Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Synechococcus Genomes Reconstructed from Freshwater Reservoirs

Freshwater picocyanobacteria including Synechococcus remain poorly studied at the genomic level, compared to their marine representatives. Here, using a metagenomic assembly approach we discovered two novel Synechococcus sp. genomes from two freshwater reservoirs Tous and Lake Lanier, both sharing 96% average nucleotide identity and displaying high abundance levels in these two lakes located at similar altitudes and temperate latitudes. These new genomes have the smallest estimated size (2.2 Mb) and average intergenic spacer length (20 bp) of any previously sequenced freshwater Synechococcus, which may contribute to their success in oligotrophic freshwater systems. Fluorescent in situ hybridization confirmed that Synechococcus sp. Tous comprises small cells (0.987 ± 0.139 μm length, 0.723 ± 0.119 μm width) that amount to 90% of the picocyanobacteria in Tous. They appear together in a phylogenomic tree with Synechococcus sp. RCC307 strain, the main representative of sub-cluster 5.3 that has itself one of the smallest marine Synechococcus genomes. We detected a type II phycobilisome (PBS) gene cluster in both genomes, which suggests that they belong to a phycoerythrin-rich pink low-light ecotype. The decrease of acidic proteins and the higher content of basic transporters and membrane proteins in the novel Synechococcus genomes, compared to marine representatives, support their freshwater specialization. A sulfate Cys transporter which is absent in marine but has been identified in many freshwater cyanobacteria was also detected in Synechococcus sp. Tous. The RuBisCo subunits from this microbe are phylogenetically close to the freshwater amoeba Paulinella chromatophora symbiont, hinting to a freshwater origin of the carboxysome operon of this protist. The novel genomes enlarge the known diversity of freshwater Synechococcus and improve the overall knowledge of the relationships among members of this genus at large.
Improvement in structural and functional echocardiographic parameters during chronic heart failure therapy guided by natriuretic peptides: mechanistic insights from the ProBNP Outpatient Tailored Chronic Heart Failure (PROTECT) study

We sought to determine if heart failure (HF) care with a goal to lower N‐terminal pro B‐type natriuretic peptide (NT‐proBNP) concentrations, compared with standard of care (SOC) management, is associated with improvement in echocardiographic parameters of cardiac structure and function.
Evidence of Oxidative Stress in Human Corneal Diseases

This study localized malondialdehyde (MDA, a toxic byproduct of lipid peroxidation), nitrotyrosine [NT, a cytotoxic byproduct of nitric oxide (NO)], and nitric oxide synthase isomers (NOS) in normal and diseased human corneas. Normal corneas (n=11) and those with clinical and histopathological diagnoses of keratoconus (n=26), bullous keratopathy (n=17), and Fuchs' endothelial dystrophy (n=12) were examined with antibodies specific for MDA, NT, eNOS (constitutive NOS), and iNOS (inducible NOS). Normal corneas showed little or no staining for MDA, NT, or iNOS, whereas eNOS was detected in the epithelium and endothelium. MDA was present in all disease groups, with each group displaying a distinct pattern of staining. NT was detected in all keratoconus and approximately one half of Fuchs' dystrophy corneas. iNOS and eNOS were evident in all the diseased corneas. Keratoconus corneas showed evidence of oxidative damage from cytotoxic byproducts generated by lipid peroxidation and the NO pathway. Bullous keratopathy corneas displayed byproducts of lipid peroxidation but not peroxynitrite (MDA but not NT). Conversely, Fuchs' dystrophy corneas displayed byproducts of peroxynitrite with little lipid peroxidation (NT » MDA). These data suggest that oxidative damage occurs within each group of diseased corneas. However, each disease exhibits a distinctive profile, with only keratoconus showing prominent staining for both nitrotyrosine and MDA. These results suggest that keratoconus corneas do not process reactive oxygen species in a normal manner, which may play a major role in the pathogenesis of this disease.
Ubiquilin-1 regulates amyloid precursor protein maturation and degradation by stimulating K63-linked polyubiquitination of lysine 688

