Miracle-dz/UniFAR-FTUs huggingface dataset:
An artificial backbone of hydrogens for finding the conformation of protein molecules

NMR experiments can provide distances between pairs of hydrogens of a protein molecule. The problem of identifying the coordinates of such hydrogens by exploiting the information on the distances is a Molecular Distance Geometry Problem (MDGP). In a previous work, we defined an artificial backbone of hydrogens related to the protein backbones, where a particular ordering was given to the hydrogens. This ordering allows to formulate the MDGP as a combinatorial optimization problem, to which we refer as the Discretizable MDGP (DMDGP) and that we efficiently solve by an exact algorithm, the Branch and Prune (BP) algorithm. Once the coordinates of the hydrogens have been found, the problem of finding the remaining backbone atoms (N, C and C) is another MDGP. In this short paper, we propose a simple method for solving the MDGP related to the backbone atoms N, C and C of a protein, where the coordinates of the hydrogens previously found by the BP algorithm are exploited.
CYSEP - a cyber-security processor for 10 Gbps networks and beyond

In this paper, we describe the architecture of a cyber-security processor (CYSEP) which can serve as a key module for enhancing security for high-speed networks/ systems. The CYSEP supports, at wire-speed, four major functions, namely, firewall/ intrusion detection, encryption/decryption, message authentication, and distributed denial of service (DDoS) attack protection. The CYSEP is to be implemented on an application-specific integrated circuit (ASIC) with the state-of-art CMOS 0.18-micron technology and expected to operate at 10 Gbit/s or higher, Massive parallelism and pipelining techniques are to be employed in the ASIC to achieve the 10 Gbit/s wire-speed operation.
Coffee and the Risk of Lymphoma: A Meta-analysis Article

Background: Coffee is implicated in the susceptibility to several cancers. However, the association between coffee and lymphoma remains unclear. This meta-analysis aimed to assess quantitatively the association between coffee and the incidence of lymphoma. Methods: A literature search was performed for cohort and case-control studies published using PubMed, Cochrane, and EMBASE databases. Studies were included if they reported relative ratios (RR) and corresponding 95% confidence intervals (CIs) of lymphoma with respect to coffee consumption. Pooled relative risk (RR) and its 95% confidence interval (CI) were calculated. All P values are two tailed Results: Seven studies met the inclusion criteria, which included three cohort and four case-control studies. Compared with did not or seldom drink coffee per day, being no significantly association between coffee and risk of lymphoma (pooled RR: 1.05, 95%CI: 0.89–1.23). In the subgroup analysis, no significant association between coffee and lymphoma risk was detected not only in different study types (cohort studies RR: 1.29; 95% CI, 0.92–1.80; case control studies RR: 0.99; 95% CI, 0.82–1.99) but also in different regions (Europe RR: 1.21; 95% CI: 0.99–1.47; USA RR: 0.85; 95% CI, 0.62–1.15; Asia RR: 1.08, 95% CI: 0.84–1.40) and coffee consumption status (≥4cups/d 1.03, 95% CI: 0.69–1.56; < 4cups/d RR: 1.06, 95% CI: 0.89–1.26). The funnel plot revealed no evidence for publication bias. Conclusion: There was no sufficient evidence to support coffee consumption association with the risk of lymphoma. Further well-designed large-scaled cohort studies are needed to provide conclusions that are more definitive.
Compass-Like Biped Robot Part I : Stability and Bifurcation of Passive Gaits

It is well-known that a suitably designed unpowered mechanical biped robot can «walk» down an inclined plane with a steady gait. The characteristics of the gait (e.g., velocity, step period, step length) depend on the geometry and the inertial properties of the robot and the slope of the plane. The energy required to maintain the steady motion comes from the conversion of the biped's gravitational potential energy as it descends. Investigation of such passive «natural» motions may potentially lead us to strategies useful for controlling active walking machines as well as to understand human locomotion. In this report we demonstrate the existence and the stability of symmetric and asymmetric passive gaits using a simple nonlinear biped robot model. Kinematically the robot is identical to a double pendulum (similar to the Acrobot and the Pendubot) and is able to walk with the so-called {\em compass gait}. We also identify period-doubling bifurcation in this passive gait which eventually leads to a chaotic regime for larger slopes.
Neuroimmunological Aberrations and Cerebral Asymmetry Abnormalities in Schizophrenia: Select Perspectives on Pathogenesis

