Miracle-dz/UniFAR-FTUs huggingface dataset:
Cartilage degradation by stimulated human neutrophils: elastase is mainly responsible for cartilage damage.

Although neutrophilic granulocytes are assumed to contribute to cartilage degradation during rheumatic diseases, there is still a discussion whether reactive oxygen species (ROS) or proteolytic enzymes that are both released by the neutrophils are most relevant to cartilage degradation. To gain further insight into these processes, an in vitro approach to study the interaction between the products of stimulated neutrophilic granulocytes and cartilage was used: Neutrophils from the blood of healthy volunteers were treated with different stimulators (e.g., Ca(2+) ionophores) in order to induce degranulation. Supernatants of neutrophils were afterward incubated with thin slices of pig articular cartilage. Some experiments were also performed in the presence of selected enzyme inhibitors. Supernatants of cartilage were subsequently assayed by one- and two-dimensional high-resolution proton NMR spectroscopy, and the content of soluble carbohydrates in the supernatant was additionally determined by biochemical methods. The selective inhibition of elastase decreased most significantly the extent of cartilage degradation, whereas all other inhibitors had much smaller effects. These results were additionally confirmed by measuring the effect of isolated elastase on articular cartilage in the absence and presence of different inhibitors. It is concluded that elastase released [EC 3.4. 21.37] by neutrophils is the most relevant enzyme for cartilage degradation.
Electrophysiological correlates associated with contributions of perceptual and conceptual fluency to familiarity

The present research manipulated the fluency of unstudied items using masked repetition priming procedures during an explicit recognition test. Based on fluency-attribution accounts, which posit that familiarity can be driven by multiple forms of fluency, the relationship between masked priming-induced fluency and familiarity was investigated. We classified pictographic characters into High-Meaningfulness (High-M) and Low-Meaningfulness (Low-M) categories on the basis of subjective meaningfulness ratings and identified the distinct electrophysiological correlates of perceptual and conceptual fluency. The two types of fluency differed in associated ERP effects: 150–250 ms effects for perceptual fluency and FN400 effects for conceptual fluency. The ERPs of Low-M MP-same (items that were preceded by matching masked items) false alarms were more positive than correct rejections during 150–250 ms, whereas the ERPs of High-M MP-same false alarms were more positive than correct rejections during 300–500 ms. The topographic patterns of FN400 effects between High-M MP-same false alarms and Low-M MP-same false alarms were not different from those of High-M hits and Low-M hits. These results indicate that both forms of fluency can contribute to familiarity, and the neural correlates of conceptual fluency are not different from those of conceptual priming induced by prior study-phase exposure. We conclude that multiple neural signals potentially contribute to recognition memory, such as numerous forms of fluency differing in terms of their time courses.
Finding Your Way from the Bed to the Kitchen: Reenacting and Recombining Sensorimotor Episodes Learned from Human Demonstration

Several simulation theories have been proposed as an explanation for how humans and other agents internalize an "inner world" that allows them to simulate interactions with the external real world -- prospectively and retrospectively. Such internal simulation of interaction with the environment has been argued to be a key mechanism behind mentalizing and planning. In the present work, we study internal simulations in a robot acting in a simulated human environment. A model of sensory-motor interactions with the environment is generated from human demonstrations, and tested on a Robosoft Kompai robot. The model is used as a controller for the robot, reproducing the demonstrated behavior. Information from several different demonstrations is mixed, allowing the robot to produce novel paths through the environment, towards a goal specified by top-down contextual information. The robot model is also used in a covert mode, where actions are inhibited and perceptions are generated by a forward model. As a result, the robot generates an internal simulation of the sensory-motor interactions with the environment. Similar to the overt mode, the model is able to reproduce the demonstrated behavior as internal simulations. When experiences from several demonstrations are combined with a top-down goal signal, the system produces internal simulations of novel paths through the environment. These results can be understood as the robot imagining an "inner world" generated from previous experience, allowing it to try out different possible futures without executing actions overtly. We found that the success rate in terms of reaching the specified goal was higher during internal simulation, compared to overt action. These results are linked to a reduction in prediction errors generated during covert action. Despite the fact that the model is quite successful in terms of generating covert behavior towards specified goals, internal simulations display different temporal distributions compared to their overt counterparts. Links to human cognition and specifically mental imagery are discussed.
Mapping binding residues in the Plasmodium vivax domain that binds Duffy antigen during red cell invasion

