Miracle-dz/UniFAR-FTUs huggingface dataset:
RBF Binding to both Canonical E2F Targets and Noncanonical Targets Depends on Functional dE2F/dDP Complexes

ABSTRACT The retinoblastoma (RB) family of proteins regulate transcription. These proteins lack intrinsic DNA-binding activity but are recruited to specific genomic locations through interactions with sequence-specific DNA-binding factors. The best-known target of RB protein (pRB) is the E2F transcription factor; however, many other chromatin-associated proteins have been described that may allow RB family members to act at additional sites. To gain a perspective on the scale of E2F-dependent and E2F-independent functions, we generated genome-wide binding profiles of RBF1 and dE2F proteins in Drosophila larvae. RBF1 and dE2F2 associate with a large number of binding sites at genes with diverse biological functions. In contrast, dE2F1 was detected at a smaller set of promoters, suggesting that it overrides repression by RBF1/dE2F2 at a specific subset of targets. Approximately 15% of RBF1-bound regions lacked consensus E2F-binding motifs. To test whether RBF1 action at these sites is E2F independent, we examined dDP mutant larvae that lack any functional dE2F/dDP heterodimers. As measured by chromatin immunoprecipitation-microarray analysis (ChIP-chip), ChIP-quantitative PCR (qPCR), and cell fractionation, the stable association of RBF1 with chromatin was eliminated in dDP mutants. This requirement for dDP was seen at classic E2F-regulated promoters and at promoters that lacked canonical E2F-binding sites. These results suggest that E2F/DP complexes are essential for all genomic targeting of RBF1.
Amplification of the association between birthweight and blood pressure with age: the Bogalusa Heart Study

Objectives Although low birthweight is associated with elevated blood pressure (BP) levels, whether the strength of this relationship is amplified with age is still debated. This study tested the hypothesis that the magnitude of the birthweight–BP association increases with age from childhood to adulthood. Methods The study cohort included 6251 individuals (64.5% whites and 35.6% blacks, 50.0% males) enrolled in the Bogalusa Heart Study. Individuals were examined 1–15 times for BP from childhood to adulthood, with 24 363 observations. Information on birthweight and gestational age was obtained from Louisiana State birth certificates. Results After adjusting for race, sex, age and gestational age, low birthweight (kg) was associated with higher SBP levels (mmHg) in adolescence (aged 12–17 years, regression coefficient β = −0.80, P = 0.004) and adulthood (aged 18–50 years, β = −1.34, P = 0.010). Adjustment for current BMI yielded considerably stronger association. Importantly, the magnitude of the birthweight–SBP relationship, measured as standardized β(unit = SD), was significantly amplified with increasing age, regardless of adjustment for current BMI and race. Further, the strengthened association (the increase in standardized β ranging 0.02–0.12) by adjustment for current BMI was closely related to the BMI–SBP and birthweight–BMI correlations, especially noted in childhood. Conclusion These findings on the potentiating effect of increasing age on the birthweight–BP relationship suggest that the fetal programming and the increasing cumulative burden with age of unhealthy lifestyle behaviors affect the development of adult hypertension in a synergistic manner.
Enforced Expression of HOXB4 in Human Embryonic Stem Cells Enhances the Production of Hematopoietic Progenitors but Has No Effect on the Maturation of Red Blood Cells

