Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins

MOTIVATION Gene expression profiling technologies can generally produce mRNA abundance data for all genes in a genome. A dearth of proteomic data persists because identification range and sensitivity of proteomic measurements lag behind those of transcriptomic measurements. Using partial proteomic data, it is likely that integrative transcriptomic and proteomic analysis may introduce significant bias. Developing methodologies to accurately estimate missing proteomic data will allow better integration of transcriptomic and proteomic datasets and provide deeper insight into metabolic mechanisms underlying complex biological systems. RESULTS In this study, we present a non-linear data-driven model to predict abundance for undetected proteins using two independent datasets of cognate transcriptomic and proteomic data collected from Desulfovibrio vulgaris. We use stochastic gradient boosted trees (GBT) to uncover possible non-linear relationships between transcriptomic and proteomic data, and to predict protein abundance for the proteins not experimentally detected based on relevant predictors such as mRNA abundance, cellular role, molecular weight, sequence length, protein length, guanine-cytosine (GC) content and triple codon counts. Initially, we constructed a GBT model using all possible variables to assess their relative importance and characterize the behavior of the predictive model. A strong plateau effect in the regions of high mRNA values and sparse data occurred in this model. Hence, we removed genes in those areas based on thresholds estimated from the partial dependency plots where this behavior was captured. At this stage, only the strongest predictors of protein abundance were retained to reduce the complexity of the GBT model. After removing genes in the plateau region, mRNA abundance, main cellular functional categories and few triple codon counts emerged as the top-ranked predictors of protein abundance. We then created a new tuned GBT model using the five most significant predictors. The construction of our non-linear model consists of a set of serial regression trees models with implicit strength in variable selection. The model provides variable relative importance measures using as a criterion mean square error. The results showed that coefficients of determination for our nonlinear models ranged from 0.393 to 0.582 in both datasets, providing better results than linear regression used in the past. We evaluated the validity of this non-linear model using biological information of operons, regulons and pathways, and the results demonstrated that the coefficients of variation of estimated protein abundance values within operons, regulons or pathways are indeed smaller than those for random groups of proteins. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Job Stress in Speech-Language Pathologists Working in Rural, Suburban, and Urban Schools: Social Support and Frequency of Interactions

CONTEMPORARY ISSUES IN COMMUNICATION SCIENCE AND DISORDERS • Volume 29 • 132–140 • Fall 2002 © NSSLHA 1092-5171/02/2902-0132 ABSTRACT: Job stress levels of speech-language pathologists (SLPs) working in rural, suburban, and urban schools were determined using a standardized inventory. The majority of SLPs (82%) rated their overall job stress levels with an overall judgement score of “barely noticeable. ” However, there were a variety of items that surfaced as chronic stressors for SLPs. The top stress items included overwhelming paperwork (82%), overwork (71%), lack of time (64%), lack of preparation time (62%), and large caseload size (55%). A Functional Social Support Scale and a Frequency of Interactions with Peers and Supervisors Scale were also administered. Regression analysis was performed on the O Job Stress in Speech-Language Pathologists Working in Rural, Suburban, and Urban Schools: Social Support and Frequency of Interactions
MERIT - The high intensity liquid mercury target experiment at the CERN PS

The MERIT experiment is a proof-of-principle test of a target system for high power proton beams to be used as front-end for a Neutrino Factory complex or a Muon Collider. The experiment took data in autumn 2007 with the fast extracted beam from the CERN Proton Synchrotron (PS) to a maximum intensity of about 30 × 1012 protons per pulse. The target system, based on a free mercury jet, allowed investigation of the interseption of a 4-MW proton beam inside a 15-T magnetic field required to capture the low-energy secondary pions as the source of the required intense muon beams. Particle detectors have been installed around the target setup to measure the secondary particle flux out of the target and probe cavitation effects in the mercury jet when exited with a beam of variable intensity. With the analysis of the data ongoing, results will be presented here that demonstrate the validity of the liquid target concept.
Mining e-contract documents to classify clauses

