules showed that they were not significantly degraded by any of the methods employed. The circular molecules were destroyed by treatment with pancreatic RNase, but were unaffected by DNase or proteinase K treatment. After complete denaturation of the RNA, the circles could be reformed under reannealing conditions. We conclude that the three size classes of RNA that comprise the Uukuniemi virus genome are circular molecules probably maintained in that form by base pairing between inverted complementary sequences at the 3' and 5' ends of linear molecules.
Multifunctional PP-Based Nanocomposites Incorporated with Organoclays, Poly(MA-alt-1-Dodecene)-g-SiO2 Nanoparticles and Bioengineering Polyesters in Melt by Reactive Extrusion

ABSTRACT Polypropylene-based multifunctional nanocomposites were fabricated in melt by a one-step reactive extrusion using a twin-screw extruder. The in situ chemical and physical processes during the extrusion of polymer blend composites consisting (1) polypropylene as a matrix polymer, (2) polypropylene–g-maleic anhydride graft copolymer compatibilizer, (3) copolymer–g-SiO2 encapsulated nanoparticles, (4) biodegradable polyesters, and (5) reactive and nonreactive organoclay nanofillers were investigated. The crystallinity, thermal stability, rheological, mechanical parameters, and surface and internal morphologies of the nanocomposites have been improved compared to polypropylene and its composites. Moreover, the colloidal copolymer–silica nanoparticles play an important role in the formation of nanocomposites with well dispersion in morphology. GRAPHICAL ABSTRACT
Word sense disambiguation by selecting the best semantic type based on Journal Descriptor Indexing: Preliminary experiment

An experiment was performed at the National Library of Medicine((R)) (NLM((R))) in word sense disambiguation (WSD) using the Journal Descriptor Indexing (JDI) methodology. The motivation is the need to solve the ambiguity problem confronting NLM's MetaMap system, which maps free text to terms corresponding to concepts in NLM's Unified Medical Language System((R)) (UMLS((R))) Metathesaurus((R)). If the text maps to more than one Metathesaurus concept at the same high confidence score, MetaMap has no way of knowing which concept is the correct mapping. We describe the JDI methodology, which is ultimately based on statistical associations between words in a training set of MEDLINE((R)) citations and a small set of journal descriptors (assigned by humans to journals per se) assumed to be inherited by the citations. JDI is the basis for selecting the best meaning that is correlated to UMLS semantic types (STs) assigned to ambiguous concepts in the Metathesaurus. For example, the ambiguity transport has two meanings: "Biological Transport" assigned the ST Cell Function and "Patient transport" assigned the ST Health Care Activity. A JDI-based methodology can analyze text containing transport and determine which ST receives a higher score for that text, which then returns the associated meaning, presumed to apply to the ambiguity itself. We then present an experiment in which a baseline disambiguation method was compared to four versions of JDI in disambiguating 45 ambiguous strings from NLM's WSD Test Collection. Overall average precision for the highest-scoring JDI version was 0.7873 compared to 0.2492 for the baseline method, and average precision for individual ambiguities was greater than 0.90 for 23 of them (51%), greater than 0.85 for 24 (53%), and greater than 0.65 for 35 (79%). On the basis of these results, we hope to improve performance of JDI and test its use in applications.
Design of additive free 3D floral shaped V2O5@ Ni foam for high performance supercapacitors

Abstract The three-dimensional (3D) floral-shaped V2O5 was directly grown on Ni foam backbones by a straightforward and additive free hydrothermal approach. The as-synthesised material can be directly investigated as electrodes for supercapacitors without inclusion of other additives, such as polymer binder and carbon black. These elegant structural features endow this material with superior electrochemical features, such as high capacitance (601 Fg−1), superior withstanding capacity at higher rates (373 Fg−1 at 5 Ag−1) and better cyclic stability. Most importantly, the symmetric supercapacitor using 3D-V2O5at Ni foam electrode exhibits specific capacitance of 142 Fg−1 with energy density of 29 WhKg−1. Thirty light-emitting diodes were illuminated using three (connected in series) 3D-VN symmetric supercapacitors. Such impressive morphology and electrochemical richness of this material encourages its usefulness as supercapacitor electrodes.
Interlaboratory Evaluation of in Vitro Cytotoxicity and Inflammatory Responses to Engineered Nanomaterials: The NIEHS Nano GO Consortium

