Miracle-dz/UniFAR-FTUs huggingface dataset:
Excitotoxic degeneration is initiated at non-random sites in cultured rat cerebellar neurons

Prolonged stimulation of cultured cerebellar neurons by kainic acid (KA) leads to death of neurons first evident from the swelling of soma and neurites. Stimulation is accompanied by increases in [Ca2+]i and [Na+]i as monitored using digital imaging microfluorimetry. “Blebs” tended to form on neurites with the highest increases in [Ca2+]i. Points of Ca2+ entry into neurites via glutamate-receptor-gated channels predicted where approximately 80% of blebs would form tens of minutes later. These sites were close to neurite intersections where there was a high likelihood of synaptic contacts and were enriched in mitochondria as revealed by rhodamine 123 staining. Ca2+, but not Na+ entry, produced a loss of mitochondrial potential. Prolonged KA, but not 50K, applications could fully dissipate the neuronal Na+ gradient. Recovery of resting [Na+]i was delayed by Ca2+ loading. We propose that blebs form at certain synaptic regions due to localized ionic fluxes and local Ca2+ overloading. Increased [Ca2+]i may hamper restoration of normal [Na+]i permitting local osmotic swelling as well as activation of Ca(2+)-dependent enzymes and other processes. Na+ may slow, block, or reverse Na/Ca exchange and enhance swelling. These conditions could not be reproduced by global changes in ion concentrations produced by Ca2+ or Na+ ionophores. The earliest stages of excitotoxicity thus appear to be manifestations of localized disruptions of ionic homeostasis mediated by Ca2+ overload and Na+ influx.
Acute renal failure in the course of HIV infection: a single-institution retrospective study of ninety-two patients and sixty renal biopsies.

BACKGROUND Acute renal failure syndromes are frequently encountered in patients with human immunodeficiency virus (HIV) infection. Most reported cases of acute renal failure are related to acute tubular necrosis, but many other causes of renal failure have been described in these patients. METHODS The present work is a single-institution retrospective study of 92 HIV-infected patients with acute or rapidly progressing renal failure. In 60 cases, a renal biopsy was performed. For each patient we analysed clinical and pathological data, as well as the short-term prognosis. RESULTS Ten different causes of acute or rapidly progressing renal failure were documented: (i) haemolytic uraemic syndrome (32 patients); (ii) acute tubular necrosis either of ischaemic-toxic origin (18 patients) or due to rhabdomyolysis (six patients); (iii) obstructive renal failure which was either extrinsic (two patients), drug-induced (13 patients) or secondary to paraprotein precipitation (one patient); (iv) HIV-associated nephropathy (14 patients); (v) acute interstitial nephritis (two patients); (vi) various glomerulonephritis (four patients). In most cases, renal failure was severe (the mean creatinine clearance at entry was 12 ml/min). Most patients had a significant improvement in renal function with only symptomatic treatment. Eighteen per cent of the patients died within 2 months of the diagnosis of renal failure. Renal biopsy seems important for the diagnosis but also for the prognosis, at least in the cases of haemolytic-uraemic syndrome, HIV-associated nephropathy and drug-induced micro-obstructive renal failure. CONCLUSION Vascular and glomerular diseases are frequent causes of acute or rapidly progressing renal failure in HIV-infected patients. Renal biopsy appears to be safe and useful for the diagnosis and the prognosis of the renal failure. High mortality rate is only observed in patients with ischaemic/toxic causes of acute renal failure.
Simultaneous irrigation and negative pressure wound therapy enhances wound healing and reduces wound bioburden in a porcine model

Infected foot wounds are one of the most common reasons for hospitalization and amputation among persons with diabetes. The objective of the study was to investigate a new wound therapy system that employs negative pressure wound therapy (NPWT) with simultaneous irrigation therapy. For this study, we used a porcine model with full‐thickness excisional wounds, inoculated with Pseudomonas aeruginosa. Wounds were treated for 21 days of therapy with either NPWT, NPWT with simultaneous irrigation therapy using normal saline or polyhexanide biguanide (PHMB) at low or high flow rates, or control. Data show that NPWT with either irrigation condition improved wound healing rates over control‐treated wounds, yet did not differ from NPWT alone. NPWT improved bioburden over control‐treated wounds. NPWT with simultaneous irrigation further reduced bioburden over control and NPWT‐treated wounds; however, flow rate did not affect these outcomes. Together, these data show that NPWT with simultaneous irrigation therapy with either normal saline or PHMB has a positive effect on bioburden in a porcine model, which may translate clinically to improved wound healing outcomes.
Detection of SNP‐SNP interactions in trios of parents with schizophrenic children

