Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of lacZ‐expressing cells in the gut of embryonic and adult DβH‐nlacZ mice

In mice that express lacZ under the control of a human dopamine β‐hydroxylase gene promoter (DβH‐nlacZ mice), the nuclei of enteric neurons express the transgene, as shown by the presence of β‐galactosidase (β‐gal) staining (Mercer et al. [1991] Neuron 7:703–716). The transgene is also expressed by neural crest‐derived cells in the developing gut before their differentiation into neurons or glial cells (Kapur et al. [1992] Development 116:167–175). However, the cell types expressing the DβH‐nlacZ transgene within the developing and adult gut have not been fully characterized. Whole‐mount preparations of embryonic and adult gut were processed for histochemistry or immunohistochemistry to reveal β‐gal plus markers of undifferentiated neural crest cells (in embryos) or enteric neurons (in adults). In embryonic mice, over 90% of undifferentiated neural crest‐derived cells (identified using antibodies to p75) were β‐gal+. Importantly, crest‐derived cells at the migratory wavefront were all β‐gal+. In adult mice, only a subpopulation of enteric neurons was β‐gal+, while glial cells showed no β‐gal staining. Considerable variation was observed between the small intestine and colon in the proportion of myenteric neurons that showed β‐gal staining. We examined whether known classes of enteric neurons varied in their expression of DβH‐nlacZ. In the myenteric plexus of the jejunum and colon, large calretinin+ neurons did not express lacZ, suggesting that the incomplete penetrance of the DβH‐nlacZ transgene observed in adult mice is not random. We conclude that the DβH‐nlacZ transgene provides a reliable marker for examining the colonization of the developing gut by neural crest cells. However, in adult mice, there is variation between mice, between gut regions, and between different classes of enteric neurons in the expression of the transgene. J. Comp. Neurol. 464:208–219, 2003. © 2003 Wiley‐Liss, Inc.
Cooperative Binning and Channel Prefixing for Secrecy in Interference Channels

This paper investigates the fundamental performance limits of the two-user interference channel in the presence of an external eavesdropper. In this setting, we construct a n inner bound, to the secrecy capacity region, based on the idea of cooperative binning and channel prefixing in whic h the two users cooperatively design their binning codebooks and jointly optimize their channel prefixing distributions. Our achiev ability scheme also utilizes messagesplitting in order to allow for partial decoding of the inter ference at the non-intended receiver. Outer bounds are then derived and used to establish the optimality of the proposed scheme in certain cases. In the Gaussian case, the previously proposed cooperative jamming and noise-forwarding techniques are shown to be special cases of our proposed approach. Overall, our results provide structural insights on how the interference can be exploited to increase the secrecy capacity of wireless networks.
Deregulation of DNA methyltransferases and loss of parental methylation at the insulin‐like growth factor II (Igf2)/H19 loci in p53 knockout mice prior to tumor development

To ascertain whether p53 deficiency in vivo leads to the deregulation of DNA methylation machinery prior to tumor development, we investigated the expression profile of DNA methyltransferases in the thymus and the liver of p53+/+, p53+/−, and p53−/− mice at 7 weeks of age before tumor development. The expression of DNA methyltransferases was examined in the thymus at 7 weeks of age, since the malignant T‐cell lymphoma develops most frequently in p53−/− mice around 20 weeks of age. Both mRNA and protein levels of Dnmt1 and Dnmt3b were increased in the thymus and the liver of p53‐deficient mice. The expression of Dnmt3a was also increased in the liver but not in the thymus of p53‐deficient mice. Dnmt3L expression was reduced in the thymus of p53+/− and p53−/− mice. The total 5‐methylcytosine (5‐MeC) in the genomic DNA of p53+/+, p53+/−, and p53−/− mice was quantitated by dot‐blot using antibody against 5‐MeC. Global methylation was increased in the thymus and the liver of p53‐deficient mice. To correlate the deregulated expression of DNA methyltransferases with the disturbance of the epigenetic integrity, we examined the DNA methylation of the imprinting control region (ICR) at the insulin‐like growth factor II (Igf2)/H19 loci in the thymus and the liver of p53+/+, p53+/−, and p53−/− mice. The region containing two CCCTC binding factor (CTCF) binding sites in the 5′‐ICR tended to be hypomethylated in the thymus of p53−/− mice, but not in the liver. The expression profile of Igf2 and H19 indicated that the thymus‐specific changes of Igf2 and H19 expression were coherent to the hypomethylation of the ICR in the thymus. Our results suggest that p53 is required for the maintenance of DNA methylation patterns in vivo. © 2004 Wiley‐Liss, Inc.
An Open Vocabulary OCR System with Hybrid Word-Subword Language Models

