Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of the Progression of Cryptococcal Meningitis on Brain Penetration and Efficacy of AmBisome in a Murine Model

Background: AmBisome is a small unilamellar vesicle containing amphotericin B. AmBisome is generally unable to pass through the blood-brain barrier, but the distribution of AmBisome in the brain is increased by inflammation, and in consequence, AmBisome exhibits activity against fungal meningitis. We investigated the influence of the progression of cryptococcal meningitis on the brain penetration and efficacy of AmBisome. Method: Mice were infected intracerebroventricularly with Cryptococcus neoformans 4 h or 5 days prior to a single dose treatment. Results: The brain tissue level and efficacy of AmBisome when administered 5 days after infection were greater than 4 h after infection. An immunohistochemical study showed that AmBisome-derived amphotericin B was localized at the infected site in the subarachnoid space. When AmBisome was compared with Fungizone at the maximum tolerated dose, 10 mg/kg AmBisome exhibited greater efficacy than 1 mg/kg Fungizone in both regimens. Conclusion: The brain penetration of AmBisome was enhanced by the progression of cryptococcal meningitis and correlated with the in vivo activity.
Cascaded 3D Full-Body Pose Regression from Single Depth Image at 100 FPS

There are increasing real-time live applications in virtual reality, where it plays an important role in capturing and retargetting 3D human pose. But it is still challenging to estimate accurate 3D pose from consumer imaging devices such as depth camera. This paper presents a novel cascaded 3D full-body pose regression method to estimate accurate pose from a single depth image at 100 fps. The key idea is to train cascaded regressors based on Gradient Boosting algorithm from pre-recorded human motion capture database. By incorporating hierarchical kinematics model of human pose into the learning procedure, we can directly estimate accurate 3D joint angles instead of joint positions. The biggest advantage of this model is that the bone length can be preserved during the whole 3D pose estimation procedure, which leads to more effective features and higher pose estimation accuracy. Our method can be used as an initialization procedure when combining with tracking methods. We demonstrate the power of our method on a wide range of synthesized human motion data from CMU mocap database, Human3.6M dataset and real human movements data captured in real time. In our comparison against previous 3D pose estimation methods and commercial system such as Kinect 2017, we achieve the state-of-the-art accuracy.
Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

In the era of personalized medical practice, understanding the genetic basis of patient-specific adverse drug reaction (ADR) is a major challenge. Clozapine provides effective treatments for schizophrenia but its usage is limited because of life-threatening agranulocytosis. A recent high impact study showed the necessity of moving clozapine to a first line drug, thus identifying the biomarkers for drug-induced agranulocytosis has become important. Here we report a methodology termed as antithesis chemical-protein interactome (CPI), which utilizes the docking method to mimic the differences in the drug-protein interactions across a panel of human proteins. Using this method, we identified HSPA1A, a known susceptibility gene for CIA, to be the off-target of clozapine. Furthermore, the mRNA expression of HSPA1A-related genes (off-target associated systems) was also found to be differentially expressed in clozapine treated leukemia cell line. Apart from identifying the CIA causal genes we identified several novel candidate genes which could be responsible for agranulocytosis. Proteins related to reactive oxygen clearance system, such as oxidoreductases and glutathione metabolite enzymes, were significantly enriched in the antithesis CPI. This methodology conducted a multi-dimensional analysis of drugs' perturbation to the biological system, investigating both the off-targets and the associated off-systems to explore the molecular basis of an adverse event or the new uses for old drugs.
Evaluation of antidepressant-like effects of aqueous and ethanolic extracts of Pimpinella anisum fruit in mice

