Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted gene knockdown in zebrafish using negatively charged peptide nucleic acid mimics

Negatively charged homo‐oligomers of alternating trans‐4‐hydroxy‐L‐proline/phosphonate polyamides with DNA bases (HypNA‐pPNA) display excellent hybridization properties toward DNA and RNA, while preserving the mismatch discrimination, nuclease resistance, and protease resistance of peptide nucleic acids (PNAs). Similar properties are associated with morpholino phosphorodiamidate (MO) DNA mimics, which have been used in the model vertebrate zebrafish (Danio rerio) for genome‐wide, sequence‐based, reverse genetic screens during embryonic development. We evaluated mixed sequence HypNA‐pPNAs as an alternative to MOs, and found that even a single central DNA mismatch lowered the HypNA‐pPNA melting temperature by 16°C. We then observed that the melting temperatures of HypNA‐pPNA 18‐mers hybridized to RNA 25‐mers were comparable to the melting temperatures of MO 25‐mers, and that two HypNA‐pPNA mismatches lowered the melting temperature with RNA by 18°C. In zebrafish embryos we observed that HypNA‐pPNA 18‐mers displayed comparable potency to MO 25‐mers as knockdown agents against chordin, notail, and uroD, with greater mismatch stringency. Finally we observed that a specific HypNA‐pPNA 18‐mer elicited the dharma (bozozok)‐/‐ phenotype in zebrafish embryos, which MO 25‐mers do not. HypNA‐pPNAs designed to inhibit translation of specific zebrafish RNA targets thus demonstrated stringent hybridization properties, relative to DNA and MO oligomers, and present a valuable alternative for reverse genetic studies, enabling the targeting of previously inaccessible genes. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Safety monitoring of ophthalmic biologics: a systematic review of pre- and postmarketing safety data.

PURPOSE The present study evaluates the safety of the biologics approved for the treatment of ocular diseases. METHODS The European medicines agency Website was searched to identify biologics with approved ophthalmologic therapeutic indications. A systematic search was performed using MEDLINE, the Cochrane Central Register of Controlled Trials (CENTRAL) and the International Clinical Trials Registry Platform up to December 2013. Pre-marketing, phase III randomized controlled trials (RCT), postmarketing clinical trials, observational longitudinal studies, and case reports involving adverse events (AE) were included. Methodological quality was assessed by Downs & Black checklist. All European spontaneous reports of AE included in the Eudravigilance up to December 2013 were also considered. AE were classified as ocular (related and non-related with the injection procedure) and non-ocular (related or non-related with vascular endothelial growth factor inhibition). Incidences of all reported AEs were estimated. RESULTS Pegaptanib, ranibizumab, and aflibercept were identified as ophthalmic biologics. Fourteen premarketing RCT, 7 postmarketing clinical trials, 31 observational studies, along with 31 case reports and 7,720 spontaneous reports were identified and included in this study. Both in pre- and postmarketing settings, ocular AEs were more frequent than non-ocular AEs. Premarketing safety data inform the most common AEs. Postmarketing studies suggest an increased number of events such as retinal pigmented epithelium tears (0.6%-24%), thromboembolic events (0.8%-5%), and mortality (2.8%-4%). CONCLUSIONS This study highlights the need to properly evaluate the risk for rare, serious, and long-term AEs, such as thromboembolic events, since they can lead to imbalances in the benefit-risk ratio of biologics in ophthalmology.
Clinical Characteristics, Outcomes, and Microbiologic Features Associated with Methicillin-Resistant Staphylococcus aureus Bacteremia in Pediatric Patients Treated with Vancomycin