E-contracts begin as legal documents and end up as processes that help organizations abide by legal rules while fulfilling contract terms. As contracts are complex, their deployment is predominantly established and fulfilled with significant human involvement. One of the key difficulties with any kind of contract processing is the legal ambiguity, which makes it difficult to address any violation of the contract terms. Thus, there is a need to track clauses for the contract activities under execution and violation of clauses. This necessitates deriving clause patterns from e-contract documents and map to their respective activities for further monitoring and fulfillment of e-contracts during their enactment. In this paper, we present a classification approach to extract clause patterns from e-contract documents. This is a challenging task as activities and clauses are mostly derived from both legal and business process driven contract knowledge.
Characterization of a descending system that enables crossed group II inhibitory reflex pathways in the cat spinal cord

In the cat, stimulation of group II afferents from hindlimb muscles evokes different crossed reflex actions depending on the integrity of the spinal cord: with the cord intact, extensor motoneurons are inhibited by activation of contralateral group II afferents; after spinal transection, the same stimuli excite these neurons (crossed extension reflex). We have investigated the mechanisms underlying this descending control. To delimit the descending pathway, the effects of funicular lesions of the thoracic cord on the crossed actions on motoneurons were examined. Bilateral lesions of the dorsolateral funiculi abolished the crossed IPSPs as effectively as complete spinal section. If either dorsolateral funiculus was spared, the IPSPs remained. To examine whether serotonergic fibers were involved, the effects of agents selective for 5-hydroxytryptamine (5-HT)1A receptors were examined. After abolishing the crossed IPSPs by spinal transection, systemic administration of the 5-HT1A receptor agonist (+/-)-8-hydroxy-2-(di-n-propylamino)tetralin hydrobromide (8-OH-DPAT; 0.1-1.3 mg/kg, i.v.) restored the crossed inhibition. This effect was antagonized by the selective 5-HT1A receptor antagonist WAY-100135 (0.7-3.7 mg/kg, i.v.). The simplest explanation of these findings is that a serotonergic pathway, descending via the dorsolateral funiculi and acting via 5-HT1A receptors, is involved: with the spinal cord intact, the pathway would be tonically active and thus enable the crossed inhibition. This raises the possibility that a serotonergic pathway is involved in the selection of specific spinal reflex patterns via 5-HT1A receptors.
Towards Retinoid Therapy for Alzheimer’s Disease

Alzheimer’s disease(AD) is associated with a variety of pathophysiological features, including amyloid plaques, inflammation, immunological changes, cell death and regeneration processes, altered neurotransmission, and age-related changes. Retinoic acid receptors (RARs) and retinoids are relevant to all of these. Here we review the pathology, pharmacology, and biochemistry of AD in relation to RARs and retinoids, and we suggest that retinoids are candidate drugs for treatment of AD.
Testing reference dependence, loss aversion and diminishing sensitivity in Spanish tourism

Based on Tversky and Kahneman’s Prospect Theory, we test the existence of reference dependence, loss aversion and diminishing sensitivity in Spanish tourism. To do this, we incorporate the reference-dependent model into a Multinomial Logit Model with Random Parameters -which controls for heterogeneity- and apply it to a sample of vacation choices made by Spaniards. We
Extensive small cell lung cancer: standard and experimental treatment approaches in elderly patients.

Small cell lung cancer (SCLC) represents 15–20% of all lungcarcinomas, with a decreasing relative frequency over the lasttwo decades [1]. According to the two-stage system of theVeterans Administration Lung Cancer Group, SCLC is deﬁnedas limited stage disease (LD), when tumor is conﬁned to onehemitorax, comprising ipsilateral, mediastinal andsupraclavicular lymph nodes, and as extensive stage disease(ED), when metastases are present in the controlateral chest orat distant sites [2]. Due to the early widespread ofmicrometastases, surgery is indicated only in few selectedpatients with very limited disease. In fact, the standardtreatment for LD and ED-SCLC, is chemotherapy plusradiotherapy or chemotherapy alone, respectively. However,most patients present with clinically obvious ED, and theirmedian overall survival (OS) is only 7–12 months long, withﬁve-year survival less than 2% [3].
The X-ray afterglow of GRB 081109A: clue to the wind bubble structure