The accuracy of a typical state-of-the-art optical character recognition (OCR) system benefits greatly from using a language model (LM). However, a conventional LM has a limited vocabulary, resulting in out-of-vocabulary (OOV) words that cannot be recognized by the OCR system. In this paper, we present an open vocabulary OCR system based on a hybrid LM. The vocabulary of the hybrid LM consists of both words and subwords. OOV words can be generated by combinations of subwords. A refined hybrid LM training scheme is applied by interpolating a standard hybrid LM, a word-based LM and a subword-based LM. An efficient word combination method is performed by modeling optional space symbols in a decoding network. The overall system deals with OOV words in a general, data-driven and language-independent way. We conduct experiments on an English handwriting OCR task. Evaluations on three testing sets demonstrate that the OCR system with the proposed method achieves a word error rate of 33.4% on an OOV-only testing set, yet without degrading the recognition accuracies on the other two testing sets mainly consisting of in-vocabulary words.
Hybrid Dynamic Moving Obstacle Avoidance Using a Stochastic Reachable Set-Based Potential Field

One of the primary challenges for autonomous robotics in uncertain and dynamic environments is planning and executing a collision-free path. Hybrid dynamic obstacles present an even greater challenge as the obstacles can change dynamics without warning and potentially invalidate paths. Artificial potential field (APF)-based techniques have shown great promise in successful path planning in highly dynamic environments due to their low cost at runtime. We utilize the APF framework for runtime planning but leverage a formal validation method, Stochastic Reachable (SR) sets, to generate accurate potential fields for moving obstacles. A small number of SR sets are computed a priori, then used to generate a potential field that represents the obstacle's stochastic motion for online path planning. Our method is novel and scales well with the number of obstacles, maintaining a relatively high probability of reaching the goal without collision, as compared to other traditional Gaussian APF methods. Here, we demonstrate our method with up to 900 hybrid dynamic obstacles and show that it outperforms the traditional Gaussian APF method by up to 60% in the holonomic case and up to 20% in the unicycle case.
A new proposal for metric in perceptual multidimensional scaling

We analyze a simpliﬁed probability model that assumes normality and homoscedasticity of vowel parameters’ distributions. We arrive at explicit formulae that describe functional relationship between a natural Euclidean distance function in the model and the confusability of vowel categories. We propose a solution to address a common case when confusabil-ity of a pair of vowel categories is very low, which leads to uncertainty of distance value. The solution is applicable when the class boundary is provided by a real-valued discriminating function. Examples of perceptual vowel diagrams obtained with new metric are presented based on vowel samples spoken by male speakers from TIMIT corpus
Predicting Presence of Offender’s Criminal Record From Antisocial Lifestyle Indicators of Homicide Victims

The aim of the present study is to explore the possibility of predicting the presence of a criminal record in the background of a homicide offender on the basis of victim characteristics. Eight victim characteristics, as well as the presence or absence of offender criminal record and offender violent criminal record, were coded for 502 Finnish homicides. A configural frequency analysis (CFA) showed that it was possible to predict the presence of a criminal record on the basis of the victim variables. The practical significance of the results for police investigations is discussed.
Pain Management in a Patient With Intractable Spinal Cord Injury Pain: A Case Report and Literature Review

