Miracle-dz/UniFAR-FTUs huggingface dataset:
Afferent baroreflex dysfunction and age-related orthostatic hypotension.

1. To test the hypothesis that in apparently healthy elderly subjects with orthostatic hypotension there is afferent baroreflex dysfunction, cardiovascular and neurohumoral responses were measured after separate stimuli which activated baroreceptor (head-up tilt) and non-baroreceptor (cold stress, isometric exercise) afferent pathways. 2. In 15 healthy elderly control subjects blood pressure did not change with 60 degrees head-up tilting and there was a moderate increase in heart rate, whereas in 13 subjects with age-related orthostatic hypotension head-up tilting was associated with a marked fall in blood pressure but a similar heart rate response to that in the elderly control group. In contrast, both groups of subjects had similar blood pressure and heart rate responses to cold stress and sustained isometric exercise. 3. Nine subjects with autonomic neuropathy also showed a marked hypotensive response to head-up tilt, but produced no pressor response to cold stress or isometric exercise. 4. The plasma concentrations of noradrenaline, adrenaline and neuropeptide-Y-like immunoreactivity rose and that of atrial natriuretic peptide fell after head-up tilt in the study population as a whole. There were no significant differences between groups despite the much greater blood pressure drops in the subjects with autonomic neuropathy and in those with age-associated orthostatic hypotension. 5. The aorto-iliac pulse wave velocity index was significantly higher in subjects with age-associated orthostatic hypotension compared with that in control subjects. 6. The pattern of responses to the separate stresses observed in the group with age-associated orthostatic hypotension is characteristic and different from that in the elderly control subjects and the subjects with autonomic neuropathy. (ABSTRACT TRUNCATED AT 250 WORDS)
The Impact of Roads on the Demography of Grizzly Bears in Alberta

One of the principal factors that have reduced grizzly bear populations has been the creation of human access into grizzly bear habitat by roads built for resource extraction. Past studies have documented mortality and distributional changes of bears relative to roads but none have attempted to estimate the direct demographic impact of roads in terms of both survival rates, reproductive rates, and the interaction of reproductive state of female bears with survival rate. We applied a combination of survival and reproductive models to estimate demographic parameters for threatened grizzly bear populations in Alberta. Instead of attempting to estimate mean trend we explored factors which caused biological and spatial variation in population trend. We found that sex and age class survival was related to road density with subadult bears being most vulnerable to road-based mortality. A multi-state reproduction model found that females accompanied by cubs of the year and/or yearling cubs had lower survival rates compared to females with two year olds or no cubs. A demographic model found strong spatial gradients in population trend based upon road density. Threshold road densities needed to ensure population stability were estimated to further refine targets for population recovery of grizzly bears in Alberta. Models that considered lowered survival of females with dependant offspring resulted in lower road density thresholds to ensure stable bear populations. Our results demonstrate likely spatial variation in population trend and provide an example how demographic analysis can be used to refine and direct conservation measures for threatened species.
Studio Classrooms and Student Centered Learning in Traditional Microscopy Courses

A studio classroom involves few traditional lectures. Instead it emphasizes collaborative/cooperative learning and active learning. The instructor acts as a facilitator while the students work together to learn. In Geology courses involving petrographic microscopes, engaging students in cooperative learning may be problematic. Microscopy traditionally involves individual students using seperate petrographic microscopes. Digital microscopy using digital cameras to provide live video feed to a video monitor can help change a microscopy lab into a studio-style classroom. Students can work together on labs, teach each other to identify common rock-forming minerals, and piece together geologic histories and environment of formations in a highly collaborative environment. Once students adjust to the classroom environment, studio-style work carries over easily into class activities that don't necessarily involve the microscope. Studio classrooms promote higher test scores and students learn the importance of group work and in class presentations.
A polycomb group protein, PHF1, is involved in the response to DNA double-strand breaks in human cell

