Miracle-dz/UniFAR-FTUs huggingface dataset:
An evaluation of the hypothesis of shifting terminals in goldfish optic tectum

It has been proposed that the terminal arbors of retinal ganglion cells continually shift positions in the optic tectum as a natural consequence of growth in larval amphibians and teleost fish. Here, we develop a detailed anatomical model of this process, based on recent observations in goldfish. The model predicts some unusual structural features of optic axons in the tectum. It was tested in two ways by use of the tracer, horseradish peroxidase (HRP). In the first, optic axons in the tectum were visualized by anterogradely transported HRP applied in the nerve or retina. As predicted, the axons had three parts: (1) fascicular segment (in the stratum opticum), (2) extrafascicular segment (in the synaptic neuropil), and (3) terminal arbor (also in the neuropil). The extrafascicular segment extended up to 1 mm caudally from the fascicle through which it entered the tectum. At its terminus, the arbor was restricted to a single lamina in which it branched extensively over an elliptical area with major axes between 100 and 200 micron long. In the second test, retinal ganglion cell bodies were labeled by retrogradely transported HRP applied to the tectum in a manner intended to label all axons and terminals in the vicinity. The pattern and locations of labeled cells varied, depending on where the HRP was applied, in detailed accord with the model's predictions. The close agreement between the model and the observations supports the hypothesis of shifting terminals.
Novel Histopathological and Molecular Effects of Natural Compound Pellitorine on Larval Midgut Epithelium and Anal Gills of Aedes aegypti

The yellow fever mosquito, Aedes aegypti, is a vector for transmitting dengue fever and yellow fever. In this study, we assessed the histopathological and molecular effects of pellitorine, an isobutylamide alkaloid, on the third instar of Ae. aegypti larvae. At 5 mg/l concentration of pellitorine, the whole body of the treated larvae became dark in color, particularly damaged thorax and abdominal regions. Pellitorine was targeted mainly on midgut epithelium and anal gills, indicating variably dramatic degenerative responses of the midgut through a sequential epithelial disorganization. The anterior and posterior midgut was entirely necrosed, bearing only gut lumen residues inside the peritrophic membranes. Pellitorine caused comprehensive damage of anal gill cells and branches of tracheole and debris was found in hemolymph of the anal gills. RT-PCR analysis indicates that the compound inhibited gene expression encoding V-type H+-ATPase and aquaporine 4 after treatment with 2.21 mg/l pellitorine. These results verify that pellitorine merits further study as a potential larvicide with a specific target site and a lead molecule for the control of mosquito populations.
Learning Generalized Plans Using Abstract Counting

Given the complexity of planning, it is often beneficial to create plans that work for a wide class of problems. This facilitates reuse of existing plans for different instances drawn from the same problem or from an infinite family of similar problems. We define a class of such planning problems called generalized planning problems and present a novel approach for transforming classical plans into generalized plans. These algorithm-like plans include loops and work for problem instances having varying numbers of objects that must be manipulated to reach the goal. Our approach takes as input a classical plan for a certain problem instance. It outputs a generalized plan along with a classification of the problem instances where it is guaranteed to work. We illustrate the utility of our approach through results of a working implementation on various practical examples.
The effect of hospital safety-net burden status on short-term outcomes and cost of care after head and neck cancer surgery.