Chronic pain is one of the more disturbing sequelae of spinal cord injury, often interfering with the basic activities, effective rehabilitation, and quality of life of the patient. Pain in the cord-injured patient is often recalcitrant to treatment. This dilemma is amplified by the limited availability of effective pharmacological and nonpharmacological treatment options. We identified relevant articles regarding pain after spinal cord injury from the Medline database from 1975 to 2005 using the search terms “spinal cord injury” or “spinal cord injuries” and “pain” or “spasticity or “muscle spasms. ” We also searched by hand the review articles in a recently published book from the International Association for the Study of Pain Press on spinal cord injury pain, and identified relevant articles through reference lists. We present a patient with intractable spinal cord injury pain who was successfully treated with a pain management plan that addressed the various aspects of spinal cord injury pain. The evidence for treatment options is reviewed.
Collaboration in Agile Software Development: Concept and Dimensions

: One of the four values listed in the Agile Manifesto emphasizes customer collaboration over contract negotiation, yet the literature has not explained what constitutes customer collaboration and how to assess it. Little research has examined the nature and dimensions of collaboration in the context of agile software development. Based on a grounded theory methodology and using interview data collected from five software development outsourcing vendors in China, we explore the nature and key underlying dimensions of collaboration in agile software development. Five major dimensions of collaboration emerged from our analysis: mutual benefits, engagement, coordination, communication, and knowledge sharing. In turn, each dimension comprises key subdimensions that provide a comprehensive view of collaboration. By revealing the underlying nature and key dimensions, we provide a conceptual basis for operationalizing collaboration that one can employ in future quantitative studies on agility and other project outcomes. Our study results suggest that collaboration in agile software development is multifaceted and mutually occurring in both directions between the customer and the vendor rather than single dimensional as the term “customer collaboration” in the Agile Manifesto indicates.
[Development and assessment of EPInfant: a rating scale of perceived exertion for the pediatric population].

Rating scales of perceived exertion (PE) have been used to measure PE during exercise in the adult population with successful results. However, in children, it is necessary to develop adapted instruments due to their cognitive immaturity. The number of Spanish-language validated instruments for the pediatric population is scarce. Our objective was to develop a new PE rating scale. Research design was divided into three stages: development, content validity, and criterion validity. For development, a panel of five expert members was summoned, who provided indications for the new instrument. A systematic review of the literature to identify other validated instruments was performed. This process resulted in the development of the new EPInfant scale to measure PE, which integrates the expert panel’s indications and the result of the literature systematic review. The evaluation of its content showed a high level of agreement regarding the quality of its design; the content validity index was 1. During the field assessment, a high concurrent criterion validity was observed in healthy adolescents due to the strong correlation shown between PE and heart rate in both boys and girls. The methodology used to develop the EPInfant scale aimed at reducing potential biases that may hinder its psychometric properties. Preliminary results suggest that this may be a validated instrument that could be implemented in healthy
Types of intensive care units with the healthiest, most productive work environments.

BACKGROUND The quality of nurses' work environments in hospitals is of great concern. The American Association of Critical-Care Nurses has specified 6 standards essential to a healthy (ie, satisfying and productive) work environment. These standards are sufficiently aligned to the Essentials of Magnetism processes to make this tool suitable for measuring healthy work environments. OBJECTIVES To identify differences in staff nurses' perceptions of the work environment by type of intensive care unit. METHODS A cross-sectional descriptive design with strategic sampling was used in this secondary analysis of data from 698 staff nurses working in 34 intensive care units in 8 magnet hospitals. Intensive care units were grouped into 4 types: medical, including coronary care; surgical, including trauma and cardiovascular; neonatal and pediatric; and medical-surgical. All nurses completed the Essentials of Magnetism instrument. Analysis of variance was used to identify initial differences; multivariate analysis of variance was used to control for covariates. RESULTS The intensive care nurses and units scored above the National Magnet Hospital Profile mean on process variables and on the Essentials of Magnetism outcome variables. Neonatal and pediatric units scored significantly higher than did the other types of intensive care units sampled. CONCLUSIONS Intensive care unit structures supported care processes and relationships that resulted in job satisfaction among nurses and high-quality care for patients in this strategic sample. Systematic study of the structures and processes present in units reporting a healthy work environment can be used to assist other clinical units in improving work environments.
Glucocorticoid receptor function; interactions, mutants and ligand responses

