Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network

The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution utilizes reaction templates to limit the space, but it suffers from coverage and efficiency issues. In this paper, we propose a template-free approach to efficiently explore the space of product molecules by first pinpointing the reaction center -- the set of nodes and edges where graph edits occur. Since only a small number of atoms contribute to reaction center, we can directly enumerate candidate products. The generated candidates are scored by a Weisfeiler-Lehman Difference Network that models high-order interactions between changes occurring at nodes across the molecule. Our framework outperforms the top-performing template-based approach with a 10\% margin, while running orders of magnitude faster. Finally, we demonstrate that the model accuracy rivals the performance of domain experts.
R plasmids which alter ultraviolet light-sensitivity and enhance ultraviolet light-induced mutability in Pseudomonas aeruginosa.

R plasmids pMG1, R2, R931 and pMG15 increased the survival of Pseudomonas aeruginosa exposed to ultraviolet radiation (u.v.) in the wild type, and uvr and polA mutants but did not alter the u.v. -response of a recA mutant. The R plasmid RPL11 reduced u.v. -survival in the wild type, and uvr and polA mutants but did not alter the u.v. -response of a recA host. All the plasmids enhanced the level of spontaneous and u.v. -induced back mutation (Trp+) in a trpB1 strain. The effect of sublethal concentration of sodium arsenite following u.v. -irradiation was examined. It was concluded that in strains trpB1(pMG1) and trpB1(R931), u.v. -protection is determined by a recA+-dependent, arsenite-sensitive repair pathway, whereas in strains trpB1(R2) and trpB1(pMG15), u.v. -protection is determined by a recA+-dependent, arsenite-insensitive step in DNA repair.
Thalamocortical interactions underlying visual fear conditioning in humans

Despite a strong focus on the role of the amygdala in fear conditioning, recent works point to a more distributed network supporting fear conditioning. We aimed to elucidate interactions between subcortical and cortical regions in fear conditioning in humans. To do this, we used two fearful faces as conditioned stimuli (CS) and an electrical stimulation at the left hand, paired with one of the CS, as unconditioned stimulus (US). The luminance of the CS was rhythmically modulated leading to “entrainment” of brain oscillations at a predefined modulation frequency. Steady‐state responses (SSR) were recorded by MEG. In addition to occipital regions, spectral analysis of SSR revealed increased power during fear conditioning particularly for thalamus and cerebellum contralateral to the upcoming US. Using thalamus and amygdala as seed‐regions, directed functional connectivity was calculated to capture the modulation of interactions that underlie fear conditioning. Importantly, this analysis showed that the thalamus drives the fusiform area during fear conditioning, while amygdala captures the more general effect of fearful faces perception. This study confirms ideas from the animal literature, and demonstrates for the first time the central role of the thalamus in fear conditioning in humans. Hum Brain Mapp 36:4592–4603, 2015. © 2015 Wiley Periodicals, Inc.
Graduate unemployment and Higher Education Institutions in South Africa

The emerging consensus regarding high and rising levels of graduate unemployment in South Africa in recent years has primarily been based on a select number of studies, all of which have serious shortcomings ranging from deficient definitions of “graduates” to the use of outdated, incomplete, or unrepresentative data. Moreover, given the heterogeneity in the quality of higher education in South Africa, existing findings regarding aggregate graduate unemployment in the country, even if accurate, mask the substantial variation in labour market outcomes which are likely to be faced by graduates from different higher education institutions. This paper attempts to address these issues by examining graduate unemployment and employment in South Africa with specific emphasis on the type and quality of higher education using multiple labour force survey and administrative datasets. Its primary contribution is to incorporate the effect of potential measures of higher education institution type and quality on the likelihood of graduate unemployment and employment by probabilistically linking graduates that are observed in labour force survey data to the institutions from which they are likely to have graduated given their time-invariant observable characteristics and the known demographic composition of the graduates produced by each of South Africa’s formal higher education institutions every year. The analysis shows that graduate unemployment in South Africa is not only low in relation to overall unemployment in the country, but that much of the racially-delineated differentials in graduate unemployment and employment outcomes can likely be attributed to heterogeneity in the quality and type of higher education institutions commonly attended by individuals from different racial backgrounds.
Enhanced Excitability of Primary Sensory Neurons and Altered Gene Expression of Neuronal Ion Channels in Dorsal Root Ganglion in Paclitaxel-induced Peripheral Neuropathy

