Miracle-dz/UniFAR-FTUs huggingface dataset:
Topology identification of undirected consensus networks via sparse inverse covariance estimation

We study the problem of identifying sparse interaction topology using sample covariance matrix of the state of the network. Specifically, we assume that the statistics are generated by a stochastically-forced undirected first-order consensus network with unknown topology. We propose a method for identifying the topology using a regularized Gaussian maximum likelihood framework where the ℓ1 regularizer is introduced as a means for inducing sparse network topology. The proposed algorithm employs a sequential quadratic approximation in which the Newton's direction is obtained using coordinate descent method. We provide several examples to demonstrate good practical performance of the method.
Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation

The activation of translation contributes to malignant transformation and is an emerging target for cancer therapies. RNA G-quadruplex structures are general inhibitors of cap-dependent mRNA translation and were recently shown to be targeted for oncoprotein translational activation. In contrast however, the G-quadruplex within the 5'UTR of the human vascular endothelial growth factor A (VEGF) has been shown to be essential for IRES-mediated translation. Since VEGF has a pivotal role in tumor angiogenesis and is a major target of anti-tumoral therapies, we investigated the structure/function relationship of the VEGF G-quadruplex and defined whether it could have a therapeutic potential. We found that the G-quadruplex within the VEGF IRES is dispensable for cap-independent function and activation in stress conditions. However, stabilization of the VEGF G-quadruplex by increasing the G-stretches length or by replacing it with the one of NRAS results in strong inhibition of IRES-mediated translation of VEGF. We also demonstrate that G-quadruplex ligands stabilize the VEGF G-quadruplex and inhibit cap-independent translation in vitro. Importantly, the amount of human VEGF mRNA associated with polysomes decreases in the presence of a highly selective stabilizing G-quadruplex ligand, resulting in reduced VEGF protein expression. Together, our results uncover the existence of functionally silent G-quadruplex structures that are susceptible to conversion into efficient repressors of cap-independent mRNA translation. These findings have implications for the in vivo applications of G-quadruplex-targeting compounds and for anti-angiogenic therapies.
A two-stage dc-dc converter for the fuel cell-supercapacitor hybrid system

A wide input range multi-stage converter is proposed with the fuel cells and supercapacitors as a hybrid system. The front-end two-phase boost converter is used to optimize the output power and to reduce the current ripple of fuel cells. The supercapacitor power module is connected by push-pull-forward half bridge (PPFHB) converter with coupled inductors in the second stage to handle the slow transient response of the fuel cells and realize the bidirectional power flow control. Moreover, this cascaded structure simplifies the power management. The control strategy for the whole system is analyzed and designed. A 1kW prototype controlled by TMS320F2808 DSP is built in the lab. Simulation and experimental results confirm the feasibility of the proposed two-stage dc-dc converter system.
PACAP and NGF regulate common and distinct traits of the sympathoadrenal lineage: effects on electrical properties, gene markers and transcription factors in differentiating PC12 cells

To determine the possible role of pituitary adenylate cyclase‐activating polypeptide (PACAP) in the development of the sympathoadrenal cell lineage, we have examined the effects of this neurotrophic peptide, in comparison to nerve growth factor (NGF), on the morphology, electrophysiological properties, expression of neuronal and neuroendocrine marker genes, and activity of transcription factors during differentiation of sympathoadrenal‐derived cells, using the rat pheochromocytoma PC12 cell model. Both PACAP and NGF elicited rapid neurite outgrowth, which was accompanied by induction of cell excitability and the development of both sodium and calcium currents. Concurrently, PACAP and NGF increased the expression of a marker of synaptic vesicles. By contrast, PACAP, but not NGF, regulated the expression of different constituents of neuroendocrine large dense core vesicles in PC12 cells. Furthermore, PACAP and NGF differentially regulated the expression of mammalian achaete‐scute homologue and paired homeobox 2b genes, transcription factors instrumental for sympathoadrenal development. To compare downstream effectors activated by PACAP and NGF, we studied the effects of these factors on the binding activity of consensus 12‐O‐tetradecanoylphorbol‐13‐acetate‐ and cAMP‐responsive elements to nuclear extracts of differentiating PC12 cells. We found that both PACAP and NGF markedly increase the binding activity of these cis‐regulatory sequences and that PACAP preferentially recruits activator protein‐1‐like transcription factors to these elements. Taken together, these results show that PACAP and NGF exert common as well as different effects on neuronal and neuroendocrine traits in differentiating PC12 cells, strongly suggesting that these two trophic factors could play complementary roles in the development of the sympathoadrenal cell lineage.
A Methodological Comparison between PLS Path Modeling and Generalized Structured Component Analysis