We present the prompt Burst Alert Telescope and afterglow X-ray Telescope data of Swift-discovered GRB 081109A up to similar to 5 x 105 s after the trigger, and the early ground-based optical followups. The temporal and spectral indices of the X-ray afterglow emission change remarkably. We interpret this as the gamma-ray burst jet first traversing the freely expanding supersonic stellar wind of the progenitor with density varying as proportional to r-2. Then, after approximately 300 s the jet traverses into a region of apparent constant density similar to that expected in the stalled-wind region of a stellar wind bubble or the interstellar medium. The optical afterglow data are generally consistent with such a scenario. Our best numerical model has a wind density parameter A(*) similar to 0.02, a density of the stalled wind n similar to 0.12 cm-3 and a transition radius similar to 4.5 x 1017 cm. Such a transition radius is smaller than that predicted by numerical simulations of the stellar wind bubbles and may be due to a rapidly evolving wind of the progenitor close to the time of its core-collapse.
SURF: Steganalysis using random forests

The success of any statistical steganalysis algorithm depends on the choice of features extracted and the classifier employed. This paper proposes steganalysis using random forests (SURF) employing HCS (Huffman Code Statistics) features and FR Index (ratio of File size to Resolution). The proposed algorithm is validated over an image database of over 30,000 images spanning various sizes, resolutions, qualities and textures to detect four widely used steganographic schemes namely LSB (Least Significant Bit) encoding, JPHS (JPEG Hide & Seek), MBS (Model Based Steganography) and PQ (Perturbed Quantization). The SURF algorithm proves random forest to be an efficient classifier for steganalysis and its performance is found to be superior compared to current steganalysis methods.
Diagnostic Accuracy of Kato–Katz, FLOTAC, Baermann, and PCR Methods for the Detection of Light-Intensity Hookworm and Strongyloides stercoralis Infections in Tanzania

Sensitive diagnostic tools are crucial for an accurate assessment of helminth infections in low-endemicity areas. We examined stool samples from Tanzanian individuals and compared the diagnostic accuracy of a real-time polymerase chain reaction (PCR) with the FLOTAC technique and the Kato–Katz method for hookworm and the Baermann method for Strongyloides stercoralis detection. Only FLOTAC had a higher sensitivity than the Kato–Katz method for hookworm diagnosis; the sensitivities of PCR and the Kato–Katz method were equal. PCR had a very low sensitivity for S. stercoralis detection. The cycle threshold values of the PCR were negatively correlated with the logarithm of hookworm egg and S. stercoralis larvae counts. The median larvae count was significantly lower in PCR false negatives than true positives. All methods failed to detect very low-intensity infections. New diagnostic approaches are needed for monitoring of progressing helminth control programs, confirmation of elimination, or surveillance of disease recrudescence.
Towards deeper understanding: Deep convex networks for semantic utterance classification

Following the recent advances in deep learning techniques, in this paper, we present the application of special type of deep architecture - deep convex networks (DCNs) - for semantic utterance classification (SUC). DCNs are shown to have several advantages over deep belief networks (DBNs) including classification accuracy and training scalability. However, adoption of DCNs for SUC comes with non-trivial issues. Specifically, SUC has an extremely sparse input feature space encompassing a very large number of lexical and semantic features. This is about a few thousand times larger than the feature space for acoustic modeling, yet with a much smaller number of training samples. Experimental results we obtained on a domain classification task for spoken language understanding demonstrate the effectiveness of DCNs. The DCN-based method produces higher SUC accuracy than the Boosting-based discriminative classifier with word trigrams.
An empirical study on the accuracy of computational effort in Genetic Programming