OBJECTIVE To determine the association between safety-net hospital care and short-term outcomes after head and neck cancer surgery. DESIGN Cross-sectional analysis. Safety-net burden was calculated as the percentage of patients with head and neck cancer with Medicaid or no insurance. SETTING Nationwide Inpatient Sample database. PATIENTS Adults who underwent an ablative procedure for a malignant oral cavity, laryngeal, hypopharyngeal, or oropharyngeal neoplasm in 2001 through 2008. MAIN OUTCOME MEASURES Associations between hospital safety-net burden and short-term morality, medical and surgical complications, length of hospitalization, and costs. RESULTS Overall, 123 662 patients underwent surgery in 2001 through 2008. Patients treated at high-safety-net burden hospitals were significantly more likely to be admitted urgently or emergently (odds ratio [OR], 1.54; 95% CI, 1.06-1.15 [P = .03]), undergo major surgical procedures (OR, 1.24; 95% CI, 1.09-1.39 [P = .001]), have advanced comorbidity (OR, 1.35; 95% CI, 1.06-1.72 [P = .02]), and be black (OR, 1.70; 95% CI, 1.29-2.23 [P < .001]), but less likely to be elderly (OR, 0.66; 95% CI, 0.53-0.82 [P < .001]). High safety-net burden hospitals were significantly more likely to be teaching hospitals (OR, 2.04; 95% CI, 1.26-3.29 [P = .004]) and less likely to be located in the West (OR, 0.18; 95% CI, 0.07-0.44 [P < .001]). Safety-net burden was not associated with in-hospital mortality, acute medical complications, surgical complications, or hospital-related costs after controlling for all other variables including hospital volume status, but was associated with a mean increase in length of hospitalization of 24 hours (P < .001). CONCLUSIONS These data suggest that safety-net hospitals provide valuable specialty care to a vulnerable population without an increase in complications or costs. Health care reform must address the economic challenges that threaten the viability of these institutions at the same time that demand for their services increases.
Phosphatidylethanol in Postmortem Brain and Serum Ethanol at Time of Death.

BACKGROUND Phosphatidylethanol (PEth) is a metabolite of ethanol (EtOH), and its concentration in whole blood samples is a direct biomarker of alcohol consumption. Because PEth is also present in the brain and incorporated in lipid membranes, it can be used to classify deceased individuals on alcohol consumption status at the time of death. The purpose of this study was to detect PEth homologs in postmortem brains of individuals known to have had alcohol use disorder (AUD) and to determine the relationship between serum alcohol at the time of death and PEth in the cerebellum (CE) and orbital frontal cortex (OFC). METHODS Postmortem brain was collected and stored according to standard protocol. Psychiatric symptoms experienced prior to death were obtained by next of kin psychological autopsy to categorize subjects. Thirty male subjects were chosen for analyses: 10 with AUD with positive serum EtOH levels present at time of autopsy (AUD-W), 10 with AUD without positive serum EtOH levels (AUD-WO), and 10 controls. PEth 16:0/18:1 and 16:0/18:2 were quantified in 50 mg of CE and OFC of human postmortem brain using HPLC and mass spectrometric detection (triple quadrupole). RESULTS Results of this study were as follows: (i) PEth 16:0/18:1 and 16:0/18:2 were detected in the CE and OFC of all subjects diagnosed with AUD, (ii) PEth 16:0/18:1 levels were about 10-fold higher than PEth 16:0/18:2 in all subjects and both areas of brain, (iii) AUD-W subjects had higher PEth homolog levels in CE and OFC than controls and AUD-WO subjects, (iv) PEth 16:0/18:1, but not PEth 16:0/18:2, levels in CE and OFC of AUD-W subjects correlated significantly with serum EtOH levels at the time of death. CONCLUSIONS Quantification of combined PEth homolog levels in postmortem human brain is a good candidate as a diagnostic factor to classify drinking status, especially for those with AUD at the time of death. For alcohol research studies with postmortem brain, verification of drinking status is essential.
Prediction of hybrid woven fabric electromagnetic shielding effectiveness

This paper deals with experimental verification of numerical models of fabric shielding effectiveness especially via analysis of leakage through the apertures (pores) in the textile structure. Equations for both solid shield and non-compact material were adopted from the literature, whereas an aperture equation based on waveguide conception was used. The experimental sample set was woven fabrics made of hybrid yarns composed of polypropylene fibers with different contents of staple stainless steel metal fibers in their structure. Geometrical characteristics of the aperture structure used for prediction were estimated with the aid of image analysis. Electric conductivity of the hybrid fabric was determined by measuring volume resistivity and plane-wave electromagnetic shielding properties of the sample set were measured by means of the coaxial transmission line method. The effect of metal fiber content on geometrical characteristics (e.g. area of pores, number of pores, cover factor), volume resistivity and electromagnetic shielding effectiveness was investigated. Results obtained by modeling of sample shielding effectiveness and experimental results achieved by measuring of shielding effectiveness were compared and discussed. It was confirmed that electromagnetic shielding effectiveness increased with a higher amount of metal fibers in the hybrid yarn structure. It was verified that the proposed numerical model is usable for predicting electromagnetic shielding effectiveness based on knowledge of dimensions of the structure apertures (pores), thickness of the fabric and volume resistivity of the material.
Endoscopic ultrasonography of nonfunctioning pancreatic islet cell tumors with histologic correlation.

