Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal in vivo two‐photon fluorescence imaging

Fluorescence microscopy is an essential technique for the basic sciences, especially biomedical research. Since the invention of laser scanning confocal microscopy in the 1980s, which enabled imaging both fixed and living biological tissue with 3D precision, high‐resolution fluorescence imaging has revolutionized biological research. Confocal microscopy, by its very nature, has one fundamental limitation. Due to the confocal pinhole, deep tissue fluorescence imaging is not practical. In contrast (no pun intended), two‐photon fluorescence microscopy allows, in principle, the collection of all emitted photons from fluorophores in the imaged voxel, dramatically extending our ability to see deep into living tissue. Since the development of transgenic mice with genetically encoded fluorescent protein in neocortical cells in 2000, two‐photon imaging has enabled the dynamics of individual synapses to be followed for up to 2 years. Since the initial landmark contributions to this field in 2002, the technique has been used to understand how neuronal structure are changed by experience, learning, and memory and various diseases. Here we provide a basic summary of the crucial elements that are required for such studies, and discuss many applications of longitudinal two‐photon fluorescence microscopy that have appeared since 2002. J. Comp. Neurol. 522:1708–1727, 2014. © 2013 Wiley Periodicals, Inc.
Effects of depression and melatonergic antidepressant treatment alone and in combination with sedative–hypnotics on heart rate variability: Implications for cardiovascular risk

Abstract Objectives: To examine heart rate variability (HRV) in unmedicated patients with major depressive disorder (MDD) and its changes after treatment with agomelatine alone and in combination with sedative–hypnotics. Methods: We recruited 152 physically healthy, unmedicated patients with MDD and 472 age- and sex-matched healthy volunteers. Frequency-domain measures of HRV were obtained during enrolment for all participants and again for MDD patients after 6 weeks of treatment with agomelatine alone and combining sedative–hypnotics. Results: Compared to the controls, unmedicated patients exhibited significantly lower mean R-R intervals, low-frequency (LF) HRV, and high-frequency (HF) HRV, but higher LF/HF ratios. Fifty-six and 49 patients successfully completed agomelatine monotherapy and the combination therapy of agomelatine and sedative–hypnotics, respectively. Between-group analyses showed significant treatment-by-group interactions for LF-HRV, HF-HRV and LF/HF ratio. The results showed a significant increase in HF-HRV after agomelatine monotherapy, a significant decrease in LF-HRV and HF-HRV, and a increase in the LF/HF ratio after combination therapy. Conclusions: MDD patients had reduced HRV, and the patterns of HRV changes differed between patients treated with agomelatine alone and in combination with sedative–hypnotics. Clinicians should consider HRV effects when adding sedative–hypnotics to agomelatine, which is important for depressed patients who already have decreased cardiac vagal tone.
Arc and Sfr functions of the Escherichia coli K-12 arcA gene product are genetically and physiologically separable

The Escherichia coli arcA gene product regulates chromosomal gene expression in response to deprivation of oxygen (Arc function; Arc stands for aerobic respiration control) and is required for expression of the F plasmid DNA transfer (tra) genes (Sfr function; Sfr stands for sex factor regulation). Using appropriate lacZ fusions, we have examined the relationship between these two genetic regulatory functions. Arc function in vivo was measured by anaerobic repression of a chromosomal sdh-lacZ operon fusion (sdh stands for succinate dehydrogenase). Sfr function was measured by activation of a plasmid traY-lacZ gene fusion. An eight-codon insertion near the 5' terminus of arcA, designated arcA1, abolished Arc function, as previously reported by S. Iuchi and E.C. C. Lin (Proc. Natl. Acad. Sci. USA 85:1888-1892, 1988), but left Sfr function largely (greater than or equal to 60%) intact. Similarly, the arcB1 mutation, which depressed sdh expression and is thought to act by abolishing the signal input that elicits ArcA function, had little effect (less than or equal to 20%) on the Sfr function of the arcA+ gene product. Conversely, a valine-to-methionine mutation at codon 203 (the sfrA5 allele) essentially abolished Sfr activity without detectably altering Arc activity. These data indicate that Sfr and Arc functions are separately expressed and regulated properties of the same protein.
Genotoxic and chemopreventive assessment of Cynara scolymus L. aqueous extract in a human-derived liver cell line