Schizophrenia (SZ) is a heritable and complex psychiatric disorder with an estimated worldwide prevalence of about 1%. Research on the risk factors for SZ has thus far yielded few clues to causes, but has pointed to a heterogeneous etiology that likely involves multiple genes and gene‐environment interactions. In this manuscript, we apply a novel method (trio logic regression, Li et al., 2009) to case‐parent trio data from a SZ candidate gene study conducted on families of Ashkenazi Jewish descent, and demonstrate the method's ability to detect multi‐gene models for SZ risk in the family‐based design. In particular, we demonstrate how this method revealed a genotype‐phenotype association that includes an allele without marginal effect. Genet. Epidemiol. 34: 396–406, 2010. © 2010 Wiley‐Liss, Inc.
An Asynchronous Projection and Summation Circuit for In-Pixel Processing in Single Photon Avalanche Diode Sensors

An asynchronous projection and summation circuit is proposed for single photon avalanche diode (SPAD) sensors. Thanks to the efficient interconnection by the asynchronous technique, the circuit can be easily implemented inside 2D SPAD arrays. As a result, the precise summation of the 1b data in one row can be parallel processed for all rows within the same cycle. A test-of-concept chip was fabricated in a 1P5M 0.18 μm CMOS process. By measurement results, the summation of a 15-pixel row can be achieved by the proposed circuit within 22 ns. Such a speed is very important for SPAD-based sensors that need fast summation operations.
Process Information and Evolution

Universal semantic communication (USC) is a theory that models communication among agents without the assumption of a fixed protocol. We demonstrate a connection, via a concept we refer to as process information, between a special case of USC and evolutionary processes. In this context, one agent attempts to interpret a potentially arbitrary signal produced within its environment. Sources of this effective signal can be modeled as a single alternative agent. Given a set of common underlying concepts that may be symbolized differently by different sources in the environment, any given entity must be able to correlate intrinsic information with input it receives from the environment in order to accurately interpret the ambient signal and ultimately coordinate its own actions. This scenario encapsulates a class of USC problems that provides insight into the semantic aspect of a model of evolution proposed by Rivoire and Leibler. Through this connection, we show that evolution corresponds to a means of solving a special class of USC problems, can be viewed as a special case of the multiplicative weights updates algorithm, and that infinite population selection with no mutation and no recombination conforms to the Rivoire–Leibler model. Finally, using process information we show that evolving populations implicitly internalize semantic information about their respective environments.
Long-Term Assessment of Hind Limb Motor Function and Neuronal Injury Following Spinal Cord Ischemia in Rats

Recent evidence suggests that brain injury caused by ischemia is a dynamic process characterized by ongoing neuronal loss for at least 14 days after ischemia. However, long-term outcome following spinal cord ischemia has not been extensively examined. Therefore, we investigated the changes of hind limb motor function and neuronal injury during a 14-day recovery period after spinal cord ischemia. Male Sprague-Dawley rats received spinal cord ischemia (n = 64) or sham operation (n = 21). Spinal cord ischemia was induced by inflation of a 2F Fogarty catheter placed into the thoracic aorta for 6, 8, or 10 minutes. The rats were killed 2, 7, or 14 days after reperfusion. Hind limb motor function was assessed with the 21-point Basso, Beattie, and Bresnahan (BBB) scale during the recovery period. The number of normal and necrotic neurons was counted in spinal cord sections stained with hematoxylin/eosin. Longer duration of spinal cord ischemia produced severer hind limb motor dysfunction at each time point. However, BBB scores gradually improved during the 14-day recovery period. Neurologic deterioration was not observed between 7 and 14 days after reperfusion. The number of necrotic neurons peaked 2 days after reperfusion and then decreased. A small number of necrotic neurons were still observed 7 and 14 days after reperfusion in some of the animals. These results indicate that, although hind limb motor function may gradually recover, neuronal loss can be ongoing for 14 days after spinal cord ischemia.
Soy phytoestrogens do not prevent bone loss in postmenopausal monkeys.