Within the wide-ranging gamut of factors that comprise gene-environment interactions postulated to underlie schizophrenia, the crosstalk between environmental factors and feto-maternal immune components has been put forth as one of the important mechanisms that increase the risk towards schizophrenia in the offspring. Interestingly, immune factors have been shown to critically modulate the brain development during the prenatal stages. Moreover the past many decades, influential theoretical propositions and evidence base (albeit not unequivocally) have compellingly linked prenatal sex hormonal status to critically provoke long lasting immunological changes and subsequently affect developmental programming of cerebral asymmetry in schizophrenia. In this review, we summarize the select perspectives emphasizing the role of neuroimmunoendocrine pathways in anomalous cerebral asymmetry in contemporary understanding of schizophrenia pathogenesis.
Towards Microeconomic Resource Sharing in End System Multicast Networks Based on Walrasian General Equilibrium

We have designed a competitive economical mechanism for application level multicast in which a number of independent services are provided to the end‐users by a number of origin servers. Each offered service can be thought of as a commodity and the origin servers and the users who relay the service to their downstream nodes can thus be thought of as producers of the economy. Also, the end‐users can be viewed as consumers of the economy. The proposed mechanism regulates the price of each service in such a way that general equilibrium holds. So, all allocations will be Pareto optimal in the sense that the social welfare of the users is maximized.
DISCOVERY OF AN UNDESCRIBED PROTOSTRONGYLID NEMATODE FROM THE ENDANGERED PAMPAS DEER (OZOTOCEROS BEZOARTICUS CELER) IN ARGENTINA

Dorsal-spined protostrongylid nematode larvae (Metastrongyloidea: Protostrongylidae) were recovered from the feces of the endangered pampas deer (Ozotocerus bezoarticus celer) in Campos del Tuyú Wildlife Reserve, Bahia Samborombón, Argentina. Partial DNA sequences from the large subunit ribosomal RNA (LSU rRNA) gene and from the second internal transcribed spacer region (ITS2) were amplified, cloned, sequenced, and compared to those of other nematodes. Nucleotide alignment and phylogenetic analysis of the sequences indicate that this protostrongylid nematode is most closely related to Parelaphostrongylus spp. as inferred from the LSU rRNA sequence analysis. Analysis of the ITS2 spacer indicated that the pampas deer protostrongylid is nested in a clade containing Parelaphostrongylus and Elaphostrongylus spp. These sequences differed considerably from those of other protostrongylid nematodes, and were most similar to those of Parelaphostrongylus spp. and Elaphostrongylus spp. in spite of clear variability from both genera. These results suggest that the protostrongylid from pampas deer is an undescribed nematode that likely belongs in the subfamily Elaphostrongylinae.
Quickly generating billion-record synthetic databases

Evaluating database system performance often requires generating synthetic databases—ones having certain statistical properties but filled with dummy information. When evaluating different database designs, it is often necessary to generate several databases and evaluate each design. As database sizes grow to terabytes, generation often takes longer than evaluation. This paper presents several database generation techniques. In particular it discusses: (1) Parallelism to get generation speedup and scaleup. (2) Congruential generators to get dense unique uniform distributions. (3) Special-case discrete logarithms to generate indices concurrent to the base table generation. (4) Modification of (2) to get exponential, normal, and self-similar distributions. The discussion is in terms of generating billion-record SQL databases using C programs running on a shared-nothing computer system consisting of a hundred processors, with a thousand discs. The ideas apply to smaller databases, but large databases present the more difficult problems.
Toward Evaluating the Usefulness of Global Illumination for Novices in Lighting Design Tasks – Supplemental Material