DNA double-strand breaks (DSBs) represent the most toxic DNA damage arisen from endogenous and exogenous genotoxic stresses and are known to be repaired by either homologous recombination or nonhomologous end-joining processes. Although many proteins have been identified to participate in either of the processes, the whole processes still remain elusive. Polycomb group (PcG) proteins are epigenetic chromatin modifiers involved in gene silencing, cancer development and the maintenance of embryonic and adult stem cells. By screening proteins responding to DNA damage using laser micro-irradiation, we found that PHF1, a human homolog of Drosophila polycomb-like, Pcl, protein, was recruited to DSBs immediately after irradiation and dissociated within 10 min. The accumulation at DSBs is Ku70/Ku80-dependent, and knockdown of PHF1 leads to X-ray sensitivity and increases the frequency of homologous recombination in HeLa cell. We found that PHF1 interacts physically with Ku70/Ku80, suggesting that PHF1 promotes nonhomologous end-joining processes. Furthermore, we found that PHF1 interacts with a number of proteins involved in DNA damage responses, RAD50, SMC1, DHX9 and p53, further suggesting that PHF1, besides the function in PcG, is involved in genome maintenance processes.
Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions

Background Estimating the historical and demographic parameters that characterize modern human populations is a fundamental part of reconstructing the recent history of our species. In addition, the development of a model of human evolution that can best explain neutral genetic diversity is required to identify confidently regions of the human genome that have been targeted by natural selection. Methodology/Principal Findings We have resequenced 20 independent noncoding autosomal regions dispersed throughout the genome in 213 individuals from different continental populations, corresponding to a total of ∼6 Mb of diploid resequencing data. We used these data to explore and co-estimate an extensive range of historical and demographic parameters with a statistical framework that combines the evaluation of multiple models of human evolution via a best-fit approach, followed by an Approximate Bayesian Computation (ABC) analysis. From a methodological standpoint, evaluating the accuracy of the parameter co-estimation allowed us to identify the most accurate set of statistics to be used for the estimation of each of the different historical and demographic parameters characterizing recent human evolution. Conclusions/Significance Our results support a model in which modern humans left Africa through a single major dispersal event occurring ∼60,000 years ago, corresponding to a drastic reduction of ∼5 times the effective population size of the ancestral African population of ∼13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ∼22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.
High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.

PURPOSE Retinal dystrophy (RD) is a broad group of hereditary disorders with heterogeneous genotypes and phenotypes. Current available genetic testing for these diseases is complicated, time consuming, and expensive. This study was conducted to develop and apply a microarray-based, high-throughput resequencing system to detect sequence alterations in genes related to inherited RD. METHODS A customized 300-kb resequencing chip, Retina-Array, was developed to detect sequence alterations of 267,550 bases of both sense and antisense sequence in 1470 exons spanning 93 genes involved in inherited RD. Retina-Array was evaluated in 19 patient samples with inherited RD provided by the eyeGENE repository and four Centre d'Etudes du Polymorphisme Humaine reference samples through a high-throughput experimental approach that included an automated PCR assay setup and quantification, efficient post-quantification data processing, optimized pooling and fragmentation, and standardized chip processing. RESULTS The performance of the chips demonstrated that the average base pair call rate and accuracy were 93.56% and 99.86%, respectively. In total, 304 candidate variations were identified using a series of customized screening filters. Among 174 selected variations, 123 (70.7%) were further confirmed by dideoxy sequencing. Analysis of patient samples using Retina-Array resulted in the identification of 10 known mutations and 12 novel variations with high probability of deleterious effects. CONCLUSIONS This study suggests that Retina-Array might be a valuable tool for the detection of disease-causing mutations and disease severity modifiers in a single experiment. Retinal-Array may provide a powerful and feasible approach through which to study genetic heterogeneity in retinal diseases.
Production of stable bispecific IgG1 by controlled Fab-arm exchange