ABSTRACT Vancomycin is the first-line therapy for methicillin-resistant Staphylococcus aureus (MRSA) bacteremia, but its efficacy in adult patients has been questioned. Less is known about the outcomes of MRSA bacteremia treated with vancomycin in pediatric patients. This study reviews the outcomes and clinical characteristics of MRSA bacteremia in children treated with vancomycin and characterizes the microbiologic and molecular features of the bloodstream isolates. A retrospective cohort study was conducted among pediatric patients with MRSA bacteremia treated with vancomycin for >5 days from 1 August 2005 to 31 May 2007 in a large tertiary care center. MRSA bloodstream isolates were characterized by antimicrobial susceptibility testing, PCR analysis of virulence genes, and Diversilab typing. Clinical records were reviewed for outcomes and comorbidities. A total of 22 pediatric patients with MRSA bacteremia were identified. Eleven cases (50.0%) were considered vancomycin treatment failures. Features significantly associated with vancomycin treatment failure were prematurity (P = 0.02) and isolates positive for Panton-Valentine leukocidin (PVL) (P = 0.008). Features typically associated with community-associated MRSA strains were identified in hospital-associated isolates. A dominant clone was not responsible for the high number of treatment failures. Further studies are needed to determine if vancomycin should be the first-line treatment for MRSA bacteremia in premature infants and for PVL-positive isolates.
Molecular epidemiology of human respiratory syncytial virus subgroup A over a six‐year period (1999–2004) in Argentina

Human respiratory syncytial virus (HRSV) is the main viral cause of acute lower respiratory tract infections in children. Little information about the molecular epidemiology of HRSV in developing countries, such as Argentina, is available. By RT‐PCR, we subgrouped 353 HRSV isolates over six consecutive epidemic seasons (1999–2004) and few isolates from 1997. Between them, 232 (65.7%) belonged to subgroup A and 121 (34.3%) to subgroup B. Therefore, the nucleotide, amino‐acid variability and phylogenetic relations of 78 HRSV subgroup A isolates, were analyzed using RFLP and sequence analysis of the G‐protein gene. The results showed that there were two main restriction patterns (PA1 and PA2) and two previously described genotypes (GA2 and GA5) cocirculating in Buenos Aires, without evidence of alternation between them during the studied period. The Argentine sequences were compared with previously reported molecular data from other countries. It showed that viruses genetically related circulated the same years within neighboring countries and the sequences from long‐distant places were closely related to Argentine sequences, but they belonged to different sampling years. The data reported here support the growing database on the molecular diversity of HRSVA circulating in Latin America in children under 2 years of age and contributes to describe the pattern of global spread of this virus. J. Med. Virol. 77:302–310, 2005. © 2005 Wiley‐Liss, Inc.
Randomized Trial of Intracardiac Echocardiography During Cavotricuspid Isthmus Ablation

Randomized Trial of ICE During CTI Ablation. Introduction: Despite a high success rate, radio‐frequency ablation (RFA) of the cavotricuspid isthmus (CTI) can be unusually challenging in some cases. We postulated that visualization of the CTI with intracardiac echocardiography (ICE) could maximize the succes rate, decrease the procedure and ablation time, and minimize the radiation exposure.
Unusual protonated structure in the homopurine.homopyrimidine tract of supercoiled and linearized plasmids recognized by chemical probes.

Plasmid pEJ4, which is a derivative of pUC19 containing an insert with 60-bp-long homopurine.homopyrimidine tract from sea urchin P. miliaris histone gene spacer, was studied by chemical probes of the DNA structure osmium tetroxide and glyoxal. The former probe reacts with pyrimidine bases, while the latter forms a stable product only with guanine residues. These probes can thus be applied as specific probes for the homopyrimidine and homopurine strands, respectively. At pH 6.0 the site-specific modification of the homopurine.homopyrimidine tract by both probes was observed at native superhelical density of the plasmid. In the linear plasmid under the same conditions this modification was absent; it appeared, however, at more acid pH values. In supercoiled DNA the hypersensitivity of the homopurine.homopyrimidine tract to osmium tetroxide did not substantially change when pH was decreased from 6.0 to 4.0. Changes in NaCl concentration at pH 4.5 did not influence the hypersensitivity to osmium tetroxide; at pH 6.0 this hypersensitivity decreased with increasing NaCl concentration. These results thus show that the chemical probes recognize an unusual protonated structure containing unpaired bases or non-Watson-Crick base pairs. At pH 5.6 the site-specific modification occurred at or near to the middle of the homopurine.homopyrimidine tract, suggesting that a hairpin may be involved in the unusual structure under the given conditions. From the models suggested so far for the unusual structure of homopurine.homopyrimidine tracts our results fit best the protonated triplex H form suggest by V.I. Lyamichev, S.M. Mirkin and M.D. Frank-Kamenetskii, J. Biomol. Struct. Dyn. 3,667 (1986).
An experimental investigation of the motor cortex and pyramidal tract of Echidna aculeata.