The putative skeletal effects of dietary soy phytoestrogens (SPE) were examined in comparison with those of conjugated equine estrogens (CEE; Premarin) in a 3-yr longitudinal study in ovariectomized female monkeys. Controls received alcohol-extracted soy protein with low phytoestrogen content, and treatment groups received either CEE (admixed into the control diet) or unextracted soy protein isolate containing SPE. The acknowledged bone protective effect of CEE was reflected by higher bone mass (by dual energy x-ray absorptiometry) and lower bone turnover marker levels. In contrast, control and SPE groups lost significant lumbar spine bone mineral content and density and whole body bone mineral content within the first year, resulting in reduced bone mass for both groups compared with CEE (P < 0.0005). No effect of SPE was observed for any bone mass measure (P > 0.44), although transient, estrogen-like effects of SPE on serum alkaline phosphatase, calcium, and C-terminal cross-link of type I collagen were observed at 3 months (P < 0.02). These results suggest that SPE may be poor substitutes for mammalian estrogens in protecting against bone loss resulting from estrogen deficiency.
TEOS plasma polymerized films: Impact of clustered material in humidity measurement

This work aims to humidity and VOCs measurement using TEOS films or TEOS/HFE composites. Films, exposed or not to ultraviolet, were tested on cycles of relative humidity ranging from 25% to 85% and VOCs interference were also evaluated. TEOS films showed good reproducibility up to 85% relative humidity but quick reaction on 90%. The best detection limit was 100 ppm, using TEOS films exposed to UVC and TEOS/HFE composites show sensitivity of 4 Hz/% humidity, but interdigitated electrodes quickly saturate. VOCs were detected in the 1% w/w in air and do not interfere in the relative humidity detection.
Reproductive, biochemical, physiological, and population responses in perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.) downstream of two elemental chlorine‐free pulp and paper mills

Perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.) populations in a state of late vitellogenesis were studied downstream of two pulp and paper mills and at upstream references in southern Lake Saimaa, Finland. The mills used elemental chlorine‐free bleaching and activated sludge effluent treatment technologies. The exposure of fish to pulp mill effluents, as measured by concentrations of chlorophenolics in the bile and liver ethoxyresorufin‐O‐deethylase (EROD) activity, was low and almost similar to the references. Nevertheless, bile resin acid concentrations in exposed perch and roach (260–320 μg/ml) and bile β‐sitosterol concentrations in exposed roach (1.5–3.5 μg/ml) were, respectively, 10 to 30 times and 2 to 5 times higher compared with the references. Reproductive parameters like plasma 17β‐estradiol and testosterone levels were lower in exposed male and female perch but the same in roach. Vitellogenin concentrations in plasma and liver cytosol of roach were similar. Gonad weight and fecundity were lower in exposed female perch but similar in roach. The relative liver weight was higher in exposed roach but not in perch. The body condition and immunologic parameters in fish were the same. The growth and age at maturity of exposed perch and roach were similar to the references. The size and age distribution of perch in the recipient of one of the mills was shifted toward smaller and younger fish. Our results show that several reproductive variables were altered in late vitellogenic perch in the vicinity of the mills, but they were not altered in roach.
A Model for Neutral Defect Limited Electron Mobility in Strained-Silicon Inversion Layers

On the strained silicon metal–oxide–semiconductor field-effect transistors (MOSFETs), we show how to derive a formalism dealing with the scattering of a 2-D electron by a neutral defect. The corresponding neutral defect limited inversion-layer electron mobility, <inline-formula> <tex-math notation="LaTeX">$\mu _{n}$ </tex-math></inline-formula>, is calculated in the momentum relaxation time approximation. The calculated results lead to a new analytical model: <inline-formula> <tex-math notation="LaTeX">$\mu _{n} =cN_{n} ^{-1}$ </tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$N_{n}$ </tex-math></inline-formula> is the neutral defect density per unit area and <inline-formula> <tex-math notation="LaTeX">${c}$ </tex-math></inline-formula> is the coefficient independent of the inversion-layer density, the strain, and the temperature. The validity and applicability of the model are confirmed by citing three independent experiments on strained silicon MOSFETs undergoing different implantation sources and different annealing budgets. Importantly, this paper clarifies for the first time that strain will not change neutral defect limited mobility unless changing the neutral defect density. This reasonably explains the two experimental observations during implantation and annealing: 1) the implantation-induced strain relaxation in strained sample does not occur and 2) the neutral defect density is much higher in strained sample than in unstrained sample.
Differential regulation of chemokine production by Fcγ receptor engagement in human monocytes: association of CCL1 with a distinct form of M2 monocyte activation (M2b, Type 2)