Abstract Cynara scolymus L. , popularly known as artichoke, is consumed as food and used as tea infusions for pharmacological purposes to treat liver dysfunctions and other conditions. Scientific data on the safety and protective effect of artichoke in human-derived liver cells is missing. This study investigated the genotoxic and modulatory effect of a liophilized extract suspended in water of C. scolymus L. leaves. Four extract concentrations (0.62, 1.25, 2.5 and 5.0 mg/mL) were evaluated using the comet assay on human hepatocyte cultures, HepG2 cells. Genotoxicity was assessed after two treatment periods, 1 and 24 h. Antigenotoxicity was evaluated against oxidative lesions induced by hydrogen peroxide in pre-, simultaneous and post-treatment protocols. Artichoke leaves aqueous extract induced genotoxic effects in HepG2 cells after 1- and 24-h treatments. In turn, extract concentrations of 0.62, 1.25 and 2.5 mg/mL, exhibited a protective effect in pretreatment, compared to hydrogen peroxide alone. However, in simultaneous and post-treatment protocols, only the lowest concentration reduced the frequency of DNA damage induced by hydrogen peroxide. In addition, in the simultaneous treatment protocol, the highest artichoke extract concentration increased hydrogen peroxide genotoxicity. It can be concluded that artichoke is genotoxic, in vitro, to HepG2 cells, but can also modulate hydrogen peroxide DNA damage.
Synergistic Effect of Biochemical Factors and Strain on the Smooth Muscle Cell Differentiation of Adipose-Derived Stem Cells on an Elastic Nanofibrous Scaffold

Abstract Adipose-derived stem cells (ASCs) have been the subject of many tissue-engineering studies, mainly because of their multipotential properties. We have focused on the potential of human ASCs (hASCs) for smooth muscle cell (SMC) differentiation in cardiovascular tissue engineering. In this study, we investigated the combined effect of differentiation factors along with strain utilizing a customized device on hASCs proliferation and consequent differentiation into SMCs on an elastic nanofibrous scaffold. The cell proliferation increased in strain-stimulated culture and was more affected by media composition as compared to in static culture. Differentiation factors did not have an influence on SM α-actin (α-SMA) and myosin heavy chain (MHC) expression in static culture. However, α-SMA and MHC expression were affected by differentiation factors in strain culture, in particular, showing that treatment with retinoic acid significantly increased the expression of α-SMA (3.6-fold) and MHC (2-fold) as compared to strain alone. This study demonstrated the synergic effect of strain and biochemical factor on the SMC differentiation of hASCs and provided a useful method for the application of stem cells in mechano-active tissue engineering.
A comparative study of low 5-minute Apgar scores (<8) in newborns of wanted versus unwanted pregnancies in southern Tehran, Iran (2006–2007)

Objective. To compare 5-minute Apgar scores in newborns of wanted versus unwanted pregnancies. Methods. This longitudinal cohort study included 1800 pregnant women attending urban and rural health centres in southern Tehran for routine prenatal care. The subjects were divided into two equal groups as wanted and unwanted pregnancies and were followed up through their prenatal care to their delivery. Low Apgar was defined as a score of < 8. Various conditions thought to increase the risk of low Apgar were assessed by logistic regression. Results. We found a prevalence of 0.4% (4 cases) for low 5′ Apgar in wanted pregnancies and 1.7% (15 cases) in unwanted pregnancies. The difference between the two groups was significant (P value = 0.01). In logistic regression analysis, unwanted pregnancy status had a strong independent relationship with low Apgar, increasing the risk by 3-fold. The attributable risk in unwanted pregnancies was 0.54 (CI0.95 = 0.13–0.81). Conclusions. In addition to the well-established maternal complications of unwanted pregnancy (e.g. emotional stress, illegal abortions, etc) it becomes clear that such pregnancies endanger the infant's health too. It is possible that many pregnant women, especially those with unwanted pregnancies, are not attending health centres for prenatal care. Further studies with active case finding are recommended to confirm these findings.
New data on Malayometastrongylus diardinematus (Gibbons and Krishnasamy, 1986) (Metastrongyloidea: Angiostrongylidae) a lungworm occurring in Rattus tanezumi (Temminck, 1844) from South-East Asia