We have developed a robust, Good Manufacturing Practice‐compatible differentiation protocol capable of producing scalable quantities of red blood cells (RBCs) from human pluripotent stem cells (hPSCs). However, translation of this protocol to the clinic has been compromised because the RBCs produced are not fully mature; thus, they express embryonic and fetal, rather than adult globins, and they do not enucleate efficiently. Based on previous studies, we predicted that activation of exogenous HOXB4 would increase the production of hematopoietic progenitor cells (HPCs) from hPSCs and hypothesized that it might also promote the production of more mature, definitive RBCs. Using a tamoxifen‐inducible HOXB4‐ERT2 expression system, we first demonstrated that activation of HOXB4 does increase the production of HPCs from hPSCs as determined by colony‐forming unit culture activity and the presence of CD43+CD34+ progenitors. Activation of HOXB4 caused a modest, but significant, increase in the proportion of immature CD235a+/CD71+ erythroid cells. However, this did not result in a significant increase in more mature CD235a+/CD71− cells. RBCs produced in the presence of enhanced HOXB4 activity expressed embryonic (ε) and fetal (γ) but not adult (β) globins, and the proportion of enucleated cells was comparable to that of the control cultures. We conclude that programming with the transcription factor HOXB4 increases the production of hematopoietic progenitors and immature erythroid cells but does not resolve the inherent challenges associated with the production of mature adult‐like enucleated RBCs.
Improvement of Influenza A/Fujian/411/02 (H3N2) Virus Growth in Embryonated Chicken Eggs by Balancing the Hemagglutinin and Neuraminidase Activities, Using Reverse Genetics

ABSTRACT The H3N2 influenza A/Fujian/411/02-like virus strains that circulated during the 2003-2004 influenza season caused influenza epidemics. Most of the A/Fujian/411/02 virus lineages did not replicate well in embryonated chicken eggs and had to be isolated originally by cell culture. The molecular basis for the poor replication of A/Fujian/411/02 virus was examined in this study by the reverse genetics technology. Two antigenically related strains that replicated well in embryonated chicken eggs, A/Sendai-H/F4962/02 and A/Wyoming/03/03, were compared with the prototype A/Fujian/411/02 virus. A/Sendai differed from A/Fujian by three amino acids in the neuraminidase (NA), whereas A/Wyoming differed from A/Fujian by five amino acids in the hemagglutinin (HA). The HA and NA segments of these three viruses were reassorted with cold-adapted A/Ann Arbor/6/60, the master donor virus for the live attenuated type A influenza vaccines (FluMist). The HA and NA residues differed between these three H3N2 viruses evaluated for their impact on virus replication in MDCK cells and in embryonated chicken eggs. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. Thus, the balance between the HA and NA activities is critical for influenza virus replication in a different host system. The HA or NA changes that increased A/Fujian/411/02 virus replication in embryonated chicken eggs were found to have no significant impact on antigenicity of these recombinant viruses. This study demonstrated that the reverse genetics technology could be used to improve the manufacture of the influenza vaccines.
MYELINATION PATTERNS ON MAGNETIC RESONANCE OF CHILDREN WITH DEVELOPMENTAL DELAY

Magnetic resonance (MR) imaging was performed in 30 children with unexplained developmental delay who had associated neurological abnormalities such as seizures, spasticity, hypotonia, ataxia or poor vision. No child had a history of regression, preterm birth or neonatal cerebral injury. CT scans were performed before MR in all cases and were either normal or showed only mild atrophy. At least two MR sequences were obtained for all patients. Nine children had delayed or absent myelination on MR, one had patchy white‐matter abnormalities, and in one patient myelination was topographically normal, but of inappropriately low signal intensity. MR was abnormal in six of seven children who had abnormal brainstem auditory evoked potentials (BAEP), and was normal in nine of 11 patients who had a normal BAEP. MR may have a useful rôle in demonstrating abnormal white‐matter maturation in children with unexplained neurodevelopmental delay, particularly when abnormalities are found on BAEP studies.
Seasonal and within-canopy variation in shoot-scale resource-use efficiency trade-offs in a Norway spruce stand.