The manufacturing of bispecific antibodies can be challenging for a variety of reasons. For example, protein expression problems, stability issues, or the use of non-standard approaches for manufacturing can result in poor yield or poor facility fit. In this paper, we demonstrate the use of standard antibody platforms for large-scale manufacturing of bispecific IgG1 by controlled Fab-arm exchange. Two parental antibodies that each contain a single matched point mutation in the CH3 region were separately expressed in Chinese hamster ovary cells and manufactured at 1000 L scale using a platform fed-batch and purification process that was designed for standard antibody production. The bispecific antibody was generated by mixing the two parental molecules under controlled reducing conditions, resulting in efficient Fab-arm exchange of >95% at kg scale. The reductant was removed via diafiltration, resulting in spontaneous reoxidation of interchain disulfide bonds. Aside from the bispecific nature of the molecule, extensive characterization demonstrated that the IgG1 structural integrity was maintained, including function and stability. These results demonstrate the suitability of this bispecific IgG1 format for commercial-scale manufacturing using standard antibody manufacturing techniques.
Transient neurological symptoms after spinal anesthesia.

PURPOSE The aim of this study was to investigate the incidence of transient neurological symptoms (TNS) after spinal anesthesia with levobupivacaine, bupivacaine, articaine or lidocaine. METHODS The patients (n=400) were randomly assigned to receive spinal anesthesia with levobupivacaine, bupivacaine, articaine or isobaric lidocaine. Onsets of sensory and motor block were recorded. On postoperative days 1, 2 and 3, patients were interviewed by an investigator blinded to the spinal anaesthetic agent used. The patients were classified as having TNS if there was pain in the hips, thighs and/or lower limbs following recovery from anesthesia. RESULTS Time to maximum sensory block was significantly longer in the articaine group than the lidocaine group. The incidence of TNS was much less after spinal anesthesia with levobupivacaine, bupivacaine and articaine than after lidocaine.
Zinc deficiency in patients with persistent viral warts.

OBJECTIVE To determine the association of low serum zinc levels with persistent, progressive or recurrent viral warts. STUDY DESIGN A comparative study. PLACE AND DURATION OF STUDY Dermatology outpatient department of Combined Military Hospital, Abbottabad in collaboration with Department of Chemical Pathology, Army Medical College, Rawalpindi, from June 2006 to May 2007. METHODOLOGY Seventy five patients having warts of more than six months duration, more than 10 in number, who either not responded to or had recurrence after previous treatments for viral warts and not having other chronic dermatological or systemic illness were included in the study after informed consent. Seventy five age and gender matched healthy individuals were taken as control. Serum zinc analysis was carried out by atomic absorption spectrometry using Perkin elmen (USA) apparatus. Independent sample t-test was used to compare mean zinc levels in microgram/litre with significance at p < 0.05. RESULTS Age of the patients as well as controls ranged from 12-65 years with a mean of 25.88 + 8.90 years. Serum zinc level was low in 42 (56%) patients and 24 (32%) controls (p=0.003). Among the patients, serum zinc level ranged from 695-1090 micro-gram/litre with a mean of 804.38 + 100.60, whereas the level ranged from 690-1100 microgram/litre with a mean of 836.17 + 91.04 among controls (p 0.044). CONCLUSION Zinc deficiency is associated with persistent, progressive or recurrent viral warts in the studied patients. Randomized controlled trials with careful dose adjustment of oral zinc sulphate may be helpful to formulate guide lines to manage such patients.
Mediation of the single-walled carbon nanotubes induced pulmonary fibrogenic response by osteopontin and TGF-β1