Objective: Pimpinella anisum (P. anisum) has different pharmacological properties such as anticonvulsant, analgesic, tranquilizer, antidepressant and anti-anxiety effects. In this study the antidepressant-like effect of aqueous and ethanolic extracts of P. anisum fruit in mice was investigated. Materials and Methods: Forced swimming test (FST) and tail suspension test (TST) were used to determine the antidepressant effects of P. anisum (50, 100 and 200 mg/kg, i.p.) fruit extracts. Fluoxetine (20 mg/kg, i.p.) and imipramine (30 mg/kg, i.p.) were used as standard drugs. Results: All the three doses of aqueous and ethanolic extracts (except 50 mg/kg of aqueous extract in FST) significantly and dose-dependently reduced the immobility times in both FST and TST. All doses of extracts increased the swimming time dose-dependently, without any significant change in climbing time. In addition, all doses of ethanolic extract reduced immobility times and increased swimming time insignificantly higher than aqueous extract. But, the two extracts decreased the duration of climbing time similarly. Fluoxetine and imipramine decreased immobility time in both tests. Fluoxetine increased the swimming time without modifying climbing time. In contrast, imipramine increased climbing time without any significant change in swimming time. Conclusion: The results of this study suggest that P. anisum possesses an antidepressant-like activity similar to that of fluoxetine, which has a potential clinical value for application in the management of depression.
Predominance and Persistence of a Single Clone of Listeria ivanovii in a Manchego Cheese Factory Over 6 Months

In an attempt to study the diversity and persistence of molecular subtypes of pathogenic Listeria spp. in a cheese factory at the La Mancha region of Spain, 43 samples were taken from incoming raw milk (cow’s, ewe’s, goat’s and mixed species) and from certain food‐contact and environmental surfaces before and/or after sanitation. Of these samples, 12 contained pathogenic Listeria. From the chromogenic agar plates corresponding to those, 46 phosphatidylinositol‐specific phospholipase C‐positive isolates were randomly taken for further analysis, including biochemical tests and pulsed‐field gel electrophoresis (PFGE). They coincided in identifying all the 46 as Listeria ivanovii subsp. ivanovii, apparently a single PFGE type. Both ewe’s and goat’s raw milk batches from asymptomatic animals tested along the 6‐month period persistently carried the same strain, which was also obtained from inner surfaces of raw milk truck tanks and the milk dump tank at the cheese factory. Biofilm‐forming abilities of this L. ivanovii clone and interference against L. monocytogenes Scott A reference strain were tested, but failed to account for the clone’s apparent pervasive presence.
Optical coherence tomography.

This paper gives an introduction to optical coherence tomography (OCT), explains its basic principles, and discusses the information content of OCT images. Various interferometric techniques used in OCT are reviewed and a short survey of results obtained so far in different fields of application and possible future developments are presented.
Black Soldier Fly (Diptera: Stratiomyidae) Larvae Reduce Escherichia coli in Dairy Manure

Abstract Escherichia coli labeled with a green fluorescent protein was inoculated into sterile dairy manure at 7.0 log cfu/g. Approximately 125 black soldier fly larvae were placed in manure inoculated and homogenized with E. coli. Manure inoculated with E. coli but without black soldier fly larvae served as the control. For the first experiment, larvae were introduced into 50, 75, 100, or 125 g sterilized dairy manure inoculated and homogenized with E. coli and stored 72 h at 27°C. Black soldier fly larvae significantly reduced E. coli counts in all treatments. However, varying the amount of manure provided the black soldier fly larvae significantly affected their weight gain and their ability to reduce E. coli populations present. For the second experiment, larvae were introduced into 50 g manure inoculated with E. coli and stored for 72 h at 23, 27, 31, or 35°C. Minimal bacterial growth was recorded in the control held at 35°C and was excluded from the analysis. Black soldier fly larvae significantly reduced E. coli counts in manure held at remaining temperatures. Accordingly, temperature significantly influenced the ability of black soldier fly larvae to develop and reduce E. coli counts with greatest suppression occurring at 27°C.
Comparative Analysis of Internal and External-Hex Crown Connection Systems - A Finite Element Study