The pathogenesis of Alzheimer’s disease (AD) is associated with proteolytic processing of the amyloid precursor protein (APP) to an amyloidogenic peptide termed Aβ. Although mutations in APP and the secretase enzymes that mediate its processing are known to result in familial forms of AD, the mechanisms underlying the more common sporadic forms of the disease are still unclear. Evidence suggests that the susceptibility of APP to amyloidogenic processing is related to its intracellular localization, and that secretase-independent degradation may prevent the formation of cytotoxic peptide fragments. Recently, single nucleotide polymorphisms in the UBQLN1 gene have been linked to late-onset AD, and its protein product, ubiquilin-1, may regulate the maturation of full-length APP. Here we show that ubiquilin-1 inhibits the maturation of APP by sequestering it in the early secretory pathway, primarily within the Golgi apparatus. This sequestration significantly delayed the proteolytic processing of APP by secretases and the proteasome. These effects were mediated by ubiquilin-1–stimulated K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. Our results reveal the mechanistic basis by which ubiquilin-1 regulates APP maturation, with important consequences for the pathogenesis of late-onset AD.
Chromosome 3p loss of heterozygosity and mutation analysis of the FHIT and beta-cat genes in squamous cell carcinoma of the head and neck.

AIMS: To study the loss of heterozygosity at the short arm of chromosome 3 in primary tumours from patients with squamous cell carcinoma of the head and neck; to determine whether the FHIT gene, mapped to 3p14.2 and the CTNNB1 (beta-cat) gene, mapped to 3p21, are deleted or mutated in these tumours. METHODS: DNA was extracted from fresh tumours. Loss of heterozygosity was assessed by microsatellite analysis of the following markers: D3S1283 and D3S1286 (3p24), D3S966 (3p21), and D3S1300 (3P14.2). Homozygous deletion was determined by radioactive multiplex polymerase chain reaction of exons 5 and 6 of the FHIT gene. The presence of mutations in FHIT exon 5 and beta-cat exon 3 was studied by single strand conformation polymorphism. RESULTS: 50% of informative cases (25/50) showed loss of heterozygosity for at least one of the 3p markers. 3p21 was the region with the highest rate of allelic deletion (63%). No point mutation was found in FHIT exon 5 or beta-cat exon 3. No case showed homozygous deletion for the FHIT (exons 5 and 6) or the beta-cat exon 3. CONCLUSIONS: The short arm of chromosome 3 is often deleted in the head and neck squamous cell carcinomas. In the remaining alleles of the FHIT or beta-cat genes, no evidence was found for point mutations or deletions, documented in other common carcinomas. Inactivation could occur by different mechanisms such as methylation, or other genes (not studied here) could be target of allelic losses in squamous cell carcinoma of the head and neck.
Peripherin as a marker for degeneration of spiral ganglion neurons after aminoglycoside ototoxicity

Conclusion. Our data show that temporary appearance of atypical type 1 neurons, like type 3 neurons, might be another degenerating form of spiral ganglion neurons (SGNs); peripherin might be a marker of degenerating neurons. Objectives. Further morphological and biochemical studies on surviving SGNs after loss of hair cells might offer clues for preventing their degeneration. Materials and methods. We observed the ultrastructural features of surviving SGNs and analyzed the peripherin immunoreactivity at 4, 10, or 20 weeks after systemic injection of neomycin in rats. Results. Type 3 neurons, similar to type 1 neurons but unmyelinated, appeared in the spiral ganglion by 4-week survival, and showed a survival advantage in remaining SGNs by longer surviving periods. We observed neurons packed with dense intermediate filament and with multiple layers of dense myelin sheath (atypical type 1 neurons) in the degenerating neurons. Atypical type 1 neurons were observed among the degenerating neurons in the 4- and 10-week survival groups, but disappeared in longer surviving animals. By means of immunohistochemistry, only smaller SGNs of normal rats were strongly stained by anti-peripherin antibody, whereas increased immunoreactivity was observed in both large and small remaining neurons after neomycin treatment, especially in 10- and 20-week survival animals.
Assessment of Bilateral Limb Lymphedema by Bioelectrical Impedance Spectroscopy