BACKGROUND/AIMS Preoperative differentiation of benign and malignant pancreatic nonfunctioning islet cell tumors remains problematic. The present study aimed to evaluate endoscopic ultrasonography (EUS) features of benign and malignant tumors with histologic correlation. METHODOLOGY Ten patients with surgically resected nonfunctioning pancreatic islet cell tumors were retrospectively reviewed. RESULTS EUS demonstrated a homogenous hypoechoic (n=2) or hyperechoic (n=1) mass in the 3 benign tumors. EUS showed a hypoechoic mass with an irregular central hyperechoic portion (n=4), a hyperechoic mass with an irregular central hypoechoic portion (n=1), a cystic mass with a large irregular internal hypoechoic portion (n=1), or a hypoechoic mass within the entire lumen of the main pancreatic duct (MPD) (n=1) in the 7 malignant tumors. Histologically, the irregular central portions of the malignant tumors corresponded to necrosis, hemorrhage, fibrosis with hyalinosis, cystic degeneration, and/or calcification. Complete obstruction of the main pancreatic duct on EUS was observed in the 2 malignant tumors. The echogenicity of the tumors was closely associated with arrangement of tumor cells and quantity of fibrous stroma. CONCLUSIONS Heterogeneous internal structures and complete obstruction of the main pancreatic duct are considered as important EUS features that are suggestive of malignancy in nonfunctioning pancreatic islet cell tumors.
Application of Erlang distribution in cycle time estimation of toolsets with wip-dependent arrival and service in a single product-type single failure-type environment

This paper proposes a methodology based on phase type distributions and a state dependent Markov chain model to estimate the cycle time of workstations (toolsets) in semiconductor manufacturing. Due to implicit operational policies adopted by the line managers the performance of the existing queueing models for toolsets is not satisfactory. On the other hand developing accurate simulation models for toolsets can be very time consuming and hard to maintain. In this paper we propose a Markov chain model with the ability to include implicit operational rules on dispatching and maintenance. We verify the performance of this model via simulation and present the results for a variety of arrival and service distribution shapes.
Predictive Control of Networked Systems with Random Delay and Data Dropout

This paper is concerned with the stochastic stability analysis of networked control systems with random network delay. A new control scheme termed networked predictive control is proposed. This scheme mainly consists of the control prediction generator and network delay compensator. The control prediction generator provides a set of future control predictions to make the closed-loop system achieve the desired control performance and the network delay compensator removes the effects of the network transmission delay and data dropout. The stochastic stability criteria of the closed-loop networked predictive control systems are derived. A numerical example shows the effectiveness of the proposed scheme
An Attempt to Target Anxiety Sensitivity via Cognitive Bias Modification

Our goals in the present study were to test an adaptation of a Cognitive Bias Modification program to reduce anxiety sensitivity, and to evaluate the causal relationships between interpretation bias of physiological cues, anxiety sensitivity, and anxiety and avoidance associated with interoceptive exposures. Participants with elevated anxiety sensitivity who endorsed having a panic attack or limited symptom attack were randomly assigned to either an Interpretation Modification Program (IMP; n = 33) or a Control (n = 32) condition. During interpretation modification training (via the Word Sentence Association Paradigm), participants read short sentences describing ambiguous panic-relevant physiological and cognitive symptoms and were trained to endorse benign interpretations and reject threatening interpretations associated with these cues. Compared to the Control condition, IMP training successfully increased endorsements of benign interpretations and decreased endorsements of threatening interpretations at visit 2. Although self-reported anxiety sensitivity decreased from pre-selection to visit 1 and from visit 1 to visit 2, the reduction was not larger for the experimental versus control condition. Further, participants in IMP (vs. Control) training did not experience less anxiety and avoidance associated with interoceptive exposures. In fact, there was some evidence that those in the Control condition experienced less avoidance following training. Potential explanations for the null findings, including problems with the benign panic-relevant stimuli and limitations with the control condition, are discussed.
Fluoroscopic localization of the femoral head as a landmark for common femoral artery cannulation †