PLS Path Modeling and Generalized Structured Component Analysis are two component-based approaches to Structural Equation Models. Both methods aim at estimating the causal relationships linking two or more latent variables by means of a set of observed indicators. Moreover, both methods define the latent variable as a linear combination of its own observed variables, i.e. as a component. The main difference between the two approaches is in the estimation of the model parameters. In fact, PLS Path Modeling uses an iterative algorithm based on a series of interdependent regressions, while the Generalized Structured Component Analysis defines a unique algebraic formulation for the model and uses an Alternative Least Square algorithm. Despite several studies have been performed to compare the PLS Path Modeling and the covariance-based approaches to Structural Equation Modeling, only a recent simulation study involves also the Generalized Structured Component Analysis (Hwang et al., 2010). Here, a new simulation study is presented in order to asses the performances of both PLS Path Modeling and Generalized Structured Component Analysis. We discuss the links between Generalized Structured Component Analysis and the Maximum Sum of Explained Variance method (Glang, 1988), as well as the links between the Glangs’s method and the PLS Path Modeling. Moreover, in Generalized Structured Component Analysis the measurement model seems to play a major role when estimating the model parameters.
Wolves, Moose, and the Allometry of Population Cycles

After a decade of dramatic population fluctuations, protected populations of wolves and moose in Isle Royale National Park in Lake Superior returned in 1983 to the levels observed in the 1950's. Inherent lags in this predator-prey system and the strong recovery of the moose population following a wolf population crash suggest that these populations may continue to cycle with a period length of about 38 (95 percent confidence interval, �13) years. Such a long-term cycle is consistent with the proposal that period length of herbivore population cycles will characteristically scale according to the fourth root of body mass, a basic allometric relation linking physiological cycles to population processes.
The Utility of Evolving Simulated Robot Morphology Increases with Task Complexity for Object Manipulation

Embodied artificial intelligence argues that the body and brain play equally important roles in the generation of adaptive behavior. An increasingly common approach therefore is to evolve an agent's morphology along with its control in the hope that evolution will find a good coupled system. In order for embodied artificial intelligence to gain credibility within the robotics and cognitive science communities, however, it is necessary to amass evidence not only for how to co-optimize morphology and control of adaptive machines, but why. This work provides two new lines of evidence for why this co-optimization is useful: Here we show that for an object manipulation task in which a simulated robot must accomplish one, two, or three objectives simultaneously, subjugating more aspects of the robot's morphology to selective pressure allows for the evolution of better robots as the number of objectives increases. In addition, for robots that successfully evolved to accomplish all of their objectives, those composed of evolved rather than fixed morphologies generalized better to previously unseen environmental conditions.
High‐Speed Cell Sorting of Infectious Trophic and Cystic Forms of Pneumocystis carinii

ABSTRACT. The separation of Pneumocystis carinii life‐cycle stages while preserving infectivity is a hitherto unresolved challenge. We describe an original, reproducible, and efficient method for separating trophic from cystic forms of P. carinii using a high‐speed cell sorter. The large amounts of highly purified (99.6±0.3%) infectious trophic and cystic forms can now be used to elucidate the poorly understood P. carinii life cycle.
Bone Marrow Function After (131)I Therapy in Patients With Differentiated Thyroid Carcinoma.