Background: Differences in interlaboratory research protocols contribute to the conflicting data in the literature regarding engineered nanomaterial (ENM) bioactivity. Objectives: Grantees of a National Institute of Health Sciences (NIEHS)-funded consortium program performed two phases of in vitro testing with selected ENMs in an effort to identify and minimize sources of variability. Methods: Consortium program participants (CPPs) conducted ENM bioactivity evaluations on zinc oxide (ZnO), three forms of titanium dioxide (TiO2), and three forms of multiwalled carbon nanotubes (MWCNTs). In addition, CPPs performed bioassays using three mammalian cell lines (BEAS-2B, RLE-6TN, and THP-1) selected in order to cover two different species (rat and human), two different lung epithelial cells (alveolar type II and bronchial epithelial cells), and two different cell types (epithelial cells and macrophages). CPPs also measured cytotoxicity in all cell types while measuring inflammasome activation [interleukin-1β (IL-1β) release] using only THP-1 cells. Results: The overall in vitro toxicity profiles of ENM were as follows: ZnO was cytotoxic to all cell types at ≥ 50 μg/mL, but did not induce IL-1β. TiO2 was not cytotoxic except for the nanobelt form, which was cytotoxic and induced significant IL-1β production in THP-1 cells. MWCNTs did not produce cytotoxicity, but stimulated lower levels of IL-1β production in THP-1 cells, with the original MWCNT producing the most IL-1β. Conclusions: The results provide justification for the inclusion of mechanism-linked bioactivity assays along with traditional cytotoxicity assays for in vitro screening. In addition, the results suggest that conducting studies with multiple relevant cell types to avoid false-negative outcomes is critical for accurate evaluation of ENM bioactivity.
C-Reactive Protein as a Predictor of Incident Ischemic Stroke Among Patients With Preexisting Cardiovascular Disease

Background and Purpose— C-reactive protein (CRP) has emerged as an important predictor of cardiovascular disease, but there are few prospective data on its association with risk of ischemic stroke in patients at high risk. Methods— We examined the association between CRP levels and subsequent risk of incident ischemic stroke among 2979 patients with stable coronary heart disease included in a controlled clinical trial (Bezafibrate Infarction Prevention) that assessed the efficacy of bezafibrate, a fibric acid derivative, versus placebo for secondary prevention. CRP was measured by a high-sensitivity assay in plasma samples collected before randomization and again at the second follow-up year of an overall mean follow-up of 6.2 years. Results— Risk of ischemic stroke per 1000 person-years increased from 4.1% for baseline CRP in the lowest tertile (<2.3 mg/L; n=982) to 5.9% for levels at the middle tertile (2.3 to 5.4 mg/L; n=1013) and 10.5% for CRP levels at the upper tertile (>5.4 mg/L; n=984; P<0.001). With adjustment for potential confounders, baseline CRP levels in the top versus bottom tertile were associated with a 2.16-fold increased hazard (95% CI, 1.32 to 3.53) for ischemic stroke, and CRP levels measured after 2 years were associated with a hazard ratio of 2.43 (95% CI, 1.30 to 4.57). The risk of an incident ischemic stroke did not differ between the bezafibrate group compared with the placebo group regardless of baseline CRP levels. Conclusions— These findings, based on a large prospective study, demonstrate the risk prediction for incident ischemic stroke conferred by CRP levels in patients at high risk.
Interoperability with Moby 1.0--it's better than sharing your toothbrush!

The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby. org/.
Targeted Disruption of the Scavenger Receptor and Chemokine CXCL16 Accelerates Atherosclerosis