Background:The mechanism of chemotherapy-induced peripheral neuropathy after paclitaxel treatment is not well understood. Given the poor penetration of paclitaxel into central nervous system, peripheral nervous system is most at risk. Methods:Intrinsic membrane properties of dorsal root ganglion neurons were studied by intracellular recordings. Multiple-gene real-time polymerase chain reaction array was used to investigate gene expression of dorsal root ganglion neuronal ion channels. Results:Paclitaxel increased the incidence of spontaneous activity from 4.8 to 27.1% in large-sized and from 0 to 33.3% in medium-sized neurons. Paclitaxel decreased the rheobase (nA) from 1.6 ± 0.1 to 0.8 ± 0.1 in large-sized, from 1.5 ± 0.2 to 0.6 ± 0.1 in medium-sized, and from 1.6 ± 0.2 to 1.0 ± 0.1 in small-sized neurons. After paclitaxel treatment, other characteristics of membrane properties in each group remained the same except that A&dgr; neurons showed shorter action potential fall time (ms) (1.0 ± 0.2, n = 10 vs. 1.8 ± 0.3, n = 9, paclitaxel vs. vehicle). Meanwhile, real-time polymerase chain reaction array revealed an alteration in expression of some neuronal ion channel genes including up-regulation of hyperpolarization-activated cyclic nucleotide-gated channel 1 (fold change 1.76 ± 0.06) and Nav1.7 (1.26 ± 0.02) and down-regulation of Kir channels (Kir1.1, 0.73 ± 0.05, Kir3.4, 0.66 ± 0.06) in paclitaxel-treated animals. Conclusion:The increased neuronal excitability and the changes in gene expression of some neuronal ion channels in dorsal root ganglion may provide insight into the molecular and cellular basis of paclitaxel-induced neuropathy, which may lead to novel therapeutic strategies.
CHEMICAL STUDIES ON EXPERIMENTAL ALLERGIC ENCEPHALOMYELITIS

THE chemistry and immunology of experimental allergic encephalomyelitis (‘EAE’) have been the subject of so much publication that a large volume would be needed now to review their history alone. It is, therefore, possible here to recapitulate only certain significant principles, which are commonly ignored. Firstly there was the evidence of KABAT, WOLF and BEZER (1947) relating the appearance of encephalitogenicity to myelinogenesis. LAATSCH, KIES, GORDON and ALVORD (1962), using an ultracentrifugation technique controlled by electron microscopy, have clearly confirmed that the active substance is related to the lamellar myelin. Chemically, the early evidence (LUMSDEN, 1949) that at least some encephalitogenic substance resisted autoclaving and treatment with formalin, alcohol, chloroform and ether, and that some was extractable with the sphingomyelin and cerebroside fraction, was overshadowed by the later enthusiasm for soluble protein, which might have been expected to be more labile. At the Bethesda symposium (KIES and ALVORD, 1959) it was widely agreed that there were three groups of EAE ‘antigens’: (i) water-soluble proteins, (ii) fat-soluble proteolipids and (iii) a water-insoluble glycoprotein or ‘collagen-like’ protein. The prevailing conclusion (see WAKSMAN, 1959) was that ‘several substances’ were responsible. If to this list were added the possibly different agents present in the ‘sphingomyelin and cerebroside’ fraction (LUMSDEN, 1949), the neurokeratin-like substances of GOLDSTEIN, KOLB, MASON, SAYRE and KARLSEN (1953) and the active material in a dialysate of brain tissue briefly reported by HOTTLE, NEDZEL, WRIGHT and BELL (1949), the range of active substances was great and their nature disparate. Moreover, little attention has been paid to the wide difference in the minimal effective dose of the different encephalitogenic agents. Thus, with highly re-purified fractions the minimal effective intradermal dose (M.E.D.) of basic protein is about 1 pg, representing 0.4 mg of wet cord tissue. The M.E. D. of the collagen-like protein prepared according to the method of ROBOZ, HENDERSON and KIES (1958) is about 0.1 mg, representing 20 mg of wet cord; that of proteolipids is as high as 1-2 mg, representing 50-100 mg of wet cord. When these doses are set against an M.E. D. * The costs of animals and technical assistance have been borne by annual grants from the Multiple Sclerosis Society with supplements from its Hull and Portsmouth Branches. t Dr Robertson’s work was done during the tenure of the Portsmouth Fellowship of the Multiple Sclerosis Society. Holder of the I. JACK LYONS Fellowship in Multiple Sclerosis, 1959-1963. Abbreviations used: BSP, basic small polypeptide; C-L, collagen-like; EAE, experimental allergic encephalitis; M.E. D, minimal effective intradermal dose; @, at a dose of (in Figs.).
Command Robots from Orbit with Supervised Autonomy: An Introduction to the Meteron Supvis-Justin Experiment