Our interactive global illumination solution is based on the Direct-to-Indirect Transfer (DTIT) algorithm [1]. In this section, we describe the differences of our solution from the original algorithm. Please refer to the original paper for more details. Hašan et al. encode the light transfer from gather samples to view samples using three matrices (the multibounce matrix, and the final gather matrices for the diffuse and glossy components). Instead of this separation, our solution uses the ‘one-pass formulation’ of the DTIT algorithm as described in Section 3.3 of the original paper. That is to say, we encode the light transfer using a single matrix T:
Molecular Gas and Star Formation in the Nucleus of IC 342: C18O and Millimeter Continuum Imaging

We present high-resolution maps (~2'') maps of the J = 1-0 and J = 2-1 transitions of C18O in the central ~150 pc of the gas-rich nucleus, IC 342, made with the Owens Valley Millimeter Array. From the C18O maps, we are able to obtain the most accurate map of N to date for IC 342. Because of their low opacities, the transitions of C18O give a more reliable estimate of the true molecular gas column-density distribution than the more common 12CO and 13CO isotopomers. The morphology of the C18O emission in the nucleus is a minispiral similar to that of the main isotopomer, 12CO, except that it is more symmetric and lacks the enhancements to the north. We suggest that the asymmetries present in 12CO images may reflect the viewing perspective of the starburst region biased by the high optical depths of 12CO rather than true asymmetries in the amount of molecular gas present. The giant molecular clouds seen in C18O appear to be nonspherical, probably because of tidal arm shearing. Column densities determined from C18O observations, 1.3 mm dust continuum, and the virial theorem indicate that the standard Galactic conversion factor, XCO, overestimates the amount of molecular gas in the center of IC 342 by a factor of ~2-3 at the molecular cloud peaks and by more than this in the diffuse gas away from the starburst. Revised molecular masses based on this conversion factor imply that star formation efficiencies in the starburst region are very high. From the distribution of gas and star formation, it appears that the sites of star formation are dynamically determined rather than driven by density peaks. Near the central star-forming region, evidence is seen for chemical enrichment of C18O caused by massive stars.
The role of organizational climate and culture in service encounters

THE ROLE OF ORGANIZATIONAL CLIMATE AND CULTURE IN SERVICE ENCOUNTERS by BETH A. HEYART May 2011 Advisor: Dr. Matthew Seeger Major : Communication Degree: Doctor of Philosophy This study explored the link between culture and climate with res pect to customer service ratings. Two hospital units, one with high customer service ratings a d one with low customer service ratings, were identified for analysis. A mixed-met hod design was implemented to assess climate and culture on each unit. Climate was assessed with a survey that combined elements of Schneider, White, and Paul’s (1998) Assessment of Service Climate I nstrument and Litwin and Stringer’s (1968) Organizational Climate Questionnaire. An ethnogra phic approach using observation, interviews and archival data analysis was completed to understand each unit’s culture. Findings indicate high customer service environments rated the factors of warmth, identity, customer orientation and global service climate more fav orably. In addition, ethnographic elements within high service environments include the Nat ure of Time, Assumptions of Human Relationship, and values as discussed by Schein (1985). All these factors help to create and perpetuate a climate and culture of high service
Determinants of Land Tenure Contracts; Theory and Evidence from Rural India

In this paper we analyze the factors that affect the choice of land tenure contracts in the semi arid tropics of India. We develop a dynamic principal-agent model with one-sided private information to explain the co-existence of wage, rent and share-cropping contracts. We generate empirically testable hypotheses about how multiple contracts can co-exist and we identify household and plot level characteristics that explain such co-existence. Using plot level data from three Indian villages we find that increasing the age of the head of the cultivating household and the value of the plot under cultivation increases the probability that the plot is under tenant cultivation (i.e. cultivated under a share or rent contract).
The design of an OCL query-based debugger for C++

In this paper, we describe an approach to query-based debugging for C + + programs tha t uses queries formulated in the object constraint language, OCL. By using OCL, together with UML, to formulate queries, debugging can begin early in the design phase. Queries can be formulated to verify design constraints such as invariants on classes and pre and post-condit ions for member functions. These queries can be reused after code generation to verify the design contract, as par t of the test ing process, and to facilitate fault detection.
Visual comfort assessment for stereoscopic 3D images based on salient discomfort regions