THE possession of an area of cortex, which on electrical stimulation gives rise to movement in contralateral parts of the body, is well known to be a common and probably universal characteristic of the mammalian forebrain. It is equally well known that this so-called "motor area" contains cells whose axons form a long projection tract, ending, partly in the brain stem and partly in the spinal cord, in immediate or very close relationship with the neurones of the "final common path ".
Raman Spectroscopy as a Potential Tool for Detection of Brucella spp. in Milk

ABSTRACT Detection of Brucella, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible Brucella isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify Brucella from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different Brucella, Escherichia, Ochrobactrum, Pseudomonas, and Yersinia spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for Brucella from medium and 94% for Brucella from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting Brucella. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.
Effect of unilateral and bilateral auditory cortex lesions on the discrimination of vocalizations by Japanese macaques.

Ten Japanese macaques were trained to discriminate between two types of Japanese macaque coo vocalizations before and after auditory cortex ablation. Five of the animals were tested following left unilateral ablation, whereas the other five were tested following right unilateral ablation. After postoperative testing, symmetrical lesions were made in the remaining hemisphere in two animals from each group and the effect of bilateral lesions was assessed. The animals were tested using a shock avoidance procedure. Unilateral ablation of left auditory cortex consistently resulted in an initial impairment in the ability to discriminate between the vocalizations with the animals regaining normal performance in 5-15 sessions. In contrast, right unilateral ablation had no detectable effect on the discrimination. Bilateral auditory cortex ablation rendered the animals permanently unable to discriminate between the coos. Although the monkeys could learn to discriminate the coos from noise and from 2- and 4-kHz tones, they had great difficulty in discriminating between the coos and tones in the same frequency range as the coos (i.e., 500 Hz and 1 kHz). The initial impairment following left unilateral lesions indicates that the ability to perceive species-specific vocalizations is lateralized to the left hemisphere. The observation that bilateral lesions abolish the discrimination indicates that the recovery in the left lesion cases was the result of the right hemisphere mediating the discrimination.
Spatial differences of cellular origins and in vivo hypoxia modify contractile properties of pulmonary artery smooth muscle cells: lessons for arterial tissue engineering

Tissue engineering of functional arteries is challenging. Within the pulmonary artery wall, smooth muscle cells (PASMCs) have site‐specific developmental and functional phenotypes, reflecting differing contractile roles. The force generated by PASMCs isolated from the inner 25% and outer 50% of the media of intrapulmonary elastic arteries from five normal and eight chronically hypoxic (hypertensive) 14 day‐old piglets was quantified in a three‐dimensional (3D) collagen construct, using a culture force monitor. Outer medial PASMCs from normal piglets exerted more force (528 ± 50 dynes) than those of hypoxic piglets (177 ± 42 dynes; p < 0.01). Force generation by inner medial PASMCs from normal and hypoxic piglets was similar (349 ± 35 and 239 ± 60 dynes). In response to agonist (thromboxane) stimulation, all PASMCs from normal and hypoxic piglets contracted, but the increase in force generated by outer and inner hypoxic PASMCs (ranges 13–72 and 14–56 dynes) was less than by normal PASMCs (ranges 27–154 and 34–159 dynes, respectively; p < 0.05 for both). All hypoxic PASMCs were unresponsive to antagonist (sodium nitroprusside) stimulation, all normal PASMCs relaxed (range − 87 to − 494 dynes). Myosin heavy chain expression by both hypoxic PASMC phenotypes was less than normal (p < 0.05 for both), as was the activity of focal adhesion kinase, regulating contraction, in hypoxic inner PASMCs (p < 0.01). Chronic hypoxia resulted in the development of abnormal PASMC phenotypes, which in collagen constructs exhibited a reduction in contractile force and reactivity to agonists. Characterization of the mechanical response of spatially distinct cells and modification of their behaviour by hypoxia is critical for successful tissue engineering of major blood vessels. Copyright © 2007 John Wiley & Sons, Ltd.
Substance use among university students at the St Augustine campus of the University of the West Indies.