Plasmodium vivax depends on interaction with the Duffy antigen/receptor for chemokines (DARC) for invasion of human erythrocytes. The 140 kDa P. vivax Duffy‐binding protein (PvDBP) mediates interaction with DARC. The receptor‐binding domain of PvDBP maps to its N‐terminal, cysteine‐rich region, region II (PvRII), which contains approximately 300 amino acid residues including 12 conserved cysteines. Using surface plasmon resonance, we show that binding of PvRII to DARC is a high‐affinity interaction with a binding constant (KD) of 8.7 nM. The minimal binding domain of PvRII has been previously mapped to a central 170‐amino‐acid stretch that includes cysteines 5–8. Here, we have used site‐directed mutagenesis and quantitative binding assays to map amino acid residues within PvRII that make contact with DARC. Of the seven alanine replacement mutations that had an effect on binding, five were mutations in hydrophobic residues suggesting that hydrophobic interactions play a major role in the interaction of PvDBP with DARC. Genetic diversity studies have shown that six of the seven binding residues identified in PvRII are conserved in P. vivax field isolates, which provides support for their role in interaction with DARC.
Coordinated motion of two robot arms

We study the problem of planning simultaneous motion for two robot arms that are modeled on the Stanford arm. The arms have two degrees of freedom and must move in a workspace, avoiding obstacles and each other. We develop an O(n2logn) algorithm for planning motion of two arms with tips together, and an O(n3) algorithm for independent but synchronized motion. Here n is the total number of walls of the obstacles.
Messages behind the sound: real-time hidden acoustic signal capture with smartphones

With the ever-increasing use of smart devices, recent research endeavors have led to unobtrusive screen-camera communication channel designs, which allow simultaneous screen viewing and hidden screen-camera communication. Such practices, albeit innovative and effective, require well-controlled alignment of camera and screen and obstacle-free access. In this paper, we develop Dolphin, a novel form of real-time acoustics-based dual-channel communication, which uses a speaker and the microphones on off-the-shelf smartphones to achieve concurrent audible and hidden communication. By leveraging masking effects of the human auditory system and readily available audio signals in our daily lives, Dolphin ensures real-time unobtrusive speaker-microphone data communication without affecting the primary audio-hearing experience for human users, while, at the same time, it overcomes the main limitations of existing screen-camera links. Our Dolphin prototype, built using off-the-shelf smartphones, realizes real-time hidden communication, supports up to 8-meter signal capture distance and ±90° listening angle and achieves decoding rate above 80% without error correction. Further, it achieves average data rates of up to 500bps while keeping the decoding rate above 95% within a distance of 1m.
Methods of transplanting nuclei from single cultured cells to unfertilized frogs' eggs.

SUMMARY Two methods of transplanting single nuclei from monolayers of cultured cells to unfertilized eggs of Xenopus laevis are described, illustrated, and tested. The detached-cell method is simpler and quicker to operate and is suitable for homogeneous populations of cells which are easily removed from the substrate on which they are growing. The other, attached-cell, method is technically more elaborate, but is applicable to cells whose properties can be individually determined under the phase-contrast microscope and to cells which are not readily dissociated from other cells or from their substrate.
PIVKA-II is a useful tool for diagnostic characterization of ultrasound-detected liver nodules in cirrhotic patients

Abstract Protein induced by vitamin K absence-II (PIVKA-II) is a potential screening marker for hepatocellular carcinoma (HCC). Limited data are available about its utility in discriminating neoplastic from regenerative nodules at ultrasonography (US) evaluation in cirrhotic patients. Aim of this study was to investigate the diagnostic utility of PIVKA-II in cases showing liver nodules of uncertain diagnosis at US. Ninety cirrhotics with US evidence of liver nodule(s) were enrolled. All patients underwent blood sampling within 1 week of US and were thereafter followed up. HCC was confirmed in 40/90 cases, and in all cases it was in a very early/early stage. All sera were tested for PIVKA-II and alpha-fetoprotein (AFP) at the end of follow-up. PIVKA-II at a cut off of 60 mAU/mL was significantly associated with HCC at both univariate and multivariate analysis (P = .016 and P = .032, respectively). AFP at a cut off of 6.5 ng/mL was not associated with HCC at univariate analysis (P = .246). ROC curves showed that PIVKA-II had 60% sensitivity, 88% specificity, 80% positive predictive value (PPV), and 73% negative predictive value (NPV), whereas AFP had 67% sensitivity, 68% specificity, 63% PPV, and 72% NPV. AUROC curves showed that the combination of both biomarkers increased the diagnostic accuracy for HCC (AUC 0.76; sensitivity 70%, specificity 94%, PPV 91%, and NPV 79%). In conclusion, PIVKA-II is a useful tool for the diagnostic definition of US-detected liver nodules in cirrhotic patients, and it provides high diagnostic accuracy for HCC when combined with AFP.
A P ] 2 8 M ay 2 01 0 Mathematics for 2 d Interfaces