Objective: The aim of the present study was to determine if the ratio of extracellular fluid (ECF), including the lymph, to that of intracellular fluid (ICF), as measured by bioimpedance spectroscopy (BIS), could be used to assess bilateral lymphedema (LE). Background: The presence of LE is commonly determined as an increase in tissue volume due to the presence of excess lymph relative to the volume of a comparable unaffected body region or to comparative normative data. However, in bilateral LE of the limbs, a comparable body region, the contralateral limb, is also affected, precluding normalization. An alternative is to normalize the increase in lymph volume, as ECF, to that of ICF volume. Methods: Extracellular/intracellular fluid ratios, expressed as the ratio of intracellular impedance (R i) to extracellular impedance (R 0), for the limbs of 277 female and 224 male controls were determined from an accumulated database of impedance data. Equivalent data were obtained for an opportunistic cross-sectional sample of 37 female and 5 male participants with bilateral LE of the legs. The ratios of R i/R 0 in the lymphedematous legs of the affected participants were compared with the equivalent ratios in the unaffected arms of the same participants and with those of the controls using box plots and visualized as bivariate data using tolerance ellipses. Results: Despite R i/R 0 ratios varying with age, sex, and limb dominance, comparison of the ratio for affected legs (normalized to the ratio in the unaffected arms) with equivalent ratios observed in a control population (as bivariate tolerance plots) was capable of discriminating between 70% and 89% of the participants with LE. Conclusions: Bioelectrical impedance spectroscopy and determination of Ri/R0 ratios as indices of ECF/ICF ratios holds promise for the semiquantitative assessment of bilateral LE.
Plasma vaspin concentrations are elevated in metabolic syndrome in men and are correlated with coronary atherosclerosis in women

Objective Vaspin is visceral adipose‐tissue‐derived adipokine, which has an insulin‐sensitizing effect in obese type 2 diabetic rodent models. As adipokines may serve as a link between visceral adiposity and atherosclerosis, we investigated whether plasma vaspin concentrations were associated with the metabolic syndrome and coronary atherosclerosis.
Clinical, virologic and phylogenetic features of hepatitis B infection in Iranian patients.

AIM To characterize the clinical, serologic and virologic features of hepatitis B virus (HBV) infection in Iranian patients with different stages of liver disease. METHODS Sixty two patients comprising of 12 inactive carriers, 30 chronic hepatitis patients, 13 patients with liver cirrhosis and 7 patients with hepatocellular carcinoma (HCC) were enrolled in the study. The HBV S, C and basal core promoter (BCP) regions were amplified and sequenced, and the clinical, serologic, phylogenetic and virologic characteristics were investigated. RESULTS The study group consisted of 16 HBeAg-positive and 46 HBeAg-negative patients. Anti-HBe-positive patients were older and had higher levels of ALT, ASL and bilirubin compared to HBeAg-positive patients. Phylogenetic analysis revealed that all patients were infected with genotype D (mostly ayw2). The G1896A precore (PC) mutant was detected in 58.1% patients. HBeAg-negative patients showed a higher rate of PC mutant compared to HBeAg-positive patients (c2 = 9.682, P = 0.003). The majority of patients with HCC were HBeAg-negative and were infected with PC mutant variants. There was no significant difference in the occurrence of BCP mutation between the two groups, while the rate of BCP plus PC mutants was higher in HBeAg-negative patients (c2 = 4.308, P = 0.04). In the HBV S region, the genetic variability was low, and the marked substitution was P120T/S, with a rate of 9.7% (n = 6). CONCLUSION In conclusion, HBV/D is the predominant genotype in Iran, and the nucleotide variability in the BCP and PC regions may play a role in HBV disease outcome in HBeAg-negative patients.
Influence of diabetes mellitus on postoperative complications and failure in head and neck free flap reconstruction: A systematic review and meta‐analysis

We performed a systematic review and meta‐analysis to determine whether diabetic patients have an increased rate of postoperative complications compared to nondiabetic patients after head and neck free flap reconstruction. A systematic review of PubMed Database between 1966 and 2012 was performed. RevMan 5.0 was used for meta‐analysis. A retrospective medical chart review of 7890 patients to identify those who had a failed microsurgical reconstruction of the head and neck region at Chang Gung Memorial Hospital was also carried out. The result revealed that patients with diabetes mellitus have a 1.76 increased risk of complications (odds ratio [OR] = 1.76; 95% confidence interval [CI] = 1.11–2.79) with minimal heterogeneity (I 2 = 22%; p = .28). The prevalence of diabetes mellitus in patients with failed free flaps for head and neck reconstruction is 15%. The incidence of diabetes mellitus in these patients with failed free flaps is 2.3 times higher than in the general population. © 2014 Wiley Periodicals, Inc. Head Neck 37: 615–618, 2015
FoxO6 affects Plxna4-mediated neuronal migration during mouse cortical development

