Miracle-dz/UniFAR-FTUs huggingface dataset:
Proptosis from a Baerveldt Tube Shunt Implant

Purpose The purpose of this case report is to describe a patient presenting with unilateral proptosis associated with a Baerveldt tube shunt implant that had been previously implanted for treatment of elevated intraocular pressure not sufficiently responsive to pressure-lowering medications. Because this particular device is impregnated with barium, it is radio-opaque and must be discriminated from ferromagnetic and other foreign bodies in the differential diagnosis of orbital space-occupying lesion. Although the incidence of proptosis resulting from glaucoma drainage devices is rare, radiologists and ophthalmic clinicians must be aware of this possibility as well as the appearance of these devices in orbital imaging. Case Report A patient with advanced glaucoma presented for an intraocular pressure check. Upon examination, proptosis was noted in the left eye. Exophthalmometry was performed and revealed asymmetry between the eyes. The patient was sent for a computed tomography scan of the orbits that revealed a foreign object in the left eye, which was identified as a Baerveldt tube shunt with surrounding fibrosis. The patient was sent to a glaucoma specialist for a consult regarding the efficacy of the implant. Conclusions Late-onset proptosis is a rare complication of a glaucoma implant but can lead to concern for an orbital mass or other pathology, which should be ruled out. Also, because this particular device is impregnated with barium, it is radio-opaque and must be discriminated from other metallic foreign bodies.
Outbreaks of Escherichia coli O157:H7 infections among children associated with farm visits--Pennsylvania and Washington, 2000.

DURING THE SPRING AND FALL OF 2000, outbreaks of Escherichia coli O157:H7 infections among school children in Pennsylvania and Washington resulted in 56 illnesses and 19 hospitalizations. Illness was associated with school and family visits to farms where children came into direct contact with farm animals. This report summarizes the findings of investigations of these outbreaks and includes strategies to reduce the transmission of enteric pathogens from farm animals to children.
Elastic Roadmaps: Globally Task-Consistent Motion for Autonomous Mobile Manipulation in Dynamic Environments

The autonomous execution of manipulation tasks in unstructured, dynamic environments requires the consideration of various motion constraints. Any motion performed during the manipulation task has to satisfy constraints imposed by the task itself, but also has to consider kinematic and dynamic limitations of the manipulator, avoid unpredictably moving obstacles, and observe constraints imposed by the global connectivity of the workspace. Furthermore, the unpredictability of unstructured environments requires the continuous incorporation of feedback to reliably satisfy these constraints. We present a novel feedback motion planning approach, called elastic roadmap framework, capable of satisfying all of the motion constraints that arise in autonomous mobile manipulation and their respective feedback requirements. This framework is validated with simulation experiments using a mobile manipulation platform and a stationary manipulator.
High-level synthesis scheduling and allocation using genetic algorithms

In this article a scheduling method is presented which is capable of allocating supplementary resources during scheduling. This makes it very suitable in synthesis strategies based on lower bound estimations techniques. The method is based on genetic algorithms. Special coding techniques and analysis methods are used to improve the runtime and quality of the results. The scheduler can easily be extended to cover other architectural issues and (for example) provides ways to make trade-offs between functional unit allocation and register allocation. Experiments and comparisons show high quality results and fast run times that outperform results produced by other heuristic scheduling methods.
Web content management by self-organization

We present a new method for content management and knowledge discovery using a topology-preserving neural network. The method, termed topological organization of content (TOC), can generate a taxonomy of topics from a set of unannotated, unstructured documents. The TOC consists of a hierarchy of self-organizing growing chains (GCs), each of which can develop independently in terms of size and topics. The dynamic development process is validated continuously using a proposed entropy-based Bayesian information criterion (BIC). Each chain meeting the criterion spans child chains, with reduced vocabularies and increased specializations. This results in a topological tree hierarchy, which can be browsed like a table of contents directory or web portal. A brief review is given on existing methods for document clustering and organization, and clustering validation measures. The proposed approach has been tested and compared with several existing methods on real world web page datasets. The results have clearly demonstrated the advantages and efficiency in content organization of the proposed method in terms of computational cost and representation. The TOC can be easily adapted for large-scale applications. The topology provides a unique, additional feature for retrieving related topics and confining the search space.
Challenging Behaviors in Young Children: The Father's Role