The on-going work at German Aerospace Center (DLR) and European Space Agency (ESA) on the Meteron Supvis-Justin space telerobotic experiment utilizing supervised autonomy is presented. The Supvis-Justin experiment will employ a tablet UI for an astronaut on the International Space Station (ISS) to communicate task level commands to a service robot. The goal is to explore the viability of supervised autonomy for space telerobotics. For its validation, survey, navigation, inspection, and maintenance tasks will be commanded to DLR's service robot, Rollin' Justin, to be performed in a simulated extraterrestrial environment constructed at DLR. The experiment is currently slated for late 2015-2016.
Pathologic Changes of Cone Photoreceptors in Eyes With Occult Macular Dystrophy.

PURPOSE Occult macular dystrophy (OMD) is an inherited retinal disease characterized by a progressive decrease of vision and appearance of normal fundus. To determine the pathologic features of OMD, we investigated the alternation of the photoreceptors using quantitative image analysis. METHODS We studied 22 eyes of 11 OMD patients. Three of them had a mutation (R45W) in RP1L1. The relative intensities of the ellipsoid zone in the spectral-domain optical coherence tomography (SD-OCT) images and the density of the cone photoreceptors in the adaptive optics (AO) fundus images of the OMD patients were compared to those of normal controls. RESULTS The relative intensities of the ellipsoid zone in the SD-OCT images of patients with OMD were significantly lower (P < 0.001) by an average of 16% compared to that of the normal controls. Normal cone mosaics were not observed in the AO images of the macula in the eyes with OMD. The mean ± SD of cone density of the 9 OMD patients was 1970 ± 884 cells/mm2 at 2°, 1124 ± 483 cells/mm2 at 3°, and 1288 ± 715 cells/mm2 at 4° nasal to the fovea. The cone densities at 2°, 3°, and 4° nasal to the fovea of OMD were significantly lower than those of the normal controls (P < 0.001). CONCLUSIONS A sparse array of cone photoreceptors with significantly reduced density of the macula is one of the morphologic features of OMD.
The International Trade Effect of FDI-Analysis Based on China's Sector Data

This paper investigates whether FDI serves as a complement to trade or a substitute for trade based on the effects identified by the Rybczynski theorem. In the discussion part of theory, the paper sets up a simple specific-factor model and analyzes the relationship among initial condition of trade, the sector production and FDI in the specific sector. In the demonstration part, it uses China's sector data of FDI and volumes of trade to test the theory conclusions, and the results shows that the trade effect of FDI in all the sectors are significant, but the specific relationship between FDI and trade in China changes with the different periods.
Paediatrics Brain Imaging In Epilepsy: Common Presenting Symptoms And Spectrum Of Abnormalities Detected On MRI.

BACKGROUND Epilepsy, a common neurological disorder can present at any age and has a number of aetiologies with underlying brain disease being the most common aetiology. Brain imaging becomes important and mandatory in the work up for epilepsy in localization and lateralization of the seizure focus. METHODS This cross-sectional study was conducted in the department of Radiology Ayub Medical Teaching Institution Abbottabad from 1st March 2015 to 31st March 2016. A total of 209 children aged 28 days to 14 years were included in the study who presented with seizures to clinicians. Information obtained from history, clinical examination and investigations especially MRI brains were recorded in a prescribed pro forma. The data was analysed in SPSS 20. RESULTS MRI examination was unremarkable in 44.01% (n=92) and mild generalized brain atrophy was noted in 12.91% (n=27). Arachnoid cysts, mild unilateral brain atrophy and hydrocephalous due to aqueduct stenosis were recorded in 3.82% (n=8) of each group. Neoplastic lesions were the second most common abnormal MRI finding and constituted 5.74% (n=12). Leukodystrophy was diagnosed in 4.78% (n=10). MRI examination showed ring enhancing lesions (tuberculomas) and AVM in 1.43% (n=3) of each group. Perinatal ischemia and intracranial infection, (focal or generalized) were recorded in 2.87% (n=6) of each group. A 0.95% (n=2) of children in each group had agenesis of corpus callosum and cavernoma. The radiological MRI diagnosis of Raussmussen encephalitis was made in 3.34% (n=7). Single case, each of mesial temporal sclerosis, subdural haemorrhage, infarct and craniopharyngioma was recorded making 0.47% of the total patients in each case. CONCLUSIONS MRI examination was abnormal in significant number of patients (55.86%), so therefore if properly utilized, in a good clinical context, this can identify most of the structural brain abnormalities in paediatric patients presenting with seizures.
The prevalence of hepatitis B virus infection in the United States in the era of vaccination.