The abutment connection with the crown is fundamental to the structural stability of the implant system and to the prevention of mechanical exertion that can compromise the success of the implant treatment. The aim of this study is to clarify the difference in the stress distribution patterns between implants with internal and external-hex connections with the crown using the Finite Element Method (FEM). Material and Methods: The internal and external-hex connections of the Neoss and 3i implant systems respectively, are considered. The geometrical properties of the implant systems are modeled using three-dimensional (3D) brick elements. Loading conditions include a masticatory force of 200, 500 and 1000N applied to the occlusal surface of the crown along with an abutment screw torque of 110, 320 and 550Nmm. The von Mises stress distributions in the crown are examined for all loading conditions. Assumptions made in the modeling include: 1. half of the implant system is modeled and symmetrical boundary conditions applied; 2. temperature sensitive elements are used to replicate the torque within the abutment screw. Results: The connection type strongly influences the resulting stress characteristics within the crown. The magnitude of stress produced by the internal-hex implant system is generally lower than that of the external-hex system. The internal-hex system held an advantage by including the use of an abutment between the abutment screw and the crown. Conclusions: The geometrical design of the external-hex system tends to induce stress concentrations in the crown at a distance of 2.89mm from the apex. At this location the torque applied to the abutment screw also affects the stresses, so that the compressive stresses on the right hand side of the crown are increased. The internal-hex system has reduced stress concentrations in the crown. However, because the torque is transferred through the abutment screw to the abutment contact, changing the torque has greater effect on this hex system than the masticatory force. Overall the masticatory force is more influential on the stress within the crown for the external-hex system and the torque is more influential on the internal-hex system.
Extending Typestate Checking Using Conditional Liveness Analysis

The authors present a practical extension to typestate checking, which is capable of proving programs free of uninitialized variable errors even when these programs contain conditionally initialized variables where the initialization of a variable depends upon the equality of one or more tag variables to a constant. The user need not predeclare the relationship between a conditionally initialized variable and its tags, and this relationship may change from one point in the program to another. The technique generalizes liveness analysis to conditional liveness analysis. Like typestate checking, this technique incorporates a dataflow analysis algorithm in which each point in a program is labeled with a lattice point describing statically tracked information, including the initialization of variables. The labeling is then used to check for programming errors such as referencing a variable which may be uninitialized. >
An integrated performance data collection, analysis, and visualization system

The lack of tools to observe the operation and performance of message-based parallel architectures limits the user's ability to e ectively optimize application and system performance. Performance data collection, analysis, and visualization tools are needed to manage the complexity and quantity of performance data. Furthermore, these tools must be integrated with the machine hardware, the system software, and the applications support software if they are to nd pervasive use in program development and experimentation. In this paper, we describe an integrated performance environment being developed for the Intel iPSC/2 hypercube. The data collection components of the environment include software event tracing at the operating system and program levels plus a hardware-based performance monitoring system used to unobtrusively capture software events. A visualization system, based on the X window system, permits the performance analyst to browse and explore interesting data components by dynamically interconnecting new performance displays and data analysis tools.
Regulation of Mitogen-Activated Protein Kinases by Sphingolipid Products in Oligodendrocytes

Sphingolipid products such as ceramide (cer), sphingosine (sph), and sphingosine-1-phosphate (SPP) are implicated in the regulation of cell growth and apoptosis. We have recently shown that cer, sph, and SPP differentially modulate ionic events in cultured oligodendrocytes (OLGs). Cer but not sph or SPP inhibits the inward rectifier (IKir) in OLGs. To further investigate the role of sphingolipid products in OLGs, we studied the effect of cer, sph, and SPP on OLG survival and on the regulation of mitogen-activated protein kinases (MAPKs). We found that cer, sph, and SPP differentially modulate OLG survival and activation of MAPK members. Cer causes OLG apoptosis, sph causes OLG lysis, and SPP does not affect OLG survival. Cer induces a preferential activation of p38α, whereas sph and SPP induce a preferential activation of extracellular signal-regulated kinase 2 (ERK2) in OLGs. In addition, the effect of cer on p38α activity is mimicked by the inhibition of IKir with Ba2+. In contrast, exposure to cer results in increased activity of ERK2 but not of p38α in astrocytes. Cer-induced OLG apoptosis is attenuated by a p38 inhibitor, SB203580, and by expression of a p38α dominant negative mutant. We conclude that p38α is the mediator in cer-induced OLG apoptosis and that cer-induced IKir inhibition may contribute to the sustained activation of p38α in OLGs.
A comparison between FUV remote sensing of magnetotail stretching and the T01 model during quiet conditions and growth phases