ABSTRACT Purpose of the study: A number of in vivo studies have shown that pulmonary exposure to carbon nanotubes (CNTs) may lead to an acute local inflammatory response, pulmonary fibrosis, and granulomatous lesions. Among the factors that play direct roles in initiation and progression of fibrotic processes are epithelial-mesenchymal transition and myofibroblasts recruitment/differentiation, both mediated by transforming growth factor-β1 (TGF-β1). Yet, other contributors to TGF-β1 associated signaling, such as osteopontin (OPN) has not been fully investigated. Materials and Methods: OPN-knockout female mice (OPN-KO) along with their wild-type (WT) counterparts were exposed to single-walled carbon nanotubes (SWCNT) (40 µg/mouse) via pharyngeal aspiration and fibrotic response was assessed 1, 7, and 28 days post-exposure. Simultaneously, RAW 264.7 and MLE-15 cells were treated with SWCNT (24 hours, 6 µg/cm2 to 48 µg/cm2) or bleomycin (0.1 µg/ml) in the presence of OPN-blocking antibody or isotype control, and TGF-β1 was measured in supernatants. Results and Conclusions: Diminished lactate dehydrogenase activity at all time points, along with less pronounced neutrophil influx 24 h post-exposure, were measured in broncho-alveolar lavage (BAL) of OPN-KO mice compared to WT. Pro-inflammatory cytokine release (IL-6, TNF-α, MCP-1) was reduced. A significant two-fold increase of TGF-β1 was found in BAL of WT mice at 7 days, while TGF-β1 levels in OPN-KO animals remained unaltered. Histological examination revealed marked decrease in granuloma formation and less collagen deposition in the lungs of OPN-KO mice compared to WT. RAW 264.7 but not MLE-15 cells exposed to SWCNT and bleomycin had significantly less TGF-β1 released in the presence of OPN-blocking antibody. We believe that OPN is important in initiating the cellular mechanisms that produce an overall pathological response to SWCNT and it may act upstream of TGF-β1. Further investigation to understand the mechanistic details of such interactions is critical to predict outcomes of pulmonary exposure to CNT.
Exposure to cold and draught, alcohol consumption, and the NS-phenotype are associated with chronic bronchitis: an epidemiological investigation of 3387 men aged 53–75 years: the Copenhagen Male Study

OBJECTIVES This study was performed to estimate the strength of association between chronic bronchitis and lifetime exposure to occupational factors, current lifestyle, and the NS-phenotype in the MNS blood group among middle aged and elderly men. METHODS The study was carried out within the frameworks of the Copenhagen Male Study. Of 3387 men 3331 men with a mean age of 63 (range 53–75) years could be classified by prevalence of chronic bronchitis. As well as the completion of a large questionnaire on health, lifestyle, and working conditions, all participants had a thorough examination, including measurements of height and weight and blood pressure and a venous blood sample was taken for the measurement of serum cotinine and MNS typing; 16.5% of the men had the NS-phenotype. Chronic bronchitis was defined as cough and phlegm lasting 3 months or more for at least 2 years; 14.6% had chronic bronchitis. RESULTS Smoking and smoke inhalation were the factors most strongly associated with prevalence of chronic bronchitis. There were three major new findings: (a) long term (>5 years) occupational exposure to cold and draught was associated with a significantly increased prevalence of chronic bronchitis; compared with others, and adjusted for confounders, the odds ratio (OR) with 95% confidence interval (95% CI) was 1.4 (1.1 to 1.7), p=0.004; (b) a significant J shaped association existed between alcohol use and bronchitis, p<0.001, with the lowest prevalence found among moderate users; (c) a significant gene by environment association existed between smoking and the NS-phenotype in the MNS blood group; only among smokers was the NS-phenotype associated with a significantly decreased risk of chronic bronchitis, OR 0.67 (0.47-0.97), p=0.02. Other well known associations between dust, fumes, and even exposure to solvents and bronchitis were confirmed. CONCLUSION The results emphasise the multifactorial nature of chronic bronchitis, and show some hitherto unrecognised associations between cold and draught exposure, alcohol consumption, and the NS-phenotype and chronic bronchitis.
Infection of Cells with Human Cytomegalovirus during S Phase Results in a Blockade to Immediate-Early Gene Expression That Can Be Overcome by Inhibition of the Proteasome