We propose visual comfort assessment for stereoscopic 3D (S3D) images based on salient discomfort regions. Color-based saliency successfully represents visual attention because that the human visual system (HVS) focuses on the most salient region in an image. Disparity-based saliency effectively expresses visual comfort in S3D images. Based on two saliencies, we extract salient discomfort regions which mostly determine the overall visual comfort degree in S3D images. Then, we predict the visual comfort score from salient discomfort regions by a disparity feature vector which combines saliency-weighted disparity and maximum disparity. Finally, we provide visual comfort index maps of S3D images based on visual comfort scores, thus showing perceptually salient discomfort regions and their degrees. Experimental results demonstrate that the proposed method achieves significantly high accuracy in visual comfort assessment as compared to existing methods.
Self-testing 1 Learners' Choices and Beliefs about Self-testing

Students have to make scores of practical decisions when they study. We investigated the effectiveness of, and beliefs underlying, one such practical decision: the decision to test oneself while studying. Using a flashcards-like procedure, participants studied lists of word pairs. On the second of two study trials, participants either saw the entire pair again (pair mode) or saw the cue and attempted to generate the target (test mode). Participants were either asked to rate the effectiveness of each study mode (Experiment 1) or to choose between the two modes (Experiment 2). The results demonstrated a mismatch between metacognitive beliefs and study choices: Participants (incorrectly) judged that the pair mode resulted in the most learning, but chose the test mode most frequently. A post-experimental questionnaire suggested that self-testing was motivated by a desire to diagnose learning rather than a desire to improve learning.
Local Neurosteroid Production in the Hippocampus: Influence on Synaptic Plasticity of Memory

In neuroendocrinology, it is believed that steroid hormones are synthesized in the gonads and/or adrenal glands, and reach the brain via the blood circulation. In contrast to this view, we are in progress of demonstrating that estrogens and androgens are also synthesized locally by cytochrome P450s in the hippocampus, and that these steroids act rapidly to modulate neuronal synaptic plasticity. We demonstrated that estrogens were locally synthesized in the adult hippocampal neurons. In the pathway of steroidogenesis, cholesterol is converted to pregnenolone (by P450scc), dehydroepiandrosterone [by P450(17α)], androstenediol (by 17β-hydroxysteroid dehydrogenase, 17β-HSD), testosterone (by 3β-HSD) and finally to estradiol (by P450arom) and dihydrotestosterone (by 5α-reductase). The basal concentration of estradiol in the hippocampus was approximately 1 nM, which was greater than that in blood plasma. Significant expression of mRNA for P450scc, P450(17α), P450arom, 17β-HSD, 3β-HSD and 5α-reductase was demonstrated by RT-PCR. Their mRNA levels in the hippocampus were 1/200–1/5,000 of those in the endocrine organs. Localization of P450(17α) and P450arom was observed in synapses in addition to endoplasmic reticulum of principal neurons using immunoelectron microscopy. Different from slow action of gonadal estradiol which reaches the brain via the blood circulation, hippocampal neuron-derived estradiol may act locally and rapidly within the neurons. For example, 1 nM 17β-estradiol rapidly enhanced the long-term depression (LTD) not only in CA1 but also in CA3 and dentate gyrus. The density of thin spines was selectively increased within 2 h upon application of 1 nM estradiol in CA1 pyramidal neurons. Only ERα agonist propyl-pyrazole-trinyl-phenol induced the same enhancing effect as estradiol on both LTD and spinogenesis in the CA1. ERβ agonist hydroxyphenyl-propionitrile suppressed LTD and did not affect spinogenesis. Localization of estrogen receptor ERα in spines in addition to nuclei of principal neurons implies that synaptic ERα can drive rapid modulation of synaptic plasticity by endogenous estradiol.
HieNet architecture using the K-Iterations Fast Learning artificial Neural Networks