In this study, the authors examined the parenting practices, developmental expectations, and stress levels of 136 fathers and the challenging and prosocial behaviors of their 1- to 5-year-old children. In addition, the authors systematically addressed fathers' qualitative concerns about their parenting. The authors divided the participants into 4 groups and controlled for family socioeconomic status (SES) and the focus child's gender. Results showed a significantly higher use of corporal and verbal punishment and parenting stress among lower income fathers. Secondary analyses demonstrated a significant effect of paternal disciplinary practices that emphasized the frequent use of corporal and verbal punishment on child behavior problems, regardless of SES level. On a positive note, fathers from both lower and higher SES groups had reasonable developmental expectations for their boys and girls, and they reported similar frequencies of their children's prosocial behavior. The authors discuss the need for early parent education programs that include fathers and that teach specific strategies to address child behavior problems.
Porting Decipher from English to Mandarin

This paper describes our efforts in porting the SRI Decipher English system into Mandarin for transcribing telephone conversations. This includes all aspects of the system: the pronunciation phone set and lexicon, word segmentation, pitch features, discriminatively trained acoustic models with parameter sharing determined by decision trees, and web-data augmented language models.
Word Embedding Clustering for Disease Named Entity Recognition

This paper reports the use of a machine learning-based approach with word embedding features for the Disease Named Entity Recognition and Normalization subtask of the BioCreative V ChemicalDisease Relation (CDR) challenge task. Firstly, we developed a feature extraction phase with standard features used in current Named Entity Recognition (NER) systems. Then, we compared the use of the word vectors and the word clusters generated by the Word2Vec tool to add the best of both in the feature set. For this purpose, we trained the Word2Vec models over Wikipedia and MedLine as corpora. Our results suggest that the use of word clusters improves 28% in F-score in disease mention recognition and increases precision almost 49% in the normalization task over the baseline system provided by the organizers.
Interactive comment on “Comment on: “Possible source of ancient carbon in phytolith concentrates from harvested grasses” by G. M. Santos al. (2012)” by

In their comment Sullivan and Parr (2012) raise several concerns which, to their opinion, weaken the soil-derived phytOC (or phytC) hypothesis of Santos et al. (2012). They believe that their concerns are mostly justified by their own 14C phytC dates from bamboo (leaves harvested alive to decomposed litter) published in the progress report no.AINGRA08061/2008 by Sullivan et al. (2008). This report was publicly displayed on line from 2009 to 2011, and is readily available on request from AINSE (at http://www.ainse.edu.au). In the present reply, we answer those points and show that
Stamen Abscission Zone Transcriptome Profiling Reveals New Candidates for Abscission Control: Enhanced Retention of Floral Organs in Transgenic Plants Overexpressing Arabidopsis ZINC FINGER PROTEIN21[C][W][OA]