SummaryA survey of rodents from Luang Prabang Province (Lao PDR) in February 2010 and May 2012 allowed examining lungs of 95 rodents belonging to 7 different genera (Bandicota, Berylmys, Cannomys, Leopoldamys, Maxomys, Mus, Rattus). The helminth Malayometastrongylus diardinematus (Nematoda: Metastrongyloidea) was identified in Rattus tanezumi living in close contact with humans, being the first report after its original description in R. tanezumi from Malaysia. A molecular study using mitochondrial gene cytochrome c oxidase subunit I (COI) of M. diardinematus placed the genus Malayometastrongylus in a separate clade in comparison with Angiostrongylus cantonensis (subgenus Parastrongylus) and other representatives of the genus, both present in rodents of South East Asia.
Arthrotomy for the treatment of chronic purulent septic gonitis with subchondral osteolysis in two calves

Abstract CASE HISTORY: A 6-week-old German Holstein heifer calf (Case 1) and a 4-week-old Charolais bull calf (Case 2) were referred because of unilateral hind limb lameness. Both had been treated with systemic antibiotics by the referring veterinarian. CLINICAL FINDINGS AND DIAGNOSIS: Based on the results of clinical, radiographic and ultrasonographic examination, a diagnosis of chronic purulent septic gonitis with subchondral osteolysis of the lateral femoral condyle was made in both calves. In Case 2 the lateral tibial condyle also showed osteolysis. TREATMENT AND OUTCOME: Treatment consisted of arthrotomy with debridement of abnormal bone and cartilage via a craniolateral and a caudolateral approach. Case 1 was discharged from with grade 1/5 lameness 60 days after surgery. In a follow-up 15 months postoperatively, the owner reported that it had been bred at 14 months, was not lame and the affected stifle joint appeared normal. Case 2 had grade 2/5 lameness 52 days after surgery, but was sound at the time of slaughter at 22 months of age. CLINICAL RELEVANCE: Arthrotomy via a caudolateral approach is a suitable method for the treatment of septic purulent gonitis with osteolysis of the lateral femoral and tibial condyles in calves. In these cases, this treatment resulted in the elimination of localised inflammation, prevented clinically relevant spread of infection to other organs, and restored normal joint function.
CpsB Is a Modulator of Capsule-associated Tyrosine Kinase Activity in Streptococcus pneumoniae *

Tyrosine phosphorylation is associated with polysaccharide synthesis in a number of Gram-positive and Gram-negative bacteria. In Streptococcus pneumoniae, CpsB, CpsC, and CpsD affect tyrosine phosphorylation and are critical for the production of a mature capsule in vitro. To characterize the interactions between these proteins and the phosphorylation event they modulate,cps2B, cps2C, and cps2D from the capsule type 2 S. pneumoniae D39 were cloned and expressed both individually and in combination in Escherichia coli. Cps2D purified from E. coli was not phosphorylated unless it was co-expressed with its cognate transmembrane domain, Cps2C. Purified phosphorylated Cps2D had tyrosine kinase activity and could phosphorylate both dephosphorylated Cps2D and an exogenous substrate (poly-Glu-Tyr) in the absence of ATP. Cps2B exhibited phosphatase activity against both purified phosphorylated Cps2D and p-nitrophenyl phosphate. An additional role for Cps2B as an inhibitor of Cps2D phosphorylation was demonstrated in both co-expression experiments in E. coli and in vitro experiments where it blocked the transphosphorylation of Cps2D even in the presence of the phosphatase inhibitor sodium orthovanadate. cps2C and cps2D deletion mutants in S. pneumoniae produced no detectable mature capsule during laboratory culture. Both were avirulent in systemic mouse infections and were unable to colonize the nasopharynx, suggesting that the failure to produce capsule was not dependent on the environment. Based on these results, we propose a model for capsule regulation where CpsB, CpsC, CpsD, and ATP form a stable complex that enhances capsule synthesis.
Ant Colony for optimal design of PM synchronous generator for direct-drive wind turbines