Previous leaf-scale studies of carbon assimilation describe short-term resource-use efficiency (RUE) trade-offs where high use efficiency of one resource requires low RUE of another. However, varying resource availabilities may cause long-term RUE trade-offs to differ from the short-term patterns. This may have important implications for understanding canopy-scale resource use and allocation. We used continuous gas exchange measurements collected at five levels within a Norway spruce, Picea abies (L.) karst. , canopy over 3 years to assess seasonal differences in the interactions between shoot-scale resource availability (light, water and nitrogen), net photosynthesis (An ) and the use efficiencies of light (LUE), water (WUE) and nitrogen (NUE) for carbon assimilation. The continuous data set was used to develop and evaluate multiple regression models for predicting monthly shoot-scale An . These models showed that shoot-scale An was strongly dependent on light availability and was generally well described with simple one- or two-parameter models. WUE peaked in spring, NUE in summer and LUE in autumn. However, the relative importance of LUE for carbon assimilation increased with canopy depth at all times. Our results suggest that accounting for seasonal and within-canopy trade-offs may be important for RUE-based modelling of canopy carbon uptake.
Pathologic Features of Pediatric Head and Neck Melanoma

Although malignant melanoma is rare in children, its incidence is steadily increasing, and it is potentially lethal. Few studies have examined head and neck melanoma in children, and even fewer have focused on the histopathologic features of melanoma within this anatomic region. To further the understanding of this entity, we examined pathology specimens from nine subjects age 18 years and younger with an original diagnosis of head or neck melanoma. The anatomic locations of these primary melanomas were the face and nose (n = 4), scalp and neck (n = 4), and ear (n = 1). The cases included seven superficial spreading melanomas, one unclassified (possible nodular) melanoma, and one melanoma in situ. No melanomas demonstrating desmoplastic or spindle cell morphologies were noted upon review. Breslow depth ranged from 0 to 2.9 mm (mean 1.3 mm, median 0.6 mm), with Clark level ranging from I to V. Pagetoid scatter was found in eight cases. Other notable features included regression (n = 5), ulceration (n = 1), and associated melanocytic nevus (n = 4). We did not observe any small cell variants; all nine cases had an epithelioid appearance. Nor was any melanoma‐associated mortality observed at last follow‐up (mean 60.4 mos, median 48 mos, range 2–174 mos). These histopathologic features were consistent with adult‐type melanoma, which is in agreement with other histopathologic studies of melanoma in children.
Behavioral evaluation of microwave irradiation.

Establishing safe exposure levels for microwave irradiation is important since new, more powerful emitters are developed and the potential for accidental exposure is increasing. Analysis of the behavior of exposed laboratory animals has proven to be an accurate and repeatable metric for assessing the effects of microwave irradiation. Determining the specific absorption rate (SAR) at which an animal will cease an ongoing behavior has proven useful in the development of safe exposure levels for humans. Behaviors that have been used are simple tasks, and the point at which behavior changes significantly or ceases has often been referred to as "work stoppage. " The tasks have been used to evaluate the overwhelming effects of heating produced by microwave irradiation. Both whole-body exposures and partial-body exposures with hotspots have been evaluated. Recent studies have suggested that microwave effects on specific cognitive aspects of behavior such as attention, learning, memory, discrimination, and time perception may occur at SAR levels far below the SARs needed to cause work stoppage. New research studies are underway to evaluate microwave-induced cognitive effects.
Morphine kinetics after diamorphine infusion in premature neonates.

1. The pharmacokinetics of morphine were studied in 26 newborn premature neonates (26-38 weeks gestational age) who were given a loading dose of 50 micrograms kg-1 of diamorphine followed by an intravenous infusion of 15 micrograms kg-1 h-1 of diamorphine. Plasma concentrations of morphine were measured during the infusion at steady-state and for 24 h after the cessation of the diamorphine infusion. 2. The mean steady-state plasma morphine concentration (+/- s.d.) for a diamorphine infusion rate of 15 micrograms kg-1 h-1 was 62.5 +/- 22.8 ng ml-1. 3. Morphine clearance was 3.6 +/- 0.9 ml min-1 kg-1, the elimination half-life was 8.9 +/- 3.3 h and the volume of distribution was 2.7 +/- 1.01 kg-1. 4. Morphine elimination kinetics were described by a mono-exponential function. 5. There was a direct relationship between the gestational age of the patients and the clearance (r2 = 0.31, P = 0.003) and half-life (r2 = 0.35, P = 0.01) of morphine, but no relationship was found between gestational age and volume of distribution. 6. The results suggest that the currently used dosing regimen of diamorphine achieves a safe and effective morphine concentration in the premature newborn but that the loading dose could be modified to achieve a more rapid onset of analgesia.
Alkaline phosphatase and percentage body fat predict circulating C-reactive protein in premenopausal women