Organ detachment requires cell separation within abscission zones (AZs). Physiological studies have established that ethylene and auxin contribute to cell separation control. Genetic analyses of abscission mutants have defined ethylene-independent detachment regulators. Functional genomic strategies leading to global understandings of abscission have awaited methods for isolating AZ cells of low abundance and very small size. Here, we couple laser capture microdissection of Arabidopsis thaliana stamen AZs and GeneChip profiling to reveal the AZ transcriptome responding to a developmental shedding cue. Analyses focus on 551 AZ genes (AZ551) regulated at the highest statistical significance (P ≤ 0.0001) over five floral stages linking prepollination to stamen shed. AZ551 includes mediators of ethylene and auxin signaling as well as receptor-like kinases and extracellular ligands thought to act independent of ethylene. We hypothesized that novel abscission regulators might reside in disproportionately represented Gene Ontology Consortium functional categories for cell wall modifying proteins, extracellular regulators, and nuclear-residing transcription factors. Promoter-β-glucuronidase expression of one transcription factor candidate, ZINC FINGER PROTEIN2 (AtZFP2), was elevated in stamen, petal, and sepal AZs. Flower parts of transgenic lines overexpressing AtZFP2 exhibited asynchronous and delayed abscission. Abscission defects were accompanied by altered floral morphology limiting pollination and fertility. Hand-pollination restored transgenic fruit development but not the rapid abscission seen in wild-type plants, demonstrating that pollination does not assure normal rates of detachment. In wild-type stamen AZs, AtZFP2 is significantly up-regulated postanthesis. Phenotype data from transgene overexpression studies suggest that AtZFP2 participates in processes that directly or indirectly influence organ shed.
Carbon Isotopes (δ13C and Δ14C) in Shell Carbonate, Conchiolin, and Soft Tissues in Eastern Oyster (Crassostrea Virginica)

Abstract Biogeochemical analyses of eastern oysters (Crassostrea virginica) are frequently included in environmental monitoring and paleoecological studies because their shells and soft tissues record environmental and dietary signals. Carbon isotopes in the mineral phase of the shell are derived from ambient bicarbonate and dissolved inorganic carbon (DIC), while organic carbon present in soft tissue is of dietary origin. Mineral-bound organic matter within the carbonate shell matrix (“conchiolin”) is studied less frequently. The purpose of this study was to compare carbon isotope composition (δ13C and Δ14C) of conchiolin to those of shell carbonates and soft tissues in eastern oysters and assess the extent to which conchiolin can provide insight into paleoecological records. Eleven oyster specimens were live-collected from Apalachicola Bay, USA, as well as a set of environmental samples (water, sediment, and terrestrial plants). Overall, the δ13C values in all studied oyster tissue types record environmental signals related to carbon sources, with conchiolin being enriched in 13C by an average of 2.3‰ relative to bulk soft tissues. Δ14C values in oyster shell carbonates generally reflect the marine versus riverine source of DIC, while conchiolin Δ14C values are impacted by variable relative contributions of young and old organic matter. Environmental samples indicate a significantly large difference in Δ14C among sources, from –127‰ in particulate organic matter to approximately +15‰ in DIC. Conchiolin is significantly depleted in 14C relative to other tissue types, by as much as 56.6‰, posing a major obstacle to the use of conchiolin as an alternative material for radiocarbon dating.
Learning tapestries, a statistical learning substrate for open chaotic systems measured with error

The problem of statistical inference for open chaotic systems measured with error is complicated by the interaction of the uncertainty introduced by chaos, and the various sources of random or external variation. Here a method of representing measured data from large open chaotic systems subject to error as collections of threads of plausible pseudo future histories to enable statistical analysis is described. This representation provides asymptotically consistent predictive distributions, for use in developing predictive likelihood methods which: 1. provide a framework for variable selection, 2. provide a framework for Bayesian updating, so for example 4 season ahead predictions learn naturally as the 3rd season ahead is measured. 3. allows examination of conditional scenarios along the future histories for planning purposes. 4. allows the ranking of variable, delay combinations with higher signal to noise ratio. The method is tested for learning and variable selection by examining its behavior in predicting 9 years across 4 seasons of climate variables, including local temperature and rainfall measurements at two locations, predicting up to 4 seasons ahead.
Ouabain, a Cardiac Glycoside, Inhibits the Fanconi Anemia/BRCA Pathway Activated by DNA Interstrand Cross-Linking Agents