We present here a survey of recent results concerning the mathematical analysis of instabilities of the interface between two incompressible, non viscous, fluids of constant density and vorticity concentrated on the interface. This configuration includes the so-called Kelvin-Helmholtz (the two densities are equal), Rayleigh-Taylor (two different, nonzero, densities) and the water waves (one of the densities is zero) problems. After a brief review of results concerning strong and weak solutions of the Euler equation, we derive interface equations (such as the Birkhoff-Rott equation) that describe the motion of the interface. A linear analysis allows us to exhibit the main features of these equations (such as ellipticity properties); the consequences for the full, non linear, equations are then described. In particular, the solutions of the Kelvin-Helmholtz and Rayleigh-Taylor problems are necessarily analytic if they are above a certain threshold of regularity (a consequence is the illposedness of the initial value problem in a non analytic framework). We also say a few words on the phenomena that may occur below this regularity threshold. Finally, special attention is given to the water waves problem, which is much more stable than the Kelvin-Helmholtz and Rayleigh-Taylor configurations. Most of the results presented here are in 2d (the interface has dimension one), but we give a brief description of similarities and differences in the 3d case.
Subcutaneous Interferon β-1a May Protect against Cognitive Impairment in Patients with Relapsing–Remitting Multiple Sclerosis: 5-Year Follow-up of the COGIMUS Study

Objective To assess the effects of subcutaneous (sc) interferon (IFN) -1a on cognition over 5 years in mildly disabled patients with relapsing–remitting multiple sclerosis (RRMS). Methods Patients aged 18–50 years with RRMS (Expanded Disability Status Scale score ≤4.0) who had completed the 3-year COGIMUS study underwent standardized magnetic resonance imaging, neurological examination, and neuropsychological testing at years 4 and 5. Predictors of cognitive impairment at year 5 were identified using multivariate analysis. Results Of 331 patients who completed the 3-year COGIMUS study, 265 participated in the 2-year extension study, 201 of whom (75.8%; sc IFN β-1a three times weekly: 44 µg, n = 108; 22 µg, n = 93) completed 5 years' follow-up. The proportion of patients with cognitive impairment in the study population overall remained stable between baseline (18.0%) and year 5 (22.6%). The proportion of patients with cognitive impairment also remained stable in both treatment groups between baseline and year 5, and between year 3 and year 5. However, a significantly higher proportion of men than women had cognitive impairment at year 5 (26.5% vs 14.4%, p = 0.046). Treatment with the 22 versus 44 µg dose was predictive of cognitive impairment at year 5 (hazard ratio 0.68; 95% confidence interval 0.48–0.97). Conclusions This study suggests that sc IFN β-1a dose-dependently stabilizes or delays cognitive impairment over a 5-year period in most patients with mild RRMS. Women seem to be more protected against developing cognitive impairment, which may indicate greater response to therapy or the inherently better prognosis associated with female sex in MS.
Prevalence of Leucocytozoon spp, in the endangered yellow-eyed penguin Megadyptes antipodes