Background— The uptake of oxidized low-density lipoprotein (OxLDL) by macrophage scavenger receptors is thought to be a key process in the formation of foam cells, the hallmark of early atherosclerotic lesions. CXCL16/scavenger receptor for phosphatidylserine and OxLDL is a multifunctional chemokine that exhibits scavenger receptor activity toward oxidized lipids in a membrane-bound configuration and may be shed to serve as a chemoattractant for T helper 1–polarized T lymphocytes. These properties, as well as the expression of CXCL16 in human and mouse atheroma, suggest that CXCL16 plays a role in atherosclerosis. Methods and Results— To examine the role of CXCL16 in plaque formation, we created CXCL16-deficient mice (CXCL16−/−) and bred them with mice deficient in the LDL receptor (LDLR−/−). In vitro, macrophages from CXCL16−/− mice have a significant reduction in the capacity to bind and internalize OxLDL. We found that CXCL16−/−/LDLR−/− mice have accelerated atherosclerosis, enhanced macrophage recruitment to the aortic arch, and more abundant mRNA for monocyte chemotactic protein-1 and tumor necrosis factor-α. Conclusions— These data suggest that scavenger receptor activity mediated by CXCL16 in vivo is atheroprotective, and they contrast with studies that document protection from atherosclerosis in scavenger receptor class A– and CD36-deficient mice.
Two-parameter Quantum Group of Exceptional Type G_2 and Lusztig's Symmetries

We give the defining structure of two-parameter quantum group of type G_2 defined over a field {\Bbb Q}(r,s) (with r\ne s), and prove the Drinfel'd double structure as its upper and lower triangular parts, extending an earlier result of [BW1] in type A and a recent result of [BGH1] in types B, C, D. We further discuss the Lusztig's Q-isomorphisms from U_{r,s}(G_2) to its associated object U_{s^{-1},r^{-1}}(G_2), which give rise to the usual Lusztig's symmetries defined not only on U_q(G_2) but also on the centralized quantum group U_q^c(G_2) only when r=s^{-1}=q. (This also reflects the distinguishing difference between our newly defined two-parameter object and the standard Drinfel'd-Jimbo quantum groups). Some interesting (r,s)-identities holding in U_{r,s}(G_2) are derived from this discussion.
Expression α Enhanced Retinoic Acid Receptor and Growth-inhibitory Response to Retinoids without Estrogen Receptor Expression Activates the Transcriptional Updated

Estrogen receptor (KR)-positive human breast cancer cells are hormonally regulated and are inhibited by retinoids, whereas most ER-negative breast cancer cells arc not. Here, we compared retinoid-induced transcriptional activation and growth inhibition in the ER-negative breast cancer cell line \1DA-MB-231, stably transfected to express wild-type ER (S3Ãœ),with that of the ER-positive MCE-7 line and the ER-negative parental line. Retinoids inhibited growth of the ER-expressing S30 clone but not of the parental MDA-MB-231 cells. Unlike a previously reported MDA-MB-231 subclone that was transfected to express a mutated ER (G40ÃœV),S30 did not express increased levels of retinoid receptor RNA or protein, nor was there increased binding activity to retinoid-responsive DNA elements. However, stable expression of ER increased retinoid acti vation of transcription of a retinole acid (RA) response elements from the low level in MDA-MB-231 to approach the level of MCF-7. The restored growth inhibition and transcriptional regulation by RA were unaffected by treatment with ER agonists or antagonists. Transient expression of ER but not of other nuclear receptors in MDA-MB-231 cells also activated retinoid-induced transcription, showing that this response is specific to ER. Furthermore, the effect of exogenously expressed ER on retinoid response was much greater than that obtained by overexpression of RA receptor a and/or retinoid X receptor a. Finally, a panel of ER mutants showed that enhancement of retinoid-induced transcriptional activity was dependent on the integrity of the DNA binding domain.
Effects of the acanthocephalan Polymorphus minutus and the microsporidian Dictyocoela duebenum on energy reserves and stress response of cadmium exposed Gammarus fossarum