OBJECTIVE The primary objective was to evaluate the short- and long-term toxic effects of radioiodine ((131)I) therapy on bone marrow function in differentiated thyroid carcinoma (DTC) patients. The secondary objective was to define characteristics of patients at risk for impaired bone marrow function after (131)I treatment. PATIENTS AND METHODS DTC patients treated with (131)I between 1989 and 2013 were included. We excluded patients with morbidities or treatments that could have influenced blood count parameters. Baseline platelets, leukocytes, and hemoglobin levels were compared with blood counts at 3 and 6 months and at 1 and 5 years after treatment. Logistic multivariate regression analyses were performed to determine patient characteristics associated with thrombocytopenia. RESULTS We included 331 patients. Mean ± SD age was 47.5 ± 17.2 years, and 74.0% were female. Posttreatment platelets were significantly decreased at 6 months and 1 year, as compared with baseline. Leukocyte counts were also decreased at 3 and 6 months and at 1 year after treatment. No decreases in hemoglobin were found. Five years after treatment, platelet and leukocyte counts were comparable with baseline. Fourteen patients (4.2%) developed transient posttreatment thrombocytopenia. Risk factors for thrombocytopenia were older age, T4 tumor stage, male gender, and cumulative dose (131)I. After a multivariate regression analysis, the cumulative dose (131)I remained independently associated with thrombocytopenia. CONCLUSION Posttreatment platelets and leukocytes were transiently decreased compared with pretreatment values in a general DTC population. Cumulative (131)I dose was independently associated with thrombocytopenia. Platelets and leukocytes normalized to baseline levels 5 years after treatment, implying that in most patients the clinical effects of bone marrow toxicity are limited.
High-Level Nickel Resistance in Alcaligenes xylosoxydans 31A and Alcaligenes eutrophus KTO2

Two new nickel-resistant strains of Alcaligenes species were selected from a large number (about 400) of strains isolated from ecosystems polluted by heavy metals and were studied on the physiological and molecular level. Alcaligenes xylosoxydans 31A is a heterotrophic bacterium, and Alcaligenes eutrophus KTO2 is an autotrophic aerobic hydrogen-oxidizing bacterium. Both strains carry—among other plasmids—a megaplasmid determining resistance to 20 to 50 mM NiCl2 and 20 mM CoCl2 (when growing in defined Tris-buffered media). Megaplasmids pTOM8, pTOM9 from strain 31A, and pGOE2 from strain KTO2 confer nickel resistance to the same degree to transconjugants of all strains of A. eutrophus tested but were not transferred to Escherichia coli. However, DNA fragments carrying the nickel resistance genes, cloned into broad-hostrange vector pVDZ'2, confer resistance to A. eutrophus derivatives as well as E. coli. The DNA fragments of both bacteria, TBA8, TBA9, and GBA (14.5-kb BamHI fragments), appear to be identical. They share equal size, restriction maps, and strong DNA homology but are largely different from fragment HKI of nickel-cobalt resistance plasmid pMOL28 of A. eutrophus CH34.
Cerebral metabolism in man after acute stroke: New observations using localized proton NMR spectroscopy

Localized proton NMR spectroscopy at 1.5 T using stimulated echoes has been applied to study metabolic alterations in the postischemic phase of patients with acute cerebral infarction. A complete depletion of N‐acetyl aspartate in the area of infarction has been observed in a patient studied 4 days after stroke. This finding was paralleled by a dramatic increase in the concentration of lactic acid to about 16 mM within the lesion, indicating continued anaerobic glycolysis. The diluting effect of the edema has been estimated to reduce average metabolite concentrations by about a factor of 3. © 1989 Academic Press, Inc.
Effects of C4 null alleles and homoduplications on quantitative expression of C4A and C4B

The availability of MoAbs now allows the accurate quantification of the individual C4 isotypes, C4A and C4B. Using a sensitive two‐site immunoradiometric technique to measure serum levels of C4A and C4B, we studied the relationship between genotype and phenotype and physiological factors affecting C4 expression in 129 fully genotyped healthy subjects. Our results confirm that there is extensive phenotypic overlap between genotypic groups and it was not possible to determine the presence of single null alleles from total serum C4. Of the factors which may influence C4 expression, we found that age contributes a very small influence but that gender has no effect and there was no evidence for the presence of feedback of null alleles on the expression of remaining genes. Potential problems in quantifying C4 arising from the complex relationship between isotypic identity and serotypic recognition were highlighted by the finding of reversed antigenic expression of a C4B*5 molecule which was recognized as C4A by the anti‐Rg: 1 monoclonal used in these studies. We also confirmed that the extended MHC haplotype associated with Felty's syndrome, HLA‐B44, C4A*3. C4BQ*O, HLA‐DR4, encodes an expressed, duplicated, C4A gene.
Esophageal Dysmotility and its Relation to Systemic Sclerosis Variant