BACKGROUND Our objective was to assess trends in the prevalence of hepatitis B virus (HBV) infection in the United States after widespread hepatitis B vaccination. METHODS The prevalence of HBV infection and immunity was determined in a representative sample of the US population for the periods 1999-2006 and 1988-1994. National Health and Nutrition Examination Surveys participants 6 years of age were tested for antibody to hepatitis B core antigen (anti-HBc), hepatitis B surface antigen (HBsAg), and antibody to hepatitis B surface antigen (anti-HBs). Prevalence estimates were weighted and age-adjusted. RESULTS During the period 1999-2006, age-adjusted prevalences of anti-HBc (4.7%) and HBsAg (0.27%) were not statistically different from what they were during 1988-1994 (5.4% and 0.38%, respectively). The prevalence of anti-HBc decreased among persons 6-19 years of age (from 1.9% to 0.6%; P < .01) and 20-49 years of age (from 5.9% to 4.6%; P < .01) but not among persons 50 years of age (7.2% vs 7.7%). During 1999-2006, the prevalence of anti-HBc was higher among non-Hispanic blacks (12.2%) and persons of "Other" race (13.3%) than it was among non-Hispanic whites (2.8%) or Mexican Americans (2.9%), and it was higher among foreign-born participants (12.2%) than it was among US-born participants (3.5%). Prevalence among US-born children 6-19 years of age (0.5%) did not differ by race or ethnicity. Disparities between US-born and foreign-born children were smaller during 1999-1996 (0.5% vs 2.0%) than during 1988-1994 (1.0% vs 12.8%). Among children 6-19 years of age, 56.7% had markers of vaccine-induced immunity. CONCLUSIONS HBV prevalence decreased among US children, which reflected the impact of global and domestic vaccination, but it changed little among adults, and approximately 730,000 US residents (95% confidence interval, 550,000-940,000) are chronically infected.
Relationship of eggshell ultrastructure and shell strength to the soundness of shell eggs.

Factors affecting the soundness of shell eggs are of primary concern to egg processors due to substantial financial losses from cracked and leaker eggs. Ultrastructural analyses were used to examine the palisade layer width and mammillary knob layer thickness of sound, cracked, and leaker eggshells. Subjective observations were also made. There was no significant difference (P > 0.05) in the width of the palisade layer or the mammillary knob layer among sound, cracked, and leaker eggshells. The eggshell strengths of sound, cracked, and leaker eggs were evaluated using puncture force and shell thickness measurements. Sound eggshells were found to have a significantly (P < 0.05) higher mean puncture force (35.3 N) than cracked (30.4 N) and leaker (28.4 N) eggshells. The mean puncture force values for cracked and leaker eggshells were not significantly different from each other (P > 0.05). Regression and correlation analyses indicated a significant correlation (P < 0.01; r = 0.61) between palisade layer width and puncture force. The mean shell thickness values for cracked (0.36 mm) and leaker (0.35 mm) eggs were significantly lower (P < 0.05) than those of sound eggs (0.38 mm), although cracked and leaker eggshell thickness did not differ significantly (P > 0.05). The correlation coefficient between puncture force and shell thickness was significant (P < 0.01; r = 0.56), indicating a possible relationship.
400 000 Observations on Inflation Perceptions and Expectations in the EU What Will They Tell Us