CC chemokine ligand 1 (CCL1; I‐309) is a CC chemokine that interacts with CC chemokine receptor 8, which is preferentially expressed in polarized T helper cell type 2 and Tc2 cells, in eosinophils, and in T regulatory cells. The present study, prompted by transcriptional profiling of human monocytes undergoing different forms of activation, was designed to characterize the production of CCL1 in monocytes compared with the production of other chemokines (CCL2, CCL22, and CCL18) differentially regulated by distinct activation signals. Lipopolysaccharide (LPS), interferon‐γ (IFN‐γ), interleukin (IL)‐1β, tumor necrosis factor α, IL‐4, IL‐13, IL‐10, IL‐6, IL‐18, and combinations thereof did not induce CCL1 production in monocytes, and some of these signals stimulated production of reference chemokines. Induction of CCL1 in monocytes required engagement of Fc receptor for immunoglobulin G (FcγR)II and exposure to IL‐1β or LPS. This combination of stimuli results in a form of M2 (M2b, Type 2) macrophage activation. FcγR engagement also induced CCL22 and amplified its stimulation by IL‐4. In contrast, FcγR stimulation inhibited the IL‐10‐ and LPS‐mediated induction of CCL18. IL‐10, IL‐4, and IFN‐γ inhibited induction of CCL1 by FcγR ligation and IL‐1β. CCL1 was present in synovial fluids and macrophages in juvenile idiopathic arthritis. Thus, regulation of CCL1 in human monocytes is unique, with an obligate requirement of FcγR engagement and costimulation by signals (IL‐1β and LPS), which use the myeloid differentiation primary‐response protein 88 adaptor protein. Thus, CCL1 is a CC chemokine with a unique pattern of regulation associated with a distinct form of M2 (Type 2, M2b) monocyte activation, which participates in macrophage‐dependent regulatory circuits of innate and adaptive immunity.
Additive survival least‐squares support vector machines

This work studies a new survival modeling technique based on least‐squares support vector machines. We propose the use of a least‐squares support vector machine combining ranking and regression. The advantage of this kernel‐based model is threefold: (i) the problem formulation is convex and can be solved conveniently by a linear system; (ii) non‐linearity is introduced by using kernels, componentwise kernels in particular are useful to obtain interpretable results; and (iii) introduction of ranking constraints makes it possible to handle censored data. In an experimental setup, the model is used as a preprocessing step for the standard Cox proportional hazard regression by estimating the functional forms of the covariates. The proposed model was compared with different survival models from the literature on the clinical German Breast Cancer Study Group data and on the high‐dimensional Norway/Stanford Breast Cancer Data set. Copyright © 2009 John Wiley & Sons, Ltd.
Anxious and depressive components of Edinburgh Postnatal Depression Scale in maternal postpartum psychological problems1)

Abstract Background: The Edinburgh Postnatal Depression Scale (EPDS) is a widely used instrument for screening for postpartum depression, but it might also detect anxiety symptoms. Objective: To investigate the factor structure of the EPDS administered immediately after delivery and to understand which factors predict a high EPDS score 3 months later. Methods: A cohort of 594 Italian mothers delivering a healthy baby at Versilia Hospital completed the EPDS at two points in time: 2 days after delivery (T0) and 3 months later (T1) by telephone interview. Results: EPDS scores were higher at T0 than at T1. Overall, 15.7% of women at 2 days postpartum and 7.6% at 3 months later reported a score >9. The factor analysis of EPDS at T0 indicated a three-factor structure: “depression” (items 7–10), “anxiety” (items 3–6) and “anhedonia” (items 1–2). Anxious symptoms were quantitatively more important than depressive ones (mean 3.9 vs. 1.2) but tended to spontaneously ameliorate at T1, whereas total EPDS score at T1 was better predicted by depressive symptoms at T0 (discriminative ability 0.75 vs. 0.68). Conclusions: This study suggests that EPDS subscales immediately after delivery help understand the spectrum of maternal postpartum psychological problems. Anxious symptoms immediately after delivery are frequent but transient, linked probably to maternity blues or atypical depression, whereas the presence of depressive symptomatology at T0 suggests higher risk of later depressive disorders.
The effects of HIF-1 alpha on gene expression profiles of NCI-H 446 human small cell lung cancer cells