SUMMARY Yellow-eyed penguins on Stewart Island were identified with a Leucocytozoon spp. of a novel lineage in association with a high regional incidence of chick mortality (n=32, 100% mortality) during the November 2006 to January 2007 breeding season. Fourteen chicks from Stewart Island were examined post-mortem and histologically for Leucocytozoon infection. In addition, a survey of blood to detect Leucocytozoon spp. infections using PCR was performed on 107 yellow-eyed penguins from 4 distinct nesting areas on the South Island (Oamaru, Otago Peninsula, and Catlins) (n=95), and Stewart Island (n=12). The results of the study revealed that 2 of the 14 (14%) chicks necropsied showed severe, disseminated megaloschizont formation in the liver, spleen, lung, kidney and other tissues characteristic of leucocytozoonosis. Eighty-three percent (83%) of blood samples collected from Stewart Island penguins contained Leucocytozoon DNA, whereas samples from the 3 other nesting areas were negative for the blood parasite. Leucocytozoon spp. DNA sequences isolated from blood and tissues of adults (n=10) and chicks (n=7) were similar and grouped with other published Leucocytozoon spp. sequences but in a distinct cluster together with closely related isolates from a Western march harrier (Circus aerginosus) and common loon (Gavia immer). These findings suggest that yellow-eyed penguins on Stewart Island are infected with a regionally isolated, host-specific Leucocytozoon spp. which may contribute to the high chick mortality observed during this period.
The Role of Sialyl Glycan Recognition in Host Tissue Tropism of the Avian Parasite Eimeria tenella

Eimeria spp. are a highly successful group of intracellular protozoan parasites that develop within intestinal epithelial cells of poultry, causing coccidiosis. As a result of resistance against anticoccidial drugs and the expense of manufacturing live vaccines, it is necessary to understand the relationship between Eimeria and its host more deeply, with a view to developing recombinant vaccines. Eimeria possesses a family of microneme lectins (MICs) that contain microneme adhesive repeat regions (MARR). We show that the major MARR protein from Eimeria tenella, EtMIC3, is deployed at the parasite-host interface during the early stages of invasion. EtMIC3 consists of seven tandem MAR1-type domains, which possess a high specificity for sialylated glycans as shown by cell-based assays and carbohydrate microarray analyses. The restricted tissue staining pattern observed for EtMIC3 in the chicken caecal epithelium indicates that EtMIC3 contributes to guiding the parasite to the site of invasion in the chicken gut. The microarray analyses also reveal a lack of recognition of glycan sequences terminating in the N-glycolyl form of sialic acid by EtMIC3. Thus the parasite is well adapted to the avian host which lacks N-glycolyl neuraminic acid. We provide new structural insight into the MAR1 family of domains and reveal the atomic resolution basis for the sialic acid-based carbohydrate recognition. Finally, a preliminary chicken immunization trial provides evidence that recombinant EtMIC3 protein and EtMIC3 DNA are effective vaccine candidates.
4E-binding Proteins, the Suppressors of Eukaryotic Initiation Factor 4E, Are Down-regulated in Cells with Acquired or Intrinsic Resistance to Rapamycin*

To determine whether inhibition of either the ribosomal p70 S6 kinase or eukaryotic initiation factor (eIF) 4E pathways downstream of the mammalian target of rapamycin, mTOR, contributes to rapamycin-induced growth arrest, clones of Rh30 rhabdomyosarcoma cells were selected for rapamycin resistance. Expression of c-Myc and anchorage-independent growth were enhanced in resistant cells. Resistance was unstable in each of three clones characterized. In resistant cells, as compared with parental cells, ∼10-fold less 4E-binding protein (4E-BP) was bound to eIF4E, and total cellular 4E-BP was markedly reduced. Levels of eIF4E were unchanged. Steady-state levels of 4E-BP transcript remained unaltered, but the rate of 4E-BP synthesis was reduced in resistant cells. In cells that reverted to rapamycin sensitivity, levels of total 4E-BP returned to those of parental cells. Compared with parental cells, resistant clones had either similar or lower levels and activity of ribosomal p70 S6 kinase, but c-Myc levels were elevated in both resistant and revertant clones. Several colon carcinoma cell lines with intrinsic rapamycin resistance were found to have low 4E-BP:eIF4E ratios. In stable clones of HCT8 carcinoma engineered to overexpress 4E-BP, rapamycin sensitivity increased markedly (>1000-fold) as 4E-BP expression increased. These results suggest that the 4E-BP:eIF4E ratio is an important determinant of rapamycin resistance and controls certain aspects of the malignant phenotype.
Effects of hemostatic agents on the histomorphologic response of human dental pulp capped with calcium hydroxide.