The ability to accurately measure inflation expectations is more than of an academic interest; it is an integral part of central bank policy. According to the present approach to monetary policy making, founded on inflation targeting, central banks should be forward-looking, framing their policies today on basis of forecasts of the future rate of inflation one to two years ahead. This approach requires access to reliable and frequently reported data on inflationary expectations of the public. Furthermore, expectations about the future course of the price level are important to decision-makers in all markets: for goods, labour, money, financial assets and currencies. Decisions on these markets determine the actual rate of inflation, nominal wage rates, interest rates, exchange rates as well as real variables such as the rate of unemployment. Expectations actually determine all types of economic behaviour, as human action is forward-looking. Such information, however, is difficult to compile for the simple reason that inflationary expectations are not directly measurable in a way similar to variables such as interest rates, monetary aggregates, rates of unemployment, consumer and producer prices etc. The expectations of the future behaviour of prices are held by individuals in their minds. To measure them in a representative way is a major challenge for economists and for policy-makers.
Physicians' opinions about medications to treat alcoholism.

AIMS Medications play a limited role in the treatment of alcoholism. This paper examines physicians' opinions about and use of two alcoholism medications currently approved in the US--disulfiram and naltrexone--and one alcoholism medication--acamprosate--that might be approved. DESIGN A total of 1388 substance abuse specialist physicians who were members of the American Academy of Addiction Psychiatry or the American Society of Addiction Medicine completed a questionnaire in 2001 (65% response rate). FINDINGS The average percentages of physicians' patients with alcoholism who were prescribed the following medications were: 13% (naltrexone), 9% (disulfiram), 46% (antidepressants) and 11% (benzodiazepines). Almost all physicians had heard of naltrexone and disulfiram, but their self-reported level of knowledge about these medications was lower than for antidepressants. Physicians estimated that naltrexone had a small-to-medium effect size, which was similar in magnitude to the effect size reported in recent meta-analyses of randomized clinical trials. Physicians identified the following three courses of action as the most likely to result in greater use of medications to treat alcohol dependence: more research to develop new medications (33%), more education of physicians about existing medications (17%), and increased involvement of physicians in alcoholism treatment (17%). CONCLUSIONS Physicians' low rate of use of naltrexone may reflect its small-to-medium effect size.
Residential water demand analysis of a Low‐Income Rate Assistance Program in California, United States

This paper presents a statistical analysis of residential water demand in a Low‐Income Rate Assistance (LIRA) Program. A comparison of 10 years of monthly household level water use data (2002–2011) for LIRA versus non‐LIRA customers revealed significant differences in water use patterns in four of the five study cities. In addition, seasonal index (averages summer versus winter water use) were investigated for LIRA versus non‐LIRA. There was a statistically significant difference for some cities; however, the level of difference was not large enough to conclusively demonstrate an outstanding difference between the two groups. Finally, the peaking factor approach coupled with the statistical modelling of demand elaborated in this paper will provide a more realistic way of representing residential water demand variations in system performance assessment/evaluations.
xIAP Induces Cell-Cycle Arrest and Activates Nuclear Factor-&kgr;B: New Survival Pathways Disabled by Caspase-Mediated Cleavage During Apoptosis of Human Endothelial Cells

Abstract— Survival of human vascular endothelial cells depends on their ability to activate the transcription factor nuclear factor-&kgr;B (NF-&kgr;B), a regulator of antiapoptotic genes, such as the X chromosome–linked inhibitor of apoptosis protein (xIAP). In the present study, we demonstrated expression of xIAP in the endothelial lining of normal human arteries and veins and elevated levels in highly malignant human endothelial tumors. Using retroviral infection of human endothelial cells, we identified two novel survival mechanisms mediated by xIAP in endothelial cells. First, xIAP can activate the transcription factor NF-&kgr;B, a known survival factor for human endothelial cells. This positive feedback loop induced by xIAP is mediated via phosphorylation and sustained degradation of inhibitor (I) &kgr;B&agr;. Second, xIAP can inhibit cell proliferation via downregulation of cyclins A and D1 and induction of the cyclin-dependent kinase inhibitors p21Cip1/Waf1 and p27Kip1. Cleavage of xIAP by caspases during endothelial cell apoptosis disables both of these biological functions of xIAP. Thus, caspase-mediated cleavage of xIAP interrupts a positive regulatory cytoprotective loop between NF-&kgr;B and xIAP and increases the vulnerability of the cell to apoptosis by releasing it from an xIAP-mediated quiescent state.