Background: Gene targeted therapy refers to any therapy focused on one of the many biological features of the tumor. Such features are mediated by specific genes that are involved in tumor metastasis, recurrence, poor response to chemotherapy and others. Hypoxia is an important pathognomonic feature of many malignant tumors including SCLC (small cell lung cancer). HIF1alpha, which is induced by hypoxia, is the most important regulatory factor of many specific genes that can influence the biological features of tumors. Methods: In this study, we tried to elucidate the changes in gene expression profiles of SCLC NCIH446 cells mediated by HIF-1alpha. According to different treatments of cells, three experimental pairwise comparisons were designed: hypoxia group vs. control group, Ad5-HIF-1alpha group vs. Ad5 group, and Ad5-siHIF-1 alpha group Vs Ad5 group. Results: Results from the analysis of gene expression profiles indicated that there were 65 genes upregulated and 28 genes downregulated more than two-fold in all three experimental pairwise comparisons. These genes were involved in transport, signal-transduction, cell adhesion/motility, growth factor/cytokines, transcription, inflammatory response, metabolic process, in addition to others. SOCS1, IGFBP5, IL-6 and STAT3 were also upregulated at protein level. SOCS1 could significantly induce apoptosis and suppress growth of NCI-H446 cells but HIF-1alpha could induce growth and suppress apoptosis. Conclusions: Through this research, we are trying to find novel functional genes that are mediated by HIF-1alpha and provide the theoretical basis for new therapeutic targets. HIF-1 alpha maybe upregulate the expression of SOCS1 through mediation of STAT3 and IL-6. In addition, SOCS1 could significantly induce apoptosis and suppress growth of NCI-H446 cells. This was contrary to HIF-1alpha and it indicated that there might be an antagonism effect between HIF1alpha and SOCS1 on regulating growth and apoptosis of NCI-H446 cells. Background Lung cancers used to be categorized into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). About 13%-15% of all lung cancers worldwide are SCLC. As a type of malignant tumor, SCLC shows many general clinical manifestations such as early metastasis, frequent Published: 10 December 2009 Journal of Experimental & Clinical Cancer Research 2009, 28:150 doi:10.1186/1756-9966-28-150 Received: 4 October 2009 Accepted: 10 December 2009 This article is available from: http://www.jeccr. com/content/28/1/150 © 2009 Wan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Faecal elastase‐1 test is superior to faecal lipase test in the assessment of exocrine pancreatic function in cystic fibrosis

Background and aims: Direct tests are characterized by the highest sensitivity and specificity. However, their practical use, especially in children, is limited. Among the indirect tests, the highest sensitivity and specificity was documented for faecal elastase‐1 test, yet the value of faecal lipase test in cystic fibrosis (CF) has not been defined. Therefore, the aim of the present study was to compare the sensitivity and the specificity of the faecal lipase test to the faecal elastase‐1 test in the assessment of exocrine pancreatic function in children with CF. Methods: The study comprised 90 CF patients and 95 healthy subjects (HS). In all subjects, faecal elastase‐1 concentrations (ELISA) and lipase activities (ELISA) were measured. The presence of pancreatic insufficiency was documented by the determination of faecal fat excretion in 78 pancreatic insufficient and by the secretin‐cholecystokinin test in 12 CF patients without steatorrhoea. Sensitivity and specificity of the faecal elastase‐1 test and faecal lipase test were analysed and, in 50 HS, sample‐to‐sample and day‐to‐day variations were determined. Results: With cut‐off levels providing the same specificity for both tests (95.8%), the sensitivity of the faecal elastase‐1 test (91.1%) was significantly higher (p > 0.0036) than that of the faecal lipase test (76.7%). Sample‐to‐sample (mean ± SEM: 13.2 ± 1.2% vs 23.4 ± 2.2%) and day‐to‐day variations (mean ± SEM: 16.3 ± 1.2% vs 32.5 ± 2.6%) were significantly lower (p > 0.0001) for elastase‐1 than for lipase measurements.