C-reactive protein (CRP) is considered a marker of inflammation, which is a risk factor for many chronic diseases. However, determinants of CRP remain unclear and were studied in a strictly defined cohort of healthy premenopausal women (n=233) using multiple regression models. Independent predictors of serum CRP (model R2=0.59) were percentage body fat, serum alkaline phosphatase (ALP), sex hormone-binding globulin and white blood cell count. The close association between CRP and ALP suggests that enzymatic activity of ALP may be important for the anti-inflammatory effects of CRP, which should be confirmed with additional studies.
Comparison of Cellular and Biomass Specific Activities of Dominant Bacterioplankton Groups in Stratified Waters of the Celtic Sea

ABSTRACT A flow-sorting technique was developed to determine unperturbed metabolic activities of phylogenetically characterized bacterioplankton groups with incorporation rates of [35S]methionine tracer. According to fluorescence in situ hybridization with rRNA targeted oligonucleotide probes, a clade of α-proteobacteria, related to Roseobacter spp. , and aCytophaga-Flavobacterium cluster dominated the different groups. Cytometric characterization revealed both these groups to have high DNA (HNA) content, while the α-proteobacteria exhibited high light scatter (hs) and the Cytophaga-Flavobacteriumcluster exhibited low light scatter (ls). A third abundant group with low DNA (LNA) content contained cells from a SAR86 cluster of γ-proteobacteria. Cellular specific activities of the HNA-hs group were 4- and 1.7-fold higher than the activities in the HNA-ls and LNA groups, respectively. However, the higher cellular protein synthesis by the HNA-hs could simply be explained by their maintenance of a larger cellular protein biomass. Similar biomass specific activities of the different groups strongly support the main assumption that underlies the determination of bacterial production: different bacteria in a complex community incorporate amino acids at a rate proportional to their protein synthesis. The fact that the highest growth-specific rates were determined for the smallest cells of the LNA group can explain the dominance of this group in nutrient-limited waters. The metabolic activities of the three groups accounted for almost the total bacterioplankton activity, indicating their key biogeochemical role in the planktonic ecosystem of the Celtic Sea.
Cognitive sequelae in acute respiratory distress syndrome patients with and without recall of the intensive care unit

Some critically ill patients have dramatic recollections of the intensive care unit (ICU), whereas 23–50% have little or no recollection of their ICU stay. In addition, cognitive impairments are common following critical illness and ICU treatment. Little is known regarding the relationship between cognitive sequelae and ICU recall. We assessed recall of the ICU and its relationship to cognitive functioning at hospital discharge and 1 and 2 years after discharge in 70 consecutive acute respiratory distress syndrome (ARDS) patients. Seventeen patients (24%) had no recall of the ICU. Patients without ICU recall had increased rates of cognitive sequelae at hospital discharge and 1-year follow-up compared with the ICU recall group. Patients without ICU recall had a greater magnitude of cognitive impairments at hospital discharge, but not at 1- or 2-year follow-up. Profile analysis showed significant group differences in general intellectual functioning, executive function, processing speed, and spatial skills at hospital discharge, but not at 1- or 2-year follow-up. Estimated premorbid intelligence scores were inversely related to the magnitude of cognitive sequelae, suggesting greater “cognitive reserve” in patients with fewer cognitive decrements. (JINS, 2007, 13, 595–605.)
Impact of the F508del mutation on ovine CFTR, a Cl− channel with enhanced conductance and ATP‐dependent gating