OBJECTIVE Substance use and abuse is a well known public health risk that peaks in persons between 18 and 25 years of age and is prevalent among university students. While this has been repeatedly documented in developed nations, there have been limited studies in the English-speaking Caribbean. This study therefore sought to assess the prevalence of alcohol, tobacco and marijuana use among university students in the English-speaking Caribbean and any associated risk factors. METHODS The study was designed as a descriptive, cross-sectional study to assess substance use in full-time, undergraduate students of The University of the West Indies (UWI), Trinidad and Tobago, over a six-month period. Questionnaires were distributed and students asked to self-report on their use of alcohol, tobacco and marijuana during the preceding six months. RESULTS The six-month prevalence rate for alcohol was 70% and 28% of students were identified as regular users. Binge drinking was estimated at 31%. Muslims were least likely to have used alcohol when compared to other religious groupings. The prevalence rate for tobacco and marijuana was 17% and 13%, respectively Ten per cent used all three substances. The use of all three substances was associated with multiple problems. CONCLUSION We conclude that substance use is common among many students of the UWI but generally lower than reports from other regions of the world. Despite this, substance use is associated with a number of problems and immediate educational interventions may be necessary to assist students in making informed and responsible choices.
An IRE-Like AGC Kinase Gene, MtIRE, Has Unique Expression in the Invasion Zone of Developing Root Nodules in Medicago truncatula1[OA]

The AGC protein kinase family (cAMP-dependent protein kinases A, cGMP-dependent protein kinases G, and phospholipid-dependent protein kinases C) have important roles regulating growth and development in animals and fungi. They are activated via lipid second messengers by 3-phosphoinositide-dependent protein kinase coupling lipid signals to phosphorylation of the AGC kinases. These phosphorylate downstream signal transduction protein targets. AGC kinases are becoming better studied in plants, especially in Arabidopsis (Arabidopsis thaliana), where specific AGC kinases have been shown to have key roles in regulating growth signal pathways. We report here the isolation and characterization of the first AGC kinase gene identified in Medicago truncatula, MtIRE. It was cloned by homology with the Arabidopsis INCOMPLETE ROOT HAIR ELONGATION (IRE) gene. Semiquantitative reverse transcription-polymerase chain reaction analysis shows that, unlike its Arabidopsis counterpart, MtIRE is not expressed in uninoculated roots, but is expressed in root systems that have been inoculated with Sinorhizobium meliloti and are developing root nodules. MtIRE expression is also found in flowers. Expression analysis of a time course of nodule development and of nodulating root systems of many Medicago nodulation mutants shows MtIRE expression correlates with infected cell maturation during nodule development. During the course of these experiments, nine Medicago nodulation mutants, including sli and dnf1 to 7 mutants, were evaluated for the first time for their microscopic nodule phenotype using S. meliloti constitutively expressing lacZ. Spatial localization of a pMtIRE-gusA transgene in transformed roots of composite plants showed that MtIRE expression is confined to the proximal part of the invasion zone, zone II, found in indeterminate nodules. This suggests MtIRE is useful as an expression marker for this region of the invasion zone.
Avoiding cultural trauma: climate change and social inertia