ABSTRACT Cells infected with human cytomegalovirus (HCMV) after commencing DNA replication do not initiate viral immediate-early (IE) gene expression and divide before arresting. To determine the nature of this blockade, we examined cells that were infected 24 h after release from G0 using immunofluorescence, laser scanning cytometry, and fluorescence-activated cell sorting (FACS) analysis. Approximately 40 to 50% of the cells had 2N DNA content, became IE+ in the first 12 h, and arrested. Most but not all of the cells with >2N DNA content did not express IE antigens until after mitosis. To define the small population of IE+ cells that gradually accumulated within the S and G2/M compartments, cells were pulsed with bromodeoxyuridine (BrdU) just prior to S-phase infection and analyzed at 12 h postinfection for IE gene expression, BrdU positivity, and cell cycle position. Most of the BrdU+ cells were IE− and had progressed into G2/M or back to G1. The majority of the IE+ cells in S and G2/M were BrdU−. Only a few cells were IE+ BrdU+, and they resided in G2/M. Multipoint BrdU pulse-labeling revealed that, compared to cells actively synthesizing DNA at the beginning of the infection, a greater percentage of the cells that initiated DNA replication 4 h later could express IE antigens and proceed into S. Synchronization of the cells with aphidicolin also indicated that the blockade to the activation of IE gene expression was established in cells soon after initiation of DNA replication. It appears that a short-lived protein in S-phase cells may be required for IE gene expression, as it is partially restored by treatment with the proteasome inhibitor MG132.
PBC: A Partially Buffered Crossbar Packet Switch

The crossbar fabric is widely used as the interconnect of high-performance packet switches due to its low cost and scalability. There are two main variants of the crossbar fabric: unbuffered and internally buffered. On one hand, unbuffered crossbar fabric switches exhibit the advantage of using no internal buffers. However, they require a complex scheduler to solve input and output ports contention. Internally, buffered crossbar fabric switches, on the other hand, overcome the scheduling complexity by means of distributed schedulers. However, they require expensive internal buffers-one per crosspoint. In this paper, we propose a novel architecture, namely, the partially buffered crossbar (PBC) switching architecture, where a small number of separate internal buffers are maintained per output. Our goal is to design a PBC switch having the performance of buffered crossbars and a cost comparable to that of unbuffered crossbars. We propose a class of round robin scheduling algorithms for the PBC architecture. Simulations results show that using as few as eight buffers per fabric column and irrespective of the number N of input ports of the switch, we can achieve similar performance to buffered crossbars that use N buffers per fabric output.
Recalcitrant Beh Errybark Oak Seed: an Ft-ir Study of Desiccation Sensitivity in Quercus Pagoda Raf. Acorns

The recalcitrant behavior of cherrybark oak (Quercus pagoda Raf.) acorns was examined in terms of effects of moisture content on seed storage longevity and (short term) seed germination. Seed samples collected over two consecutive years were fully hydrated, then subjected to drying under ambient conditions of temperature and relative humidity on the lab bench and sampled regularly for moisture determination (gravimetric analysis) and germination (greenhouse conditions). Fourier transform infrared spectroscopy (FT-IR) was used to follow changes in macromolecular structure as moisture and viability were lost. Transmission spectra were collected on dry and rehydrated samples of separate embryonic axis and cotyledon tissue. Long-term storage longevity was highly dependent on initial acorn moisture content. Germination was also highly dependent on short-term moisture content, and severely declined when seed moisture dropped below 17% (fresh weight basis). FT-IR analyses revealed significant differences in moisture and lipid profiles between embryonic axis and cotyledon tissue during short term drying. A strong absorbance near Ii’40 cm-t in cotyledon tissue indicated a high concentration of ester carbonyl groups (storage lipids). Membrane lipid structure exhibited reversible shifts between gel and liquid crystalline phases upon drying and rehydration in both axes and cotyledons (peak frequency and bandwidth near 2850 cm-t); however, reversibility declined as viability was lost. Irreversible changes in protein secondary structure, illustrated by shifts in the amide absorbance near 1650 cm-r, were the most sensitive indicators of viability loss.