The protein that is investigated in this thesis is the glucocorticoid receptor (GR), which belongs to the nuclear hormone receptor superfamily of ligand activated transcription factors. The nuclear receptors share three conserved structural domains, the N-terminal transactivating domain, the central DNA-binding domain and the C-terminal ligandbinding domain. GCs are well known for their anti-inflammatory and apoptotic effects and are therefore used as treatment for a multitude of diseases including, asthma, rheumatoid arthritis, ulcerative colitis and leukemia’s. GR mediates the effects of GCs not only by the activation and repression of specific target genes that play important roles in several physiological processes such as metabolism, cell proliferation and inflammatory and immune responses but also through protein-protein interactions with other signalling pathways, referred to as crosstalk mechanisms. In the first study, we described a method to investigate new GR interacting proteins on a large scale using 2-dimensional gel electrophoresis in combination with MALDITOF/TOF mass spectrometry. We found 27 novel potentially important proteins that interacted with the GR receptor complex. Our data suggests that those interactions are variable depending on the presence or absence of GCs and that they also are present in different GR multiprotein complexes of different composition, indicating the existence of new GR cross-talk mechanisms. In the second study, we characterized the interaction between GR and FMS-like tyrosine kinase 3 (Flt3). We showed that the DNA-binding domain of GR is sufficient for the Flt3 interaction. Addition of Flt3 ligand also proved to be necessary for potentiation of GC dependent transcription. The data presented in the third study aimed to detect GC regulated genes from blood samples within a short time frame. We also measured the amount of GR in different subpopulations of peripheral blood leucocytes with flow cytometry. Together these results serve as a starting point for a quick determination of GC responsiveness in patients. In the fourth study, we characterized the functional properties of the two GR mutations, R477H and G679S. We showed that both R477H and G679S have a dominant negative effect on wild-type GR and that R477H has impaired DNA-binding which explains the severe clinical phenotypes of cortisol resistance that are associated with these mutations.
An Improved Discrete Complex Image Method Based on a Special Sampling Path

A special sampling path is proposed to improve the accuracy of the discrete complex image method (DCIM) in evaluating the lateral wave. Different from all the previous DCIM implementations, the proposed sampling path goes through the branch point directly, which helps to evaluate its contribution to the lateral wave more accurately. In this communication, different sampling paths of DCIM have been implemented and compared. It is found that in the situations where the lateral wave dominates the far-field region, DCIM with the new path gives more accurate and stable results.
Hair embolism in lungs of rat and rabbit caused by intravenous injection

Among 1422 Sprague-Dawley rats treated daily for 28 consecutive days by i.v. injection, 144 animals (10·1%) showed particles of hair in thrombi at the site of injection. 381 rats (26·8%) had pulmonary emboli with fragments of hair and skin in arterial thrombi or in giant cell granulomas. 6 weeks after cessation of treatment lesions were still found in lungs from 5 of 90 rats (5·6%) allowed to recover. After the experimental administration of 0·75 ml/100 g body wt of a hair suspension (3000 hair particles/ml) to rats, there was no influence on phagocytosis whether endogenous or foreign hairs were injected. In 8 of 64 Himalayan rabbits (12·5%) given 28 injections each into ear veins pulmonary embolism was observed.
Do Clients' Problem-Solving Appraisals Predict Career Counseling Outcomes or Vice Versa? A Reanalysis of Heppner, et al.