OBJECTIVE To evaluate the response of human pulps capped with a calcium hydroxide [Ca(OH)2] cement after bleeding control with 2 hemostatic agents. METHOD AND MATERIALS Pulps were exposed on the occlusal floor, and the bleeding was controlled either with saline solution (SS) or 2.5% sodium hypochlorite (NaOCl) (SH). After that, the pulp was capped with Ca(OH)2 cement and restored with resin composite. After 30 (groups SS30 and SH30) and 60 (groups SS60 and SH60) days, the teeth were extracted and processed with hematoxylin-eosin and categorized in a histologic score system. The data were subjected to Kruskal-Wallis and Mann-Whitney tests (alpha = .05). RESULTS Regarding dentin bridge formation, an inferior response of SH60 group was observed when compared to SS60 (P < .05). The response of the SH30 group generally was similar to that of the groups treated with saline solution. However, after 60 days, 2.5% NaOCl showed a trend toward having an inferior response. CONCLUSION Using saline solution as a hemostatic agent before pulp capping with Ca(OH)2 resulted in a significantly better histomorphologic response than using 2.5% NaOCl as a hemostatic agent before capping with Ca(OH)2.
Single Nucleotide Polymorphisms in the Tumor Necrosis Factor-Alpha Gene Promoter Region Alter the Risk of Psoriasis Vulgaris and Psoriatic Arthritis: A Meta-Analysis

Background It has been confirmed that tumor necrosis factor-alpha (TNFα), a macrophage-derived pro-inflammatory cytokine, plays an important role in the pathogenesis of psoriasis vulgaris and psoriatic arthritis (PsV&PsA). In contrast, the reported association of TNFα gene promoter region single nucleotide polymorphisms (SNPs) and PsV&PsA has remained controversial. Accordingly, we performed a meta-analysis to provide new evidence that SNPs in the TNFα gene promoter region alter not only the risk of psoriasis vulgaris (PsV) or psoriatic arthritis (PsA) but also of PsV&PsA. Methods Interrelated literature dated to October 2012 was acquired from the PubMed, ScienceDirect, and SpringerLink databases. The number of the genotypes and/or alleles for the TNFα promoter in the PsV and PsA and control subjects was obtained. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to calculate the risk of PsV and/or PsA with TNFα promoter SNPs. Results A total of 26 papers of 2159 for PsV (2129 normal controls) and 2360 for PsA (2997 normal controls) were included in our meta-analysis. The results showed that the variant genotype and allele of TNFα -308A/G was protective in pooled groups of patients with PsV&PsA (OR = 0.682, 0.750; 95% CI, 0.596-0.779, 0.653-0.861). However, the variant genotypes and alleles of TNFα -238A/G and -857T/C had an increased risk of PsV&PsA (OR = 2.493, 2.228, 1.536, 1.486, 95% CI, 1.777-3.498, 1.628-3.049, 1.336-1.767, 1.309-1.685). Moreover, the meta-analysis revealed a significant association between TNFα -238A/G and -857T/C polymorphism and PsA susceptibility (OR = 2.242, 2.052, 1.419, 1.465; 95% CI, 1.710-2.941, 1.614-2.610, 1.214-1.658, 1.277-1.681). In contrast, the variant genotypes and alleles of TNFα -308A/G proved to be protective against PsV (OR = 0.574, 0.650, 95% CI, 0.478-0.690, 0.556-0.759), whereas TNFα -238A/G was found to have a risk association (OR = 2.636, 2.223, 95% CI, 1.523-4.561, 1.317-3.751). Conclusions SNPs in the TNFα gene promoter region alter the risk of PsV and/or PsA.
A New General Method to Generate Random Modal Formulae for Testing Decision Procedures

The recent emergence of heavily-optimized modal decision procedures has highlighted the key role of empirical testing in this domain. Unfortunately, the introduction of extensive empirical tests for modal logics is recent, and so far none of the proposed test generators is very satisfactory. To cope with this fact, we present a new random generation method that provides benefits over previous methods for generating empirical tests. It fixes and much generalizes one of the best-known methods, the random CNF? m test, allowing for generating a much wider variety of problems, covering in principle the whole input space. Our new method produces much more suitable test sets for the current generation of modal decision procedures. We analyze the features of the new method by means of an extensive collection of empirical tests.