Significance The molecular basis of radial migration of cortical neurons is a well-studied process showing prominent roles for axon guidance, cell adhesion, cell polarity, and cytoskeleton remodeling. Remarkably, knowledge about transcriptional control of such processes is scarce. In this study, we show that the forkhead transcription factor FoxO6 influences Plexin A4 (Plxna4) expression, a key component of the Semaphorin signaling pathway, known for its role in axonal guidance and cortical migration. FoxO6 knockdown animals show a hampered migration of embryonic day 14.5-born neurons, which can be rescued by recombinant Plxna4 expression constructs. Altogether, our data provide insights into the molecular mechanisms whereby transcriptional programs influence cortical development. The forkhead transcription factor FoxO6 is prominently expressed during development of the murine neocortex. However, its function in cortical development is as yet unknown. We now demonstrate that cortical development is altered in FoxO6+/− and FoxO6−/− mice, showing migrating neurons halted in the intermediate zone. Using a FoxO6-directed siRNA approach, we substantiate the requirement of FoxO6 for a correct radial migration in the developing neocortex. Subsequent genome-wide transcriptome analysis reveals altered expression of genes involved in cell adhesion, axon guidance, and gliogenesis upon silencing of FoxO6. We then show that FoxO6 binds to DAF-16–binding elements in the Plexin A4 (Plxna4) promoter region and affects Plxna4 expression. Finally, ectopic Plxna4 expression restores radial migration in FoxO6+/− and siRNA-mediated knockdown models. In conclusion, the presented data provide insights into the molecular mechanisms whereby transcriptional programs drive cortical development.
Decline in the frequency of Burkitt's lymphoma relative to other childhood malignancies in Ibadan, Nigeria

Abstract Burkitt's lymphoma is the commonest childhood malignancy in tropical Africa and the predisposing factors include malaria and infection with the Epstein-Barr virus. Recent studies suggest that the prevalence of this neoplasm is declining in this environment. The present study was undertaken to investigate whether there is a real decrease in the occurrence of Burkitt's lymphoma. We analysed 665 cases of childhood malignancies reported in the Ibadan Cancer Registry between 1991 and 1999. Burkitt's lymphoma and retinoblastoma remained the two commonest specific childhood malignancies, accounting for 19.4% and 17.9% of all childhood cancers, respectively. However, this represents a significant decline in the relative frequency of Burkitt's lymphoma when compared with similar surveys for the periods 1960 to 1972 and 1973 to 1990 when Burkitt's lymphoma accounted for 51.5% and 37.1%, respectively, of all childhood malignancies. In Ibadan, it seems that what appeared to be minor changes might actually be a real decline in the incidence of Burkitt's lymphoma and that it might be partly ascribed to improved living conditions and greater control of malaria.
Testing of digital filters for power-line interference removal from ECG signals

A procedure for testing digital filters for power line interference removal from ECG signals is proposed in this article. The testing procedure is developed in a MatLab environment. It allows different filters to be tested and compared based on the residual error from the filtration. A procedure for measurement the frequency and the amplitude of the power line interference is also developed.
Low Rate of Mother‐to‐Child Transmission of HIV‐1 After Nevirapine Intervention in a Pilot Public Health Program in Yaoundé, Cameroon

Objective: To determine the percentage of infected children for whom nevirapine (NVP) was used to prevent peripartum mother‐tochild transmission (MTCT) of HIV in Yaoundé, Cameroon. Design: The study was a prospective Public Health Pilot Program covering a 3‐year period (January 2000‐December 2002). Methods: Counseled and consenting HIV‐1‐positive pregnant women were given a single dose of NVP at the onset of labor. Babies were given 2 mg/kg NVP syrup within the first 72 hours of life. NVPtreated children were regularly followed up and examined for HIV‐1 infection at 6‐8 weeks and 5‐6 months through plasma viral load (VL) quantification with the bDNA system. Results: One hundred twenty‐three children were diagnosed with perinatal HIV‐1 infection at 6‐8 weeks and 5‐6 months. Thirteen children (10.6% [13/123]; 95% confidence interval, 5.1‐16) were infected and presented with high VLs, in general >500,000 copies/mL. Two children had intermediate VLs (between 50 and 3500 copies/mL) at both time points. One hundred seven children (87%) were considered not infected at 6‐8 weeks of age. Conclusions: Our results indicate that the HIV‐1 MTCT rate 6‐8 weeks after NVP administration was not >13% (16/123), thus demonstrating the effectiveness of NVP for lowering the risk of HIV‐1 MTCT in real‐life settings.
Ghrelin and cholecystokinin in term and preterm human breast milk