Amphipods are commonly parasitized by acanthocephalans and microsporidians and co-infections are found frequently. Both groups of parasites are known to have severe effects on their host. For example, microsporidians can modify host sex ratio and acanthocephalans can manipulate the behavior of the amphipod to promote transmission to the final host. These effects influence host metabolism in general and will also affect the ability of amphipods to cope with additional stressors such as environmental pollution, e.g., by toxic metals. Here we tested the effects of sub-lethal concentrations of cadmium on glycogen and lipid levels, as well as on the 70kDa heat shock protein (hsp70) response of field collected Gammarus fossarum, which were naturally infected with microsporidians and the acanthocephalan Polymorphus minutus. Infected and uninfected G. fossarum were exposed to a nominal Cd concentration of 4 µg/L, which resembled measured aqueous Cd concentration of 2.9 µg/L in reconstituted water for 7 d at 15 °C in parallel to an unexposed control. After exposure gammarids were snap frozen, weighed, sexed and tested for microsporidian infection by PCR. Only individuals containing the microsporidian Dictyocoela duebenum were used for the further biochemical and metal analyses. P. minutus infected amphipods were significantly smaller than their uninfected conspecifics. Mortality was insignificantly increased due to cadmium exposure, but not due to parasite infection. Microsporidian infection in combination with cadmium exposure led to increased glycogen levels in female gammarids. An increase of glycogen was also found due to interaction of acanthocephalan and microsporidian infection. Elevated lipid levels were observed in all groups infected with microsporidians, while acanthocephalans had the opposite effect. A positive correlation of lipid and glycogen levels was observed. The general stress response measured in form of hsp70 was significantly increased in microsporidian infected gammarids exposed to cadmium. P. minutus did not affect the stress response of its host. Lipid levels were correlated negatively with hsp70 response, and indicated a possible increased stress susceptibility of individuals with depleted energy reserves. The results of our study clearly demonstrate the importance of parasitic infections, especially of microsporidians, for ecotoxicological research.
Ablation of Vacuole Protein Sorting 18 (Vps18) Gene Leads to Neurodegeneration and Impaired Neuronal Migration by Disrupting Multiple Vesicle Transport Pathways to Lysosomes

Background: The physiological function of Vps18 in mammals is unknown. Results: Deleting Vps18 in mice leads to neurodegeneration by disrupting multiple vesicle transport pathways to lysosomes and impairs neuron migration via accumulation of β1 integrin. Conclusion: Vps18 contributes to neuron survival and migration. Significance: This study demonstrates the critical functions of Vps18-mediated vesicle transport pathways in mammalian brain development. Intracellular vesicle transport pathways are critical for neuronal survival and central nervous system development. The Vps-C complex regulates multiple vesicle transport pathways to the lysosome in lower organisms. However, little is known regarding its physiological function in mammals. We deleted Vps18, a central member of Vps-C core complex, in neural cells by generating Vps18F/F; Nestin-Cre mice (Vps18 conditional knock-out mice). These mice displayed severe neurodegeneration and neuronal migration defects. Mechanistic studies revealed that Vps18 deficiency caused neurodegeneration by blocking multiple vesicle transport pathways to the lysosome, including autophagy, endocytosis, and biosynthetic pathways. Our study also showed that ablation of Vps18 resulted in up-regulation of β1 integrin in mouse brain probably due to lysosome dysfunction but had no effects on the reelin pathway, expression of N-cadherin, or activation of JNK, which are implicated in the regulation of neuronal migration. Finally, we demonstrated that knocking down β1 integrin partially rescued the migration defects, suggesting that Vps18 deficiency-mediated up-regulation of β1 integrin may contribute to the defect of neuronal migration in the Vps18-deficient brain. Our results demonstrate important roles of Vps18 in neuron survival and migration, which are disrupted in multiple neural disorders.
Orphan nuclear receptor NR4A2 inhibits hepatic stellate cell proliferation through MAPK pathway in liver fibrosis

Hepatic stellate cells (HSCs) play a crucial role in liver fibrosis, which is a pathological process characterized by extracellular matrix accumulation. NR4A2 is a nuclear receptor belonging to the NR4A subfamily and vital in regulating cell growth, metabolism, inflammation and other biological functions. However, its role in HSCs is unclear. We analyzed NR4A2 expression in fibrotic liver and stimulated HSCs compared with control group and studied the influence on cell proliferation, cell cycle, cell apoptosis and MAPK pathway after NR4A2 knockdown. NR4A2 expression was examined by real-time polymerase chain reaction, Western blotting, immunohistochemistry and immunofluorescence analyses. NR4A2 expression was significantly lower in fibrotic liver tissues and PDGF BB or TGF-β stimulated HSCs compared with control group. After NR4A2 knockdown α-smooth muscle actin and Col1 expression increased. In addition, NR4A2 silencing led to the promotion of cell proliferation, increase of cell percentage in S phase and reduced phosphorylation of ERK1/2, P38 and JNK in HSCs. These results indicate that NR4A2 can inhibit HSC proliferation through MAPK pathway and decrease extracellular matrix in liver fibrogenesis. NR4A2 may be a promising therapeutic target for liver fibrosis.