In this paper, an optimal design procedure of radial surface permanent-magnet generator (PMSG) with an outer rotor for wind energy application is investigated. Firstly, an analytical model based on the resolution of the Maxwell's equations using the separation of variable method is presented. From the same model analytical expressions of four constraint functions dedicated for the optimal design of the PMSG are developed. These constraints are: electromagnetic torque, electromotive force (EMF), flux density saturation in stator/rotor yoke and saturation in stator tooth. The Ant Colony Optimization (ACO) method is then employed to optimize two objective functions (weight and power loss of the generator) with the respect of the above mentioned constraints. Finally, the finite element method is used to validate the designed PMSG.
Vascular abnormalities in reflex sympathetic dystrophy (CRPS I): mechanisms and diagnostic value.

Complex regional pain syndrome type I (CRPS I, formerly known as reflex sympathetic dystrophy) is a painful neuropathic disorder that develops after trauma affecting the limbs without overt nerve injury. Clinical features are spontaneous pain, hyperalgesia, impairment of motor function, swelling, changes in sweating, and vascular abnormalities. In this study, the pathophysiological mechanisms of vascular abnormalities were investigated. Furthermore, the incidence, sensitivity and specificity of side differences in skin temperature were defined in order to distinguish patients with definite CRPS I from patients with extremity pain of other origin. In 25 CRPS I patients and two control groups (20 healthy subjects and 15 patients with other types of extremity pain), cutaneous sympathetic vasoconstrictor activity was altered tonically by the use of controlled thermoregulation. Whole-body temperature changes were induced with a thermal suit in which cold or hot water circulated. The vascular reflex response (skin blood flow, laser Doppler flowmetry, skin temperature, infrared thermometry) was analysed to quantify sympathetic outflow. Measurements were performed during a complete thermoregulatory cycle, i.e. during the entire spectrum of sympathetic vasoconstrictor activity from high (whole-body cooling) to low sympathetic activity (whole-body warming). Venous noradrenalin levels were determined bilaterally in five CRPS patients. (i) Three distinct vascular regulation patterns were identified related to the duration of the disorder. In the "warm" (acute) type of regulation, the affected limb was warmer and perfusion values were higher than in the contralateral limb during the entire spectrum of sympathetic activity. In the "intermediate" type of regulation the limb was either warmer or colder. In the "cold" (chronic) type of regulation, skin temperature and perfusion values were lower on the affected side during the entire spectrum of sympathetic vasoconstrictor activity. (ii) Noradrenalin levels were lower on the affected side, even in chronic patients with considerable cutaneous vasoconstriction. (iii) Temperature and blood flow differences between the two sides were dynamic and most prominent at a high to medium level of vasoconstrictor activity. (iv) In both control groups, there were only minor side differences in flow and temperature. In conclusion, it is suggested that, in CRPS I, unilateral inhibition of sympathetic vasoconstrictor neurones leads to a warmer affected limb in the acute stage. Secondary changes in neurovascular transmission may lead to vasoconstriction and cold skin in chronic CRPS I, whereas sympathetic activity is still depressed. Vascular abnormalities are dynamic. The maximal skin temperature difference that occurs during the thermoregulatory cycle distinguishes CRPS I from other extremity pain syndromes with high sensitivity and specificity.
Mouse in red: Red fluorescent protein expression in mouse ES cells, embryos, and adult animals

Spectral variants of green fluorescent protein are widely used in live samples for a broad range of applications: from visualization of protein interactions, through following gene expression, to marking particular cells in complex tissues. Higher wavelength emissions (such as red) are preferred due to the lower background‐autofluorescence in tissues (Miyawaka et al., Nat Cell Biol Suppl S1–7, 2003). Until now, however, red fluorescent proteins (RFP) have displayed toxicity in murine embryos, which has hampered its application in this model. Here we report strong expression of a recently developed RFP variant, DsRed.T3, in mouse ES cells, embryos, and adult mice. Our results show that the red fluorescent wavelength has a superior tissue penetrance compared with spectral variants of lower wavelength. Furthermore, we have generated an ES cell line and a corresponding transgenic mouse line in which red fluorescence is activated upon Cre excision. Finally, we introduced cell type‐specifically expressed Cre transgenes into this Cre recombinase reporter cell line, and by using the tetraploid embryo complementation assay, we could directly verify the Cre recombinase specificity on ES cell‐derived embryos/animals. genesis 40:241–246, 2004. © 2004 Wiley‐Liss, Inc.
Risk of incident stroke in patients with Alzheimer disease or vascular dementia