Aim: To determine whether ghrelin and cholecystokinin (CCK) are present in significant quantities in term and preterm human breast milk, and to identify their source. Methods: Samples were collected from 10 mothers who delivered term infants and 10 mothers who delivered preterm infants. Estimated fat content was measured. Ghrelin and CCK levels were measured in whole and skim breast milk samples using radioimmunoassays (RIA). Reverse transcriptase‐polymerase chain reaction (RT‐PCR) was performed using RNA from human mammary epithelial cells (hMECs) and mammary gland with primers specific to ghrelin. Results: The median ghrelin level in whole breast milk was 2125 pg/ml, which is significantly higher than normal plasma levels. There was a direct correlation between whole milk ghrelin levels and estimated milk fat content (r=0.84, p<0.001). Both the mammary gland and hMECs produced ghrelin. While CCK was detected in some samples, levels were insignificant. Infant gestational age, birthweight, maternal age, and maternal pre‐pregnancy body mass index did not significantly affect the results.
Q-Switched ruby laser therapy of acquired bilateral nevus of Ota-like macules.

BACKGROUND Acquired bilateral nevus of Ota-like macules (ABNLM), also called nevus fuscoceruleus zygomaticus or nevus of Hori, is a relatively common disease in Asia. It is refractory to all medical treatment. OBJECTIVE To present the first report on the use of Q-switched ruby laser to treat ABNLM. METHODS One hundred and forty female patients, ages 19-62 years (mean 39 years), were included in the study. The laser fluence employed was 7-10 J/cm2, at a repetition rate of 1 Hz, and with a spot size of 2-4 mm. The number of treatment sessions ranged from 1 to 6 (mean 2.3). RESULTS Nine patients were lost to follow-up before complete clearance of the lesions, while in the remaining 131 patients complete clearance was obtained. The only complication was a long-term hypopigmentation, observed in three patients. There was no recurrence at 6 months- 4.3 years (mean 2.5 years) of follow-up. CONCLUSION Q-switched ruby laser is an effective and less invasive tool to eradicate ABNLM.
A Comparison of Mindray BC‐6800, Sysmex XN‐2000, and Beckman Coulter LH750 Automated Hematology Analyzers: A Pediatric Study

Modern automated laboratory hematology analyzers allow the measurement of over 30 different hematological parameters useful in the diagnostic and clinical interpretation of patient symptoms. They use different methods to measure the same parameters. Thus, a comparison of complete blood count made by Mindray BC‐6800, Sysmex XN‐2000 and Beckman Coulter LH750 was performed.
Hypercapnia‐induced active expiration increases in sleep and enhances ventilation in unanaesthetized rats

Expiratory muscles (abdominal and thoracic) can be recruited when respiratory drive increases under conditions of increased respiratory demand such as hypercapnia. Studying hypercapnia‐induced active expiration in unanaesthetized rats importantly contributes to the understanding of how the control system is integrated in vivo in freely moving animals. In unanaesthetized rats, hypercapnia‐induced active expiration was not always recruited either in wakefulness or in sleep, suggesting that additional factors influence the recruitment of active expiration. The pattern of abdominal muscle recruitment varied in a state‐dependent manner with active expiration being more predominant in the sleep state than in quiet wakefulness. Pulmonary ventilation was enhanced in periods with active expiration compared to periods without it.
Escalas de equivalencia en los países de América Latina

En la literatura sobre la medicion del bienestar existe consenso acerca de la conveniencia de utilizar escalas de equivalencia cuando se emplea los recursos economicos de un hogar como indicador de bienestar. Estas dan cuenta de las diferencias en el costo de vida segun el tamano y composicion del hogar y, por ello, se consideran mas adecuadas que expresar el ingreso o el gasto en terminos per capita. No obstante, tambien se reconoce que su estimacion esta sujeta a importantes limitaciones conceptuales y empiricas. Este articulo busca ilustrar las posibilidades de estimacion de escalas de equivalencia en los paises de America Latina. Para ello, se utiliza dos de los metodos de estimacion mas conocidos, Engel y Rothbarth, y un conjunto de encuestas de presupuestos familiares para 16 paises. Los resultados muestran una amplia heterogeneidad, consistente con la que se encuentra en la revision de la literatura. Segun el pais y encuesta utilizada, las escalas de equivalencia obtenidas presentan distintos grados de sensibilidad al modelo de estimacion y a las caracteristicas de los datos. En consecuencia, se propone que la aplicacion de escalas de equivalencia para la medicion del bienestar en los paises de la region se haga a traves de una escala parametrica, con una forma funcional predeterminada, que considera unicamente la presencia de economias de escala en el consumo