Modulation of the DNA repair pathway is an emerging target for the development of anticancer drugs. DNA interstrand cross-links (ICLs), one of the most severe forms of DNA damage caused by anticancer drugs such as cisplatin and mitomycin C (MMC), activates the Fanconi anemia (FA)/BRCA DNA repair pathway. Inhibition of the FA/BRCA pathway can enhance the cytotoxic effects of ICL-inducing anticancer drugs and can reduce anticancer drug resistance. To find FA/BRCA pathway inhibitory small molecules, we established a cell-based high-content screening method for quantitating the activation of the FA/BRCA pathway by measuring FANCD2 foci on DNA lesions and then applied our method to chemical screening. Using commercial LOPAC1280 chemical library screening, ouabain was identified as a competent FA/BRCA pathway inhibitory compound. Ouabain, a member of the cardiac glycoside family, binds to and inhibits Na+/K+-ATPase and has been used to treat heart disease for many years. We observed that ouabain, as well as other cardiac glycoside family members―digitoxin and digoxin―down-regulated FANCD2 and FANCI mRNA levels, reduced monoubiquitination of FANCD2, inhibited FANCD2 foci formation on DNA lesions, and abrogated cell cycle arrest induced by MMC treatment. These inhibitory activities of ouabain required p38 MAPK and were independent of cellular Ca2+ ion increase or the drug uptake-inhibition effect of ouabain. Furthermore, we found that ouabain potentiated the cytotoxic effects of MMC in tumor cells. Taken together, we identified an additional effect of ouabain as a FA/BRCA pathway-inhibiting chemosensitization compound. The results of this study suggest that ouabain may serve as a chemosensitizer to ICL-inducing anticancer drugs.
Identification of methanotrophic lipid biomarkers in cold-seep mussel gills: chemical and isotopic analysis

A lipid analysis of the tissues of a cold-seep mytilid mussel collected from the Louisiana slope of the Gulf of Mexico was used in conjunction with a compound-specific isotope analysis to demonstrate the presence of methanotrophic symbionts in the mussel gill tissue and to demonstrate the host's dependence on bacterially synthesized metabolic intermediates. The gill tissue contained large amounts of group-specific methanotrophic biomarkers, bacteriohopanoids, 4-methylsterols, lipopolysaccharide-associated hydroxy fatty acids, and type I-specific 16:1 fatty acid isomers with bond positions at delta 8, delta 10, and delta 11. Only small amounts of these compounds were detected in the mantle or other tissues of the host animal. A variety of cholesterol and 4-methylsterol isomers were identified as both free and steryl esters, and the sterol double bond positions suggested that the major bacterially derived gill sterol [11.0% 4 alpha-methyl-cholesta-8(14),24-dien-3 beta-ol] was converted to host cholesterol (64.2% of the gill sterol was cholest-5-en-3 beta-ol). The stable carbon isotope values for gill and mantle preparations were, respectively, -59.0 and -60.4% for total tissue, -60.6 and -62.4% for total lipids, -60.2 and-63.9% for phospholipid fatty acids, and -71.8 and 73.8% for sterols. These stable carbon isotope values revealed that the relative fractionation pattern was similar to the patterns obtained in pure culture experiments with methanotrophic bacteria (R.E. Summons, L.L. Jahnke, and Z. Roksandic, Geochim. Cosmochim. Acta 58: 2853-2863, 1994) further supporting the conversion of the bacteria methylsterol pool.
Fast and Efficient Second-Order Method for Training Radial Basis Function Networks

This paper proposes an improved second order (ISO) algorithm for training radial basis function (RBF) networks. Besides the traditional parameters, including centers, widths and output weights, the input weights on the connections between input layer and hidden layer are also adjusted during the training process. More accurate results can be obtained by increasing variable dimensions. Initial centers are chosen from training patterns and other parameters are generated randomly in limited range. Taking the advantages of fast convergence and powerful search ability of second order algorithms, the proposed ISO algorithm can normally reach smaller training/testing error with much less number of RBF units. During the computation process, quasi Hessian matrix and gradient vector are accumulated as the sum of related sub matrices and vectors, respectively. Only one Jacobian row is stored and used for multiplication, instead of the entire Jacobian matrix storage and multiplication. Memory reduction benefits the computation speed and allows the training of problems with basically unlimited number of patterns. Several practical discrete and continuous classification problems are applied to test the properties of the proposed ISO training algorithm.
Stabilization of Microtubule-Unbound Tau via Tau Phosphorylation at Ser262/356 by Par-1/MARK Contributes to Augmentation of AD-Related Phosphorylation and Aβ42-Induced Tau Toxicity