We sought to determine the reliability of frequently used landmarks for femoral arterial access in patients undergoing cardiac catheterization. The common femoral artery (CFA) is the most frequently used arterial access in cardiac catheterization. Arterial sheath placement into the CFA has been shown to decrease vascular complications. Some authors recommend locating the inferior border of the femoral head using fluoroscopy due to the relationship of the femoral head and the bifurcation of the CFA. We performed a descriptive study in a prospective design of 158 patients undergoing catheterization from the femoral approach. A femoral angiogram was performed, and the CFA bifurcation location was recorded in relation to the inguinal ligament, middle and inferior border of the femoral head, and the inguinal skin crease. The CFA bifurcation was distal to the inguinal ligament, middle femoral head, and inferior femoral head in most patients with mean distances (cm ± SD) of 7.5 ± 1.7, 2.9 ± 1.5, and 0.8 ± 1.2, respectively. The inguinal skin crease was below the bifurcation in 78% of patients (−1.8 ± 1.6 cm). The CFA overlies the femoral head in 92% of cases. The femoral head has a consistent relationship to the CFA, and localization using fluoroscopy is a useful landmark. © 2005 Wiley‐Liss, Inc.
Paper and pencil vs online self-administered food frequency questionnaire (FFQ) applied to university population: a pilot study.

OBJECTIVE To test the reliability of dietary intake data measured with an online food frequency questionnaires (FFQ) applied to a university population by comparing the results with those from a paper and pencil version. MATERIALS AND METHODS A total of 50 students were recruited from the second-year Food Technology course at the Universitat Politècnica de València (Comunidad Valenciana, Spain) in the academic year 2008-2009. The students were between the ages of 20-32. The participants completed both presentation modes of the FFQ (paper and pencil and online) in a cross-over study with a time interval of 3-week. To study the effect of ordering of the questionnaires, participants were randomly assigned to group A (paper and pencil FFQ first) and group B (online FFQ first). Both self-administered semi-quantitative presentations of the FFQ included 84 food items divided into six groups (dairy products; eggs, meat and fish; vegetables, legumes and fruits; bread, cereals and similar; oils, fats and sweets; beverages and pre-cooked). Participants were asked how frequently and how much each food item they had consumed in the previous year. RESULTS The response rate was 78% (39 students, 23% men and 77% women). For the total sample, the median dietary intakes were higher for the paper and pencil FFQ than the online version for energy (2,077 vs. 1,635 kcal/day), proteins (96 vs. 88 g/day), carbohydrates (272 vs. 211 g/day), and fat (70 vs. 58 g/day), respectively. These differences were statistically significant. However, there were not significant differences between the two presentations when the consumption by groups of food was calculated, except for "beverages and pre-cooked" group. CONCLUSIONS The pilot testing showed that this online FFQ is a useful tool for estimating the intake of food groups in this university population. On the other hand, the differences found in the results of the absolute quantities of energy and nutrients intakes were not clear. These differences could be due to the problems that the participants had for reporting portion size in the paper and pencil FFQ as photographs of portion sizes were not presented.
Clinical Characteristics and Prognosis of Nonleukemic Myeloid Sarcoma

Abstract:Myeloid sarcoma (MS) is an extramedullary mass that is composed of immature myeloid cells. The objectives of this study was to describe the frequency, clinical characteristics and the prognostic factors of patients with nonleukemic MS. Twenty-three cases of nonleukemic MS were recorded in the authors’ institution between April 2006 and March 2012. Most of the patients received systemic antiacute myeloid leukemia chemotherapy and the overall response rate was 91.3%, and 56.5% patients experienced complete remission. The anticipated 3-year progression-free survival and overall survival rates are 23% and 41%, respectively. The prognostic impact of nonleukemic MS is unclear. The cytogenetic and molecular abnormalities of malignant cells may be the most important prognostic factor because these are not always available because of cost and technical reason. In this case, the remission state, Ki67 score of tumor cells and number and size of the lesions might act as independent prognostic factors; this finding requires further confirmation.
The xaxAB Genes Encoding a New Apoptotic Toxin from the Insect Pathogen Xenorhabdus nematophila Are Present in Plant and Human Pathogens*