In a previous study, Blockx et al. (2005) showed that the SI12 camera on board the IMAGE spacecraft is an excellent tool to remotely determine the position of the isotropy boundary (IB) in the ionosphere, and thus is able to provide a reasonable estimate of the amount of stretching of the magnetic field lines in the magetotail. By combining an empirical model of the magnetospheric configuration with Sergeev's criterion for non-adiabatic motion, it is also possi- ble to obtain a theoretical position of IB in the ionosphere, for known conditions in the solar wind. Earlier studies have demonstrated the inadequacy of the Tsyganenko-1989 (T89) model to quantitatively reproduce the field line stretching, particularly during growth phases. In this study, we reexam- ine this question using the T01 model which considers the time history of the solar wind parameters. We compare the latitude of IB derived from SI12 global images near local midnight with that calculated from the T01 model and the Sergeev's criterion. Observational and theoretical results are found to frequently disagree. We use in situ measurements of the magnetic field with the GOES-8 satellite to discrimi- nate which of the two components in the calculation of the theoretical position of the IB (the T01 model or Sergeev's criterion) induces the discrepancy. For very quiet magnetic conditions, we find that statistically the T01 model approxi- mately predicts the correct location of the maximum proton precipitation. However, large discrepancies are observed in individual cases, as demonstrated by the large scatter of pre- dicted latitudes. For larger values of the AE index, the model fails to predict the observed latitude of the maximum pro- ton intensity, as a consequence of the lack of consideration of the cross-tail current component which produces a more elongated field configuration at the location of the proton in- jection along the field lines. We show that it is possible to match the observed location of the maximum proton precip- itation by decreasing the current sheet half-thickness D pa- rameter. We thus conclude that underestimation of the field line stretching leads to inadequately prediction of the bound- ary latitude of the non-adiabatic proton precipitation region.
Fully Delexicalized Contexts for Syntax-Based Word Embeddings

Word embeddings induced from large amounts of unannotated text are a key resource for many NLP tasks. Several recent studies have proposed extensions of the basic distributional semantics approach where words form the context of other words, adding features from e.g. syntactic dependencies. In this study, we look in a different direction, exploring models that leave words out entirely, instead basing the context representation exclusively on syntactic and morphological features. Remarkably, we ﬁnd that the resulting vectors still capture clear semantic aspects of words in addition to syntactic ones. We assess the properties of the vectors using both intrinsic and extrinsic evaluations, demonstrating in a multilingual parsing experiment using 55 treebanks that fully delexicalized syntax-based word representations give a higher average parsing performance than conventional word2vec embeddings.
Case–Control Study of the Metabolic Syndrome and Metabolic Risk Factors for Endometrial Cancer