Some commonly used performance measures in Genetic Programming are those defined by John Koza in his first book. These measures, mainly computational effort and number of individuals to be processed, estimate the performance of the algorithm as well as the difficulty of a problem. Although Koza's performance measures have been widely used in the literature, their behaviour is not well known. In this paper we study the accuracy of these measures and advance in the understanding of the factors that influence them. In order to achieve this goal, we report an empirical study that attempts to systematically measure the effects of two variability sources in the estimation of the number of individuals to be processed and the computational effort. The results obtained in those experiments suggests that these measures, in common experimental setups, and under certain circumstances, might have a high relative error.
A Case of Intraductal Papillary Neoplasm of the Bile Duct with Stromal Invasion

Intraductal papillary neoplasm of the bile duct (IPNB) represents biliary papillary tumors mainly growing and is considered to be of relatively low-grade malignancy. Here we report a case of IPNB in whom the poorly differentiated component deeply infiltrated the bile duct wall. A 77-year-old male had an invasive carcinoma of the bile duct 3 cm in size. He underwent right hemihepatectomy with combined resection of the extrahepatic bile duct. Papillary growing tumor was observed in the common bile duct and the right posterior Glisson’s pedicle was invaded. Histologic finding showed papillary adenocarcinoma in the surface layer superficially extending to the epithelium of the surrounding bile duct. In the subserosal layer, the tumor represented poorly differentiated adenocarcinoma. The tumor was diagnosed as invasive bile duct carcinoma arising from IPNB.
Finite state automata: A geometric approach

Recently, finite state automata, via the advent of hyperbolic and automatic groups, have become a powerful tool in geometric group theory. This paper develops a geometric approach to automata theory, analogous to various techniques used in combinatorial group theory, to solve various problems on the overlap between group theory and monoid theory. For instance, we give a geometric algorithm for computing the closure of a rational language in the profinite topology of a free group. We introduce some geometric notions for automata and show that certain important classes of monoids can be described in terms of the geometry of their Cayley graphs. A long standing open question, to which the answer was only known in the simplest of cases (and even then was non-trivial), is whether it is true, for a pseudovariety of groups H, that a J -trivial co-extension of a group in H must divide a semidirect product of a J -trivial monoid and a group in H. We show the answer is affirmative if H is closed under extension, and may be negative otherwise.
Neural Circuit in the Dorsal Raphe Nucleus Responsible for Cannabinoid-Mediated Increases in 5-HT Efflux in the Nucleus Accumbens of the Rat Brain

In vivo microdialysis was used in this study to reveal the role of cannabinoids in regulating serotonin (5-HT) efflux in the nucleus accumbens (NAcc) and dorsal raphe nucleus (DRN). The cannabinoid CB1 receptor agonists WIN55212-2 and CP55940 systematically administered to rats caused significant increases in 5-HT efflux in the NAcc but failed to have an effect in the DRN. To reveal mechanisms underlying regionally selective responses, we tested the hypothesis that cannabinoids have both direct and indirect effects on 5-HT efflux, depending on the location of CB1 receptors in the neural circuit between DRN and NAcc. We showed that the direct effect of cannabinoids caused a reduction in 5-HT efflux whereas the indirect effect resulted in an increase. Furthermore, the indirect effect was blocked by the GABAA receptor antagonist bicuculline in the DRN, suggesting that the action is likely due to a presynaptic inhibition on GABAergic activity that exerts a tonic influence on neuronal circuits regulating 5-HT efflux. Involvement of GABAergic neurons was confirmed by measuring changes in GABA efflux. Taken together, our study suggests that cannabinoids may have direct and indirect effects on the 5-HT regulatory circuits, resulting in regionally selective changes of 5-HT efflux in the brain.
Near real-time stereo based on effective cost aggregation

Recent research activity on stereo matching has proved the efficacy of local approaches based on advanced cost aggregation strategies in accurately retrieving 3D information. However, accuracy is typically achieved at expense of computational efficiency, with best methods being far from meeting real-time requirements. On the other side, basic real-time local algorithms relying on a rectangular correlation window suffer from significant ambiguity along depth borders and untextured areas. This work proposes a novel local approach aimed at maximizing the speed-accuracy trade-off by means of an efficient segmentation-based cost aggregation strategy.
Shortest Paths and Distances with Differential Privacy