ABSTRACT The failure of societies to respond in a concerted, meaningful way to climate change is a core concern of the social science climate literature. Existing explanations of social inertia display little coherence. Here, a theoretical approach is suggested that integrates disparate perspectives on social inertia regarding climate change. Climate change constitutes a potential cultural trauma. The threat of cultural trauma is met with resistance and attempts to restore and maintain the status quo. Thus, efforts to avoid large-scale social changes associated with climate change constitute an effort to avoid cultural trauma, and result in social inertia regarding climate change at individual, institutional, and societal levels. Existing approaches to social inertia are reviewed. An intellectual framework utilizing the work of Pierre Bourdieu is proposed to integrate these different levels of social interaction. Social processes that maintain social order and thus avoid cultural trauma create social inertia regarding climate change.
Phosphoinositide 3-Kinase Catalytic Subunit Deletion and Regulatory Subunit Deletion Have Opposite Effects on Insulin Sensitivity in Mice

ABSTRACT Studies ex vivo have shown that phosphoinositide 3-kinase (PI3K) activity is necessary but not sufficient for insulin-stimulated glucose uptake. Unexpectedly, mice lacking either of the PI3K regulatory subunits p85α or p85β exhibit increased insulin sensitivity. The insulin hypersensitivity is particularly unexpected in p85α−/− p55α−/− p50α−/− mice, where a decrease in p110α and p110β catalytic subunits was observed in insulin-sensitive tissues. These results raised the possibility that decreasing total PI3K available for stimulation by insulin might circumvent negative feedback loops that ultimately shut off insulin-dependent glucose uptake in vivo. Here we present results arguing against this explanation. We show that p110α+/− p110β+/− mice exhibit mild glucose intolerance and hyperinsulinemia in the fasted state. Unexpectedly, p110α+/− p110β+/− mice showed a ∼50% decrease in p85 expression in liver and muscle. Consistent with this in vivo observation, knockdown of p110 by RNA interference in mammalian cells resulted in loss of p85 proteins due to decreased protein stability. We propose that insulin sensitivity is regulated by a delicate balance between p85 and p110 subunits and that p85 subunits mediate a negative role in insulin signaling independent of their role as mediators of PI3K activation.
Reduction of DNA Fragmentation and Hydroxyl Radical Production by Hyaluronic Acid and Chondroitin-4-sulphate in Iron Plus Ascorbate-induced Oxidative Stress in Fibroblast Cultures

Glycosaminoglycans (GAGs), components of extracellular matrix, are thought to play important roles in cell proliferation and differentiation in the repair process of injured tissue. Oxidative stress is one of the most frequent causes of tissue and cell injury and the consequent lipid peroxidation is the main manifestation of free radical damage. It has been found to play an important role in the evolution of cell death. Since several reports have shown that hyaluronic acid (HYA) and chondroitin-4-sulphate (C4S) are able to inhibit lipid peroxidation during oxidative stress, We investigated the antioxidant capacity of these GAGs in reducing oxidative damage in fibroblast cultures. Free radicals production was induced by the oxidizing system employing iron (Fe2+) plus ascorbate. We evaluated cell death, membrane lipid peroxidation, DNA damage, protein oxidation, hydroxyl radical (OH•) generation and endogenous antioxidant depletion in human skin fibroblast cultures. The exposition of fibroblasts to FeSO4 and ascorbate caused inhibition of cell growth and cell death, increased OH• production determined by the aromatic trap method; furthermore it caused DNA strand breaks and protein oxidation as shown by the DNA fragments analysis and protein carbonyl content, respectively. Moreover, it enhanced lipid peroxidation evaluated by the analysis of conjugated dienes (CD) and decreased antioxidant defenses assayed by means of measurement of superoxide dismutase (SOD) and catalase (CAT) activities. When fibroblasts were treated with two different doses of HYA or C4S a protective effect, following oxidative stress induction, was shown. In fact these GAGs were able to limit cell death, reduced DNA fragmentation and protein oxidation, decreased OH• generation, inhibited lipid peroxidation and improved antioxidant defenses. Our results confirm the antioxidant activity of HYA and C4S and this could represent a useful step in the understanding of the exact role played by GAGs in living organisms.