Objective: To explore the risk of ischemic stroke, hemorrhagic stroke, or TIA in patients with Alzheimer disease (AD) or vascular dementia (VD). Methods: We conducted a follow-up study with a nested case-control analysis using the UK-based General Practice Research Database. We included patients aged 65 years and older with an incident diagnosis of AD or VD between 1998 and 2008 and a comparison group of dementia-free patients. We estimated incidence rates of ischemic stroke, hemorrhagic stroke, or TIA in patients with AD, VD, or without dementia, and we calculated odds ratios with 95% confidence intervals (CIs) of developing such an outcome in patients with AD or VD, stratified by use of antipsychotic drugs. Results: We followed 6,443 cases with AD, 2,302 with VD, and 9,984 dementia-free patients over time and identified 281 cases with incident ischemic stroke, 139 with hemorrhagic stroke, and 379 with TIA. The incidence rates of ischemic stroke for patients with AD, VD, or no dementia were 4.7/1,000 person-years (PYs) (95% CI 3.8–5.9), 12.8/1,000 PYs (95% CI 9.8–16.8), and 5.1/1,000 PYs (95% CI 4.3–5.9), respectively. Compared with dementia-free patients, the odds ratio of developing a TIA for patients with AD treated with atypical antipsychotic drugs was 4.5 (95% CI 2.1–9.2). Conclusions: Patients with VD, but not AD, have a markedly higher risk of developing an ischemic stroke than those without dementia. In patients with AD, but not VD, use of atypical antipsychotic drugs was associated with an increased risk of TIA.
Evaluating apatite formation and osteogenic activity of electrospun composites for bone tissue engineering

Significant interest has been in examining calcium phosphate ceramics, specifically β‐tricalcium phosphate (β‐TCP) (Ca3(PO4)2) and synthetic hydroxyapatite (HA) (Ca10(PO4)6(OH)2), in composites and more recently, in fibrous composites formed using the electrospinning technique for bone tissue engineering applications. Calcium phosphate ceramics are sought because they can be bone bioactive, which means an apatite forms on their surface that facilitates bonding to bone tissue, and are osteoconductive. However, studies examining the bioactivity of electrospun composites containing calcium phosphates and their corresponding osteogenic activity have been limited. In this study, electrospun composites consisting of (20/80) HA/TCP nanoceramics and poly (ϵ‐caprolactone) (PCL) were fabricated. Solvent and solvent combinations were evaluated to form scaffolds with a maximum concentration and dispersion of ceramic and pore sizes large enough for cell infiltration and tissue growth. PCL was dissolved in either methylene chloride (Composite‐MC) or a combination of methylene chloride (80%) and dimethylformamide (20%; Composite‐MC + DMF). Composites were evaluated in vitro for degradation, apatite formation, and osteogenic differentiation of human mesenchymal stem cells (MSCs) with an emphasis on temporal gene expression of osteogenic markers and the pluripotent gene Sox‐2. Apatite formation and the osteogenic differentiation was the greatest for Composite‐MC as determined by gene expression, protein production and biochemical markers, even without the presence of osteoinductive factors in the media, in comparison to Composite‐MC + DMF and unfilled PCL mats. Sox‐2 levels also reduced over time. The results of this study demonstrate that the solvent or solvent combination used in preparing the electrospun composite mats plays a critical role in determining their bioactivity which may, in turn, affect cell behavior. Biotechnol. Biotechnol. Bioeng. 2014;111: 1000–1017. © 2013 Wiley Periodicals, Inc.
Fast full search equivalent encoding algorithms for image compression using vector quantization

Three fast search routines to be used in the encoding phase of vector quantization (VQ) image compression systems are presented. These routines, which are based on geometric considerations, provide the same results as an exhaustive (or full) search. Examples show that the proposed algorithms need only 3-20% of the number of mathematical operations required by a full search and fewer than 50% of the operations required by recently proposed alternatives.