Xenorhabdus nematophila, a member of the Enterobacteriaceae, kills many species of insects by strongly depressing the immune system and colonizing the entire body. A peptide cytotoxin has been purified from X. nematophila broth growth, and the cytolytic effect on insect immunocytes and hemolytic effect on mammalian red blood cells of this toxin have been described (Ribeiro, C., Vignes, M., and Brehélin, M. (2003) J. Biol. Chem. 278, 3030–3039). We show here that this toxin, Xenorhabdus α-xenorhabdolysin (Xax), triggers apoptosis in both insect and mammalian cells. We also report the cloning and sequencing of two genes, xaxAB, encoding this toxin in X. nematophila. The expression of both genes in recombinant Escherichia coli led to the production of active cytotoxin/hemolysin. However, hemolytic activity was observed only if the two peptides were added in the appropriate order. Furthermore, we report here that inactivation of xaxAB genes in X. nematophila abolished the major cytotoxic activity present in broth growth, called C1. We also show that these genes are present in various entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus, in Pseudomonas entomophila, in the human pathogens Yersinia enterocolitica and Proteus mirabilis, and in the plant pathogen Pseudomonas syringae. This toxin cannot be classified in any known family of cytotoxins on the basis of amino acid sequences, locus organization, and activity features. It is, therefore, probably the prototype of a new family of binary toxins.
Scientific software process improvement decisions: A proposed research strategy

Scientific research is hard enough; software shouldn't make it harder. While traditional software engineering development and management practices have been shown to be effective in scientific software projects, adoption of these practices has been limited. Rather than presume to create a prescriptive scientific software process improvement manual or leave scientists to determine their own plans with only minimal references as support, we posit that a hybrid approach is required to adequately support and guide scientific SPI decisions. This paper presents a grounded theory approach for determining the driving factors of scientific software process planning activities in order to generate supporting data for a proposed Scientific Software Process Improvement Framework (SciSPIF).
Synaptojanin-2 Binding Protein Stabilizes the Notch Ligands DLL1 and DLL4 and Inhibits Sprouting Angiogenesis

Rationale: The formation of novel blood vessels is initiated by vascular endothelial growth factor. Subsequently, DLL4-Notch signaling controls the selection of tip cells, which guide new sprouts, and trailing stalk cells. Notch signaling in stalk cells is induced by DLL4 on the tip cells. Moreover, DLL4 and DLL1 are expressed in the stalk cell plexus to maintain Notch signaling. Notch loss-of-function causes formation of a hyperdense vascular network with disturbed blood flow. Objective: This study was aimed at identifying novel modifiers of Notch signaling that interact with the intracellular domains of DLL1 and DLL4. Methods and Results: Synaptojanin-2 binding protein (SYNJ2BP, also known as ARIP2) interacted with the PDZ binding motif of DLL1 and DLL4, but not with the Notch ligand Jagged-1. SYNJ2BP was preferentially expressed in stalk cells, enhanced DLL1 and DLL4 protein stability, and promoted Notch signaling in endothelial cells. SYNJ2BP induced expression of the Notch target genes HEY1, lunatic fringe (LFNG), and ephrin-B2, reduced phosphorylation of ERK1/2, and decreased expression of the angiogenic factor vascular endothelial growth factor (VEGF)-C. It inhibited the expression of genes enriched in tip cells, such as angiopoietin-2, ESM1, and Apelin, and impaired tip cell formation. SYNJ2BP inhibited endothelial cell migration, proliferation, and VEGF-induced angiogenesis. This could be rescued by blockade of Notch signaling or application of angiopoietin-2. SYNJ2BP-silenced human endothelial cells formed a functional vascular network in immunocompromised mice with significantly increased vascular density. Conclusions: These data identify SYNJ2BP as a novel inhibitor of tip cell formation, executing its functions predominately by promoting Delta-Notch signaling.