Abnormal accumulation of the microtubule-interacting protein tau is associated with neurodegenerative diseases including Alzheimer’s disease (AD). β-amyloid (Aβ) lies upstream of abnormal tau behavior, including detachment from microtubules, phosphorylation at several disease-specific sites, and self-aggregation into toxic tau species in AD brains. To prevent the cascade of events leading to neurodegeneration in AD, it is essential to elucidate the mechanisms underlying the initial events of tau mismetabolism. Currently, however, these mechanisms remain unclear. In this study, using transgenic Drosophila co-expressing human tau and Aβ, we found that tau phosphorylation at AD-related Ser262/356 stabilized microtubule-unbound tau in the early phase of tau mismetabolism, leading to neurodegeneration. Aβ increased the level of tau detached from microtubules, independent of the phosphorylation status at GSK3-targeted SP/TP sites. Such mislocalized tau proteins, especially the less phosphorylated species, were stabilized by phosphorylation at Ser262/356 via PAR-1/MARK. Levels of Ser262 phosphorylation were increased by Aβ42, and blocking this stabilization of tau suppressed Aβ42-mediated augmentation of tau toxicity and an increase in the levels of tau phosphorylation at the SP/TP site Thr231, suggesting that this process may be involved in AD pathogenesis. In contrast to PAR-1/MARK, blocking tau phosphorylation at SP/TP sites by knockdown of Sgg/GSK3 did not reduce tau levels, suppress tau mislocalization to the cytosol, or diminish Aβ-mediated augmentation of tau toxicity. These results suggest that stabilization of microtubule-unbound tau by phosphorylation at Ser262/356 via the PAR-1/MARK may act in the initial steps of tau mismetabolism in AD pathogenesis, and that such tau species may represent a potential therapeutic target for AD.
Poly[[μ3-N,N′-bis(3-pyridylmethyl)thiourea-κ3 N:N′:S]iodidocopper(I)]

In the title coordination polymer, [CuI(C13H14N4S)]n, the CuI atom is coordinated by two N atoms from two N,N′-bis(3-pyridylmethyl)thiourea ligands, as well as by the S atom of a third ligand and an I atom to confer a distorted tetrahedral coordination at the metal centre. The coordination bonds give rise to a layer structure parallel to (010).
The Basal Forebrain Cholinergic System Is Required Specifically for Behaviorally Mediated Cortical Map Plasticity

The basal forebrain cholinergic system has been implicated in the reorganization of adult cortical sensory and motor representations under many, but not all, experimental conditions. It is still not fully understood which types of plasticity require the cholinergic system and which do not. In this study, we examine the hypothesis that the basal forebrain cholinergic system is required for eliciting plasticity associated with complex cognitive processing (e.g., behavioral experiences that drive cortical reorganization) but is not required for plasticity mediated under behaviorally independent conditions. We used established experimental manipulations to elicit two distinct forms of plasticity within the motor cortex: facial nerve transections evoke reorganization of cortical motor representations independent of behavioral experience, and skilled forelimb training induces behaviorally dependent expansion of forelimb motor representations. In animals that underwent skilled forelimb training in conjunction with a facial nerve lesion, cholinergic mechanisms were required for mediating the behaviorally dependent plasticity associated with the skilled motor training but were not necessary for mediating plasticity associated with the facial nerve transection. These results dissociate the contribution of cholinergic mechanisms to distinct forms of cortical plasticity and support the hypothesis that the forebrain cholinergic system is selectively required for modulating complex forms of cortical plasticity driven by behavioral experience.