To the Editor: Dr. Lock et al. (1) have recently published their results concerning the association between esophageal dysfunction and pulmonary functional impairment in systemic sclerosis (SSc). In the discussion section of their paper, the authors state that patients with the diffuse-variant of SSc were significantly overrepresented in the group with esophageal dysfunction. I would submit that the literature does not clearly corroborate their findings, and caution is in order in this regard. Specifically, a study published by Akesson and Wolheim (2) has shown that the frequency of esophageal dysmotility is similar in patients with limited and diffuse skin involvement. In this study, the authors used a combination of cineradiographic and radionuclide scintigraphic techniques to assess esophageal function in 37 patients with diffuse, and 67 with limited SSc. There was, however, the suggestion that patients with diffuse-variant SSc have a more pronounced motility disturbance. Garrett et al. (3) studied 124 patients and used manometry to assess for esophageal dysfunction in patients with SSc. These authors found that esophageal dysfunction was not related to the severity or extent of cutaneous or visceral SSc-involvement. In 1993, colleagues and I published the results of a prospective investigation of esophageal motility and acid reflux (pH monitoring) testing in 36 patients with SSc (4). Our study included 16 patients with diffuse SSc and 20 patients with limited SSc, as classified by previously published criteria (5). These same criteria were utilized by Lock et al. (1) in their study. For analysis, we separated our patients into two subgroups, based on the presence or absence of distal esophageal peristalsis. We found these two subgroups to be similar with regard to the relative frequency of diffuse or limited SSc (by Fisher exact test; p 5 0.718). Furthermore, mean lower esophageal sphincter pressure was not significantly different between patients with the diffuse and limited SSc variants (17.9 1 1.9 and 14.4 1 1.5 mm Hg, respectively). Lastly, Lock et al. (6) had recently quoted a fourth study, which suggested that there is no significant difference in the frequency of gastrointestinal involvement between patients with the diffuse and limited variants of SSc (7). The above study results would appear to support the conclusion that the weight of evidence suggests that the frequency and severity of esophageal dysmotility are similar in patients with the diffuse and limited variants of SSc.
Bedside Shift Reports: What Does the Evidence Say?

Bedside shift reports are viewed as an opportunity to reduce errors and important to ensure communication between nurses and communication. Models of bedside report incorporating the patient into the triad have been shown to increase patient engagement and enhance caregiver support and education. Nurse shift reports and nurse handovers are 2 of the most critical processes in patient care that can support patient safety and reduce medical errors in the United States. Nurses continue to not recognize the evidence supporting this practice and adopt bedside report into practice.
A Phytochemical Investigation of Zanthoxylum setulosum

The crude bark extract of Zanthoxylum setulosum from Monteverde, Costa Rica was notably cytotoxic (100% kill at 100 μg/mL) to MCF-7, MDA-MB-231, and MDA-MB-468 cells in vitro. Phytochemical studies of the bark extract revealed the triterpenoid lupeol, the lignan sesamin, the sesquiterpene sesquichamaenol, and the xanthone lichexanthone. This is the first report of the isolation of sesquichamaenol and lichexanthone from the bark extract of Z. setulosum. All structures were determined using NMR spectroscopic techniques (1H NMR and 13C NMR) and GCMS and by comparison with literature data. Lupeol proved to be the cytotoxic component of Z. setulosum bark.
Spinal lesions treated with Novalis shaped beam intensity-modulated radiosurgery and stereotactic radiotherapy.