Background: Metabolic syndrome may predict endometrial cancer risk better than diabetes, hypertension, dyslipidemia, dysglycemia, or weight alone, but few studies have examined this issue. Methods: We conducted a population-based case–control study in Alberta, Canada (2002–2006) that included 515 incident endometrial cancer cases and 962 frequency age-matched controls. Data were collected through in-person interviews, anthropometric measurements, and 8-hour fasting bloods drawn either pre- or postsurgery. Bloods were analyzed using quantitative colorimetric or absorbance-based assays (ELISA), specific to metabolic syndrome markers. Metabolic syndrome was defined using harmonized guidelines requiring presence of ≥3 of the following risk factors: waist circumference ≥88 cm, triglycerides ≥150 mg/dL, high-density lipoprotein cholesterol <50 mg/dL, treatment of previously diagnosed hypertension, and fasting blood glucose ≥100 mg/dL. OR and 95% CIs for endometrial cancer risk with presence of metabolic syndrome and individual metabolic syndrome components were estimated using logistic regression analysis. Results: Metabolic syndrome was significantly more prevalent among cases (62%) than controls (38%). A statistically significant increased risk for endometrial cancer was observed for metabolic syndrome (OR = 1.53; 95% CI: 1.17–2.00), as well as for some of the individual components of metabolic syndrome including waist circumference ≥88 cm (OR = 1.57; 95% CI: 1.18–2.08), hypertension (OR = 1.57; 95% CI: 1.18–2.09), and fasting blood glucose ≥100 mg/dL (OR = 1.31; 95% CI: 1.03–1.67). Some evidence for effect modification by menopausal status and body mass index was also found. Conclusion: Metabolic syndrome is clearly associated with increased endometrial cancer risk. Impact: Targeting the entire metabolic syndrome may optimize endometrial cancer risk reduction. Cancer Epidemiol Biomarkers Prev; 20(11); 2384–95. ©2011 AACR.
PSATO: a Distributed Propositional Prover and its Application to Quasigroup Problems

Abstract We present a distributed/parallel prover for propositional satisfiability (SAT), called PSATO, for networks of workstations. PSATO is based on the sequential SAT prover SATO, which is an efficient implementation of the Davis –Putnam algorithm. The master–slave model is used for communication. A simple and effective workload balancing method distributes the workload among workstations. A key property of our method is that the concurrent processes explore disjoint portions of the search space. In this way, we use parallelism without introducing redundant search. Our approach provides solutions to the problems of (i) cumulating intermediate results of separate runs of reasoning programs; (ii) designing highly scalable parallel algorithms and (iii) supporting “fault-tolerant” distributed computing. Several dozens of open problems in the study of quasigroups have been solved using PSATO. We also show how a useful technique called the cyclic group construction has been coded in propositional logic.
DNA-based vaccination induces humoral and cellular immune responses against hepatitis B virus surface antigen in mice without activation of C-myc.

AIM:To develop a safe and effective DNA vaccine for inducing humoral and cellular immunological responses against hepatitis B virus surface antigen (HBsAg). METHODS:BALB/c mice were inoculated with NV-HB/s, a recombinant plasmid that had been inserted S gene of hepatitis B virus genome and could express HBsAg in eukaryotes. HBsAg expression was measured by ABC immunohis tochemical assay, generation of anti-HBs by ELISA and cytotoxic T lymphocyte (CTL), by MTT method, existence of vaccine DNA by Southern blot hybridization and activation of oncogene C-myc by in situ hybridization.RESULTS:With NV-HB/s vaccination by intramuscular injection, anti-HBs was initially positive 2 weeks after inoculation while all mice tested were HBsAg positive in the muscles.The titers and seroconversion rate of anti-HBs were steadily increasing as time went on and were dose dependent. All the mice inoculated with 100&mgr;g NV-HB/s were anti-HBs positive one month after inoculation, the titer was 1 1024 or more. The humoral immune response was similar induced by either intramuscular or intradermal injection. CTL activities were much stronger (45.26%) in NV-HB/s DNA immunized mice as compared with those (only 6%) in plasma-derived HBsAg vaccine immunized mice. Two months after inoculation, all muscle samples were positive by Southernblot hybridization for NV-HB/s DNA detection, but decreased to 25% and all were undetectable by in situ hybridiza-tion after 6 months.No oncogene C-myc activation was found in the muscle of inoculation site.CONCLUSION:NV-HB/s could generate humoral and cellular immunolo-gical responses against HBsAg that had been safely expressed in situ by NV-HB/s vaccination.