Using Heppner, et al.'s data from 2004, this study tested career counseling clients in the United States on problem-solving appraisal scores and career-related variables. A cross-lagged panel design with structural equation modeling was used. Results supported the link between clients' precounseling problem-solving appraisal scores and career outcome. This finding held for career decision-making, but not for vocational identity. The study provided further support for Heppner, et al.'s findings, highlighting the influential role of clients' problem-solving appraisals in advancing their career decision-making processes.
IMPAIRMENT OF GROWTH AND IMMUNE FUNCTION OF AVOCET CHICKS FROM SITES WITH ELEVATED SELENIUM, ARSENIC, AND BORON

Avocets (Recurvirostra americana) hatched from eggs collected from the south Central Valley of California (USA) were studied to determine the impact of elevated concentrations of selenium, arsenic, and boron on the immune system and growth to maturity. Corcoran ponds were the reference site with low selenium (1.2 ppb) and arsenic (29 ppb) (boron not measured). Westfarmers Pond had elevated concentrations of selenium (319 ppb), arsenic (127 ppb), and boron (109 ppm). Pryse ponds also had elevated selenium, arsenic, and boron concentrations (13.9 ppb, 1,100 ppb, and 29.4 ppm, respectively). Size at hatch was significantly reduced (P < 0.05) in birds from Westfarmers and Pryse ponds. The growth rate was faster, but mean adult size was reduced in birds from Pryse ponds. Avocet chicks from Pryse and Westfarmers ponds exposed solely through in ovo transfer of these elements had significantly increased heterophil: lymphocyte ratios. The phagocytic activity of macrophages also was significantly reduced in these birds, and Pryse Pond birds had an increased proliferative ability of lymphocytes in the presence of concanavalin A, a T-cell mitogen. Avocet chicks (≤5 wk old) were captured from the various ponds and the same morphometric and immune function measurements made. The birds that were most severely impacted by exposure to these compounds were those that were collected from Pryse ponds.
Treatment of lymphoma with adoptively transferred T cells

Background: Chemotherapy-resistant lymphomas can be cured with allogeneic hematopoietic cell transplantation, demonstrating the susceptibility of these tumors to T cell mediated immune responses. However, high rates of transplant-related morbidity and mortality limit this approach. Efforts have, therefore, been made to develop alternative T cell based therapies, and there is growing evidence that adoptive therapy with T cells targeted to lymphoma-associated antigens may be a safe and effective new method for treating this group of diseases. Objective/methods: We review publications on adoptive therapy with ex vivo expanded T cells targeting viral antigens, as well as genetically modified autologous T cells, as strategies for the treatment of lymphoma, with the goal of providing an overview of these approaches. Results/conclusions: Epstein-Barr virus specific T cell therapy is an effective and safe method of treating Epstein-Barr virus associated lymphomas; however, most lymphoma subtypes do not express EBV antigens. For these diseases, adoptive immunotherapy with genetically modified T cells expressing chimeric T cell receptors targeting lymphoma-associated antigens such as CD19 and CD20 appears to be a promising alternative. Recent innovations including enhanced co-stimulation, exogenous cytokine administration and use of memory T cells promise to overcome many of the limitations and pitfalls initially encountered with this approach.
HD-CNN: Hierarchical Deep Convolutional Neural Network for Image Classification

Existing deep convolutional neural network (CNN) architectures are trained as N-way classifiers to distinguish between N output classes. This paper builds on the intuition that not all classes are equally difficult to distinguish from the true class label. Towards this end, we introduce hierarchical branching CNNs, called Hierarchical Deep CNN (HD-CNN), wherein classes that can be easily distinguished are classified in the higher-layer coarse category CNN, while the most difficult classifications are done on lower-layer fine category CNN. We propose utilizing a multinomial logistic loss and a novel temporal sparsity penalty for HD-CNN training. Together, they ensure each branching component deals with a subset of categories confusing to each other. Furthermore, conditional evaluation of branching components is introduced to substantially speed up the HD-CNN net execution. This new network architecture adopts a coarse-to-fine classification strategy and a module design principle. The proposed model achieves superior performance over standard models. We demonstrate state-of-the-art results on the CIFAR100 benchmark and also present preliminary results on ImageNet dataset.