This paper proposes a hierarchical architecture, HieNet, that utilizes the K-Iterations Fast Learning artificial Neural Network (KFLANN). Effective in its clustering capabilities, the KFLANN is capable of providing more stable and consistent clusters that are independent data presentation sequences (DPS). Leveraging on the ability to provide more consistent clusters, the KFLANN is initially used to identify the homogeneous Feature Spaces that prepare large dimensional networks for a hierarchical organization. We illustrate how this hierarchical structure can be constructed through the recurring use of the KFLANN and support our work with experimental results.
A step-down method for correcting multiple hypothesis testing in biomedical signal processing

Multiple hypothesis testing in biomedical signal analysis and genomic signal processing has been facing a difficult dilemma regarding the adjustment of significance values. Studies that report unadjusted values may fail to control false positives. On the other hand, classical correction methods may be too conservative while handling high-dimensional variable spaces, yielding a high Type II error rate. We present a novel stepwise method for estimating the adjusted p-values in applications that require multiple hypothesis testing. The method increases the statistical power of the results by refuting the assumption of independence among variables, while keeping the probability of false positives low. It is based on the spectral decomposition of the correlation matrix, from which it is possible to obtain valuable information about the dependence levels among the variables of the problem. The method is compared to other relevant stepwise adjustment models such as Holm's step-down extension of the Bonferroni/Sidak method, the False Discovery Rate method and resampling. We illustrate the effectiveness of the method in a magnetic resonance imaging study involving progressively larger sets of variables. The results show that the proposed method is able to compute adjusted p-values that are closer to the ones obtained by resampling, at a much lower computational cost.
Common Motifs in the Response of Cereal Primary Metabolism to Fungal Pathogens are not Based on Similar Transcriptional Reprogramming

During compatible interactions with their host plants, biotrophic plant–pathogens subvert host metabolism to ensure the sustained provision of nutrient assimilates by the colonized host cells. To investigate, whether common motifs can be revealed in the response of primary carbon and nitrogen metabolism toward colonization with biotrophic fungi in cereal leaves, we have conducted a combined metabolome and transcriptome study of three quite divergent pathosystems, the barley powdery mildew fungus (Blumeria graminis f.sp. hordei), the corn smut fungus Ustilago maydis, and the maize anthracnose fungus Colletotrichum graminicola, the latter being a hemibiotroph that only exhibits an initial biotrophic phase during its establishment. Based on the analysis of 42 water-soluble metabolites, we were able to separate early biotrophic from late biotrophic interactions by hierarchical cluster analysis and principal component analysis, irrespective of the plant host. Interestingly, the corresponding transcriptome dataset could not discriminate between these stages of biotrophy, irrespective, of whether transcript data for genes of central metabolism or the entire transcriptome dataset was used. Strong differences in the transcriptional regulation of photosynthesis, glycolysis, the TCA cycle, lipid biosynthesis, and cell wall metabolism were observed between the pathosystems. However, increased contents of Gln, Asn, and glucose as well as diminished contents of PEP and 3-PGA were common to early post-penetration stages of all interactions. On the transcriptional level, genes of the TCA cycle, nucleotide energy metabolism and amino acid biosynthesis exhibited consistent trends among the compared biotrophic interactions, identifying the requirement for metabolic energy and the rearrangement of amino acid pools as common transcriptional motifs during early biotrophy. Both metabolome and transcript data were employed to generate models of leaf primary metabolism during early biotrophy for the three investigated interactions.
Firing Restrictions, Government Growth, Immigration, and the NAIRU: Evidence from Fifteen OECD Countries

Using a Phillips-type equation and annual aggregate data from 15 Organization for Economic Cooperation and Development (OECD) countries, we estimate the effects of the following policies on the ‘non‐accelerating inflation rate of unemployment’ (NAIRU): restrictions on firing, growth in government ‘productive’ expenditure, growth in social security benefits, and lax immigration policy. We consider Greece separately, but treat the other 14 countries as a fixed‐effects panel. Two effects seem to be robust to changes in the sample: restrictions on firing and growth in social security benefits raise the NAIRU.