Malfunction of the cystic fibrosis transmembrane conductance regulator (CFTR), a gated pathway for chloride movement, causes the common life‐shortening genetic disease cystic fibrosis (CF). Towards the development of a sheep model of CF, we have investigated the function of sheep CFTR. We found that sheep CFTR was noticeably more active than human CFTR, while the most common CF mutation, F508del, had reduced impact on sheep CFTR function. Our results demonstrate that subtle changes in protein structure have marked effects on CFTR function and the consequences of the CF mutation F508del.
Dynamics of a feline virus with two transmission modes within exponentially growing host populations

Feline panleucopenia virus (FPLV) was introduced in 1977 on Marion Island (in the southern Indian Ocean) with the aim of eradicating the cat population and provoked a huge decrease in the host population within six years. The virus can be transmitted either directly through contacts between infected and healthy cats or indirectly between a healthy cat and the contaminated environment: a specific feature of the virus is its high rate of survival outside the host. In this paper, a model was designed in order to take these two modes of transmission into account. The results showed that a mass-action incidence assumption was more appropriate than a proportionate mixing one in describing the dynamics of direct transmission. Under certain conditions the virus was able to control the host population at a low density. The indirect transmission acted as a reservoir supplying the host population with a low but sufficient density of infected individuals which allowed the virus to persist. The dynamics of the infection were more affected by the demographic parameters of the healthy hosts than by the epidemiological ones. Thus, demographic parameters should be precisely measured in field studies in order to obtain accurate predictions. The predicted results of our model were in good agreement with observations.
Early Inflammatory Responses following Cell Grafting in the CNS Trigger Activation of the Subventricular Zone: A Proposed Model of Sequential Cellular Events

While multiple rodent preclinical studies, and to a lesser extent human clinical trials, claim the feasibility, safety, and potential clinical benefit of cell grafting in the central nervous system (CNS), currently only little convincing knowledge exists regarding the actual fate of the grafted cells and their effect on the surrounding environment (or vice versa). Our preceding studies already indicated that only a minor fraction of the initially grafted cell population survives the grafting process, while the surviving cell population becomes invaded by highly activated microglia/macrophages and surrounded by reactive astrogliosis. In the current study, we further elaborate on early cellular and inflammatory events following syngeneic grafting of eGFP mouse embryonic fibroblasts (mEFs) in the CNS of immunocompetent mice. Based on obtained quantitative histological data, we here propose a detailed mathematically derived working model that sequentially comprises hypoxia-induced apoptosis of grafted mEFs, neutrophil invasion, neoangiogenesis, microglia/macrophage recruitment, astrogliosis, and eventually survival of a limited number of grafted mEFs. Simultaneously, we observed that the cellular events following mEF grafting activates the subventricular zone neural stem and progenitor cell compartment. This proposed model therefore further contributes to our understanding of cell graft-induced cellular responses and will eventually allow for successful manipulation of this intervention.
Potential Predictive Markers in Protocol Biopsies for Premature Renal Graft Loss

Background/Aims: Protocol biopsies offer new possibilities to predict kidney allograft outcome. The aim of this study was to find clinical, laboratory, morphological and molecular predictors of short-term renal graft survival. Methods: Three-month protocol kidney graft biopsy was carried out on 257 patients. The real-time RT-PCR was used to identify intragraft mRNA expression of several cytokines and chemokines and predictive statistics was performed to find markers connected with the risk of premature graft failure. Results: Compared to patients with normal morphology at 3 months, patients with subclinical rejection including borderline changes had experienced more frequent (p < 0.001) acute rejections before 3-month biopsy, serum creatinine ≧170 µmol/l (p < 0.01), and higher intrarenal expression of RANTES, IP-10 (p < 0.001), C3, CD3, IgJ (p < 0.01) and CD20 (p < 0.05). There was a significant correlation between subclinical rejection and the occurrence of late acute rejection and graft failure at the first year after transplantation. Moreover, higher RANTES and IP-10 expressions in subclinical rejection predicted graft loss at one year after transplantation in the univariate analysis. Conclusions: Patients with subclinical rejection including borderline changes in 3-month biopsy and particularly those with higher intrarenal expression of RANTES and IP-10 mRNA were found to be at risk for premature kidney graft loss.