We introduce a model for differentially private analysis of weighted graphs in which the graph topology (υ,ε) is assumed to be public and the private information consists only of the edge weights ω : ε → R+. This can express hiding congestion patterns in a known system of roads. Differential privacy requires that the output of an algorithm provides little advantage, measured by privacy parameters ε and δ, for distinguishing between neighboring inputs, which are thought of as inputs that differ on the contribution of one individual. In our model, two weight functions w,w' are considered to be neighboring if they have l1 distance at most one. We study the problems of privately releasing a short path between a pair of vertices and of privately releasing approximate distances between all pairs of vertices. We are concerned with the approximation error, the difference between the length of the released path or released distance and the length of the shortest path or actual distance. For the problem of privately releasing a short path between a pair of vertices, we prove a lower bound of Ω(|υ|) on the additive approximation error for fixed privacy parameters ε,δ. We provide a differentially private algorithm that matches this error bound up to a logarithmic factor and releases paths between all pairs of vertices, not just a single pair. The approximation error achieved by our algorithm can be bounded by the number of edges on the shortest path, so we achieve better accuracy than the worst-case bound for pairs of vertices that are connected by a low-weight path consisting of o(|υ|) vertices. For the problem of privately releasing all-pairs distances, we show that for trees we can release all-pairs distances with approximation error $O(log2.5|υ|) for fixed privacy parameters. For arbitrary bounded-weight graphs with edge weights in [0,M] we can brelease all distances with approximation error Õ(√>(|υ|M).
Activity Theory vs Cognitive Science in the Study of Human-Computer Interaction

This paper discusses the shortcomings of the cognitive science approach to understanding human cognition particularly in its relationship to human computer interaction. Its failure to distinguish between the psychic and the information processes in human and machine has led to a view of the computer as a 'replacement' for the human in intellectual spheres and the implication that a computer program is a theory of human thinking. An alternate psychological approach, namely Activity Theory, is suggested as a more broad based and durable framework for understanding 'humans interacting with computers' as it details the importance of work activity as the unit of analysis and emphasises the contextuality of computer use.
Utility of contact detection reflexes in prosthetic hand control

Tactile sensations make grasping fragile objects a simple and unchallenging task for the human hand. Prosthetic hands lack these sensory capabilities and their users frequently struggle with such tasks. To address this problem, the benefits of compliant fingertips with contact-detection reflexes were assessed in one prosthesis user when grasping fragile objects (eggshells, foam packing peanuts, crackers, and soft clay). A commercially available myoelectric prosthetic hand was modified to include the compliant BioTac® tactile sensors (SynTouch, LLC), which have previously been demonstrated to be more sensitive to contact than the human fingertip. Upon sensing contact during hand closure on an object, the gain of the operator's EMG command signals to the prosthesis' motor was reduced to prevent excessive closing forces, a behavior similar to an inhibitory reflex. This allowed the prosthetic hand to quickly react to the presence of the object and permitted the operator to handle fragile objects with ease and without the usual dependency on visual feedback. The time required to grasp and move a set of fragile objects with this modified prosthesis was compared to the subject's usual prosthetic hand. The contact detection method demonstrated both utility and reliability through faster completion times and reduced variance in the times to complete these trials.
Human embryonal carcinoma stem cells: models of embryonic development in humans.

There are few reliable experimental systems available to study the molecular mechanisms that govern human embryonic development. Embryonal carcinoma (EC) cells are pluripotent stem cells derived from teratocarcinomas and are considered the malignant counterparts of human embryonic stem (ES) cells. Several of the existing human EC stem cell lines provide robust and simple culture systems to study certain aspects of cellular differentiation in a manner pertinent to human embryogenesis. Here we review the strategies used to derive and characterize the established and recognized human EC stem cell line TERA2.cl. SP12. Furthermore, we demonstrate the value of human EC stem cells as a model of early development and focus on cell fate determination in the embryonic ectoderm.