OBJECT Spinal radiosurgery was implemented to improve quality of life (QOL) in patients with malignancies. It may also be applicable to the treatment of benign lesions. METHODS Between July 2002 and January 2004, 14 patients harboring 22 lesions were treated; 13 received single-dose stereotactic radiosurgery. Six were women. The mean age was 60.2 years (range 48-82 years). There were 11 metastases, two neurofibromas, and one meningioma. Six lesions were cervical, 10 thoracic, and six lumbar. Ten patients suffered pain, three paresthesias, two weakness, and three were asymptomatic. Seven patients underwent spinal surgery, with four receiving instrumentation. Twelve patients underwent conventional irradiation before stereotactic radiosurgery/stereotactic radiotherapy. A mean dose of 12+/-2.7 Gy (range 8-21 Gy) was prescribed to the 91% isodose line (range 85-97%). The mean tumor volume was 25+/-27.1 ml (range 0.75-91.8 ml). Treatment was planned using intensity-modulated radiosurgery (IMRS) fields in 15 cases, dynamic arcs in five, and conformal beams in two. The mean follow-up period was 6.1+/-3.9 months (range 1-16 months). Three patients became pain free and four experienced considerable relief. Weakness improved in the two patients with this preoperative symptom and the asymptomatic patients remained so. Four lesions decreased in size, five remained stable, seven progressed, and six were not followed up (two patients died before follow up). Four patients in all died, three of systemic disease and one of thoracic lesion progression. No complications due to shaped beam and IMRS/intensity-modulated radiotherapy (IMRT) techniques were observed. CONCLUSIONS Shaped beam and IMRS/IMRT involving the Novalis system may delay neurological deterioration, improving QOL. The lack of complication suggests that higher doses can be delivered to improve the control rate in patients with metastases.
Psychometric Properties of the Body Image Scale in Turkish Ostomy Patients.

PURPOSE To investigate the validity and reliability of the Body Image Scale in Turkish ostomy patients. METHODS This study has a methodological and cross-sectional design. A hundred patients with ostomy lasting for at least 2 months were recruited from an ostomy and wound care unit. FINDINGS Confirmatory factor analyses showed that goodness-of-fit indexes were acceptable. Exploratory factor analyses showed that factor loadings of the scale items varied between 0.74 and 0.91, and a single factor was determined. The Cronbach's alpha value of the scale was 0.94. Item-to-total correlation coefficients ranged from 0.75 to 0.91. CONCLUSION The Turkish version of the Body Image Scale is a valid and reliable tool for evaluating body image in Turkish ostomy patients.
From conference abstract to full paper: differences between data presented in conferences and journals

Background: We studied the type and frequency of differences between data presented in conference abstracts and subsequent published papers in the fields of infectious diseases and microbiology. Methods: We reviewed all abstracts from the first session of 7 of 15 major research categories presented in the 1999 and 2000 Interscience Conference on Antimicrobial Agents and Chemotherapy. For each selected pair of abstract and related published paper, two independent investigators performed a detailed data comparison. Results: From 190 abstracts reviewed, 68 (36%) were subsequently published as full papers by March 2004. Fifty‐two pairs referred to the same study population and period. Differences were found in 30 of 51 pairs, which were further analyzed (point estimate = 59%, 95% C.I.: 45–73%). The identified differences were related to both the aims and conclusions of the study (3/30), the study conclusions only (2/30), numbers and/or rates of the studied patients (10/30), numbers or rates of microbiological isolates (9/30), MIC values or Ki values (5/30), other pharmacological properties of antibiotics (2/30), odds ratio (1/30), and duration of observation (1/30). Some differences were considered major. In bivariable associations, time to publication (from presentation in the conference to publication of the full paper) was associated with identifiable differences between the conference abstract and the full paper (OR=1.76, 95% CI 0.95–3.24/year of delay, P=0.07). Conclusions: It is reassuring that although we identified several reportable differences, only a very small proportion of studies exhibited differences in their aims and/or conclusions. Researchers may benefit from the above findings in improving the accuracy of presented data. —Rosmarakis, E. S. , Soteriades, E. S. , Vergidis, P. I. , Kasiakou, S. K. , Falagas, M. E. From conference abstract to full paper: differences between data presented in conferences and journals. FASEB J. 19, 673–680 (2005)