tbuckley/cabot-search huggingface dataset:
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.
Authors: Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold
Journal: Genome biology (2006)

Abstract We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.
The Acute Respiratory Distress Syndrome: Pathogenesis and Treatment
Authors: Michael A. Matthay, Rachel L. Zemans
Journal: Annual Review of Pathology Mechanisms of Disease (2011)

The acute respiratory distress syndrome (ARDS) causes 40% mortality in approximately 200,000 critically ill patients annually in the United States. ARDS is caused by protein-rich pulmonary edema that causes severe hypoxemia and impaired carbon dioxide excretion. The clinical disorders associated with the development of ARDS include sepsis, pneumonia, aspiration of gastric contents, and major trauma. The lung injury is caused primarily by neutrophil-dependent and platelet-dependent damage to the endothelial and epithelial barriers of the lung. Resolution is delayed because of injury to the lung epithelial barrier, which prevents removal of alveolar edema fluid and deprives the lung of adequate quantities of surfactant. Lymphocytes may play a role in resolution of lung injury. Mortality has been markedly reduced with a lung-protective ventilatory strategy. However, there is no effective pharmacologic therapy, although cell-based therapy and other therapies currently being tested in clinical trials may provide novel treatments for ARDS.
Anion manipulation: a new antiarrhythmic approach. Action of substitution of chloride with nitrate on ischemia- and reperfusion-induced ventricular fibrillation and contractile function.
Authors: P D Ridley, M J Curtis
Journal: Circulation Research (1992)

The role of anions in the initiation of ischemia- and reperfusion-induced arrhythmias is unknown. We examined the antiarrhythmic effects of isotonic substitution of extracellular Cl- with NO3- by using the rat Langendorff preparation (n = 12 per group). During 30 minutes of regional ischemia, the incidence of ventricular fibrillation (VF) was reduced from 50% in hearts perfused with control solution (containing a Cl-:NO3- ratio of 100:0) to 25%, 0% (p less than 0.05), 0% (p less than 0.05), and 0% (p less than 0.05) by perfusion with solution containing Cl-:NO3- ratios of 75:25, 50:50, 25:75, and 0:100, respectively. The incidence of reperfusion-induced VF was also reduced from 58% to 25%, 8% (p less than 0.05), 8% (p less than 0.05), and 0% (p less than 0.05), respectively. Similar effects were produced in hearts reperfused after briefer durations of ischemia (10 or 15 minutes). Substitution of NO3- for Cl- also facilitated spontaneous termination of VF. Heart rate and occluded zone size were not affected by anion manipulation. Coronary flow was affected by NO3-, but changes did not correlate with arrhythmias. During ischemia, electrocardiographic changes indicative of class III activity (widening of the ventricular complex) were produced by anion substitution. These changes occurred selectively in the ischemic tissue with no significant influence before ischemia onset. However, the relation between this effect and arrhythmia reduction was not linear and a cause-effect relation is therefore unlikely. In separate groups of hearts (n = 12 per group), switching from 100:0 to 0:100 Cl-:NO3- solution or vice versa 10 seconds after coronary occlusion or just before reperfusion demonstrated that 1) protection against ischemia-induced VF resulted partly from an action in the ischemic zone and partly from an action in the nonischemic zone, and 2) protection against reperfusion-induced VF resulted principally from an action occurring during reperfusion and within the reperfused tissue. To assess whether benefit was offset by deleterious effects on contractile function in nonischemic tissue, we constructed Starling curves in isolated rate hearts. The 0:100 Cl-:NO3- solution had no effect on compliance or contractility at physiological end-diastolic pressures but reduced the slope of the peak systolic pressure-volume relation by approximately 20% as end-diastolic pressure was increased above 10 mm Hg. In conclusion, anions appear to play a hitherto unrecognized role in arrhythmogenesis in ischemia and reperfusion. Manipulation of anion homeostasis may represent a novel target for antiarrhythmic drug development.
In Vivo Correction of COX Deficiency by Activation of the AMPK/PGC-1α Axis
Authors: Carlo Viscomi, Emanuela Bottani, Gabriele Civiletto, Raffaele Cerutti, Maurizio Moggio, Gigliola Fagiolari, Eric A. Schon, Costanza Lamperti, Massimo Zeviani
Journal: Cell Metabolism (2011)

Increased mitochondrial biogenesis by activation of PPAR- or AMPK/PGC-1α-dependent homeostatic pathways has been proposed as a treatment for mitochondrial disease. We tested this hypothesis on three recombinant mouse models characterized by defective cytochrome c-oxidase (COX) activity: a knockout (KO) mouse for Surf1, a knockout/knockin mouse for Sco2, and a muscle-restricted KO mouse for Cox15. First, we demonstrated that double-recombinant animals overexpressing PGC-1α in skeletal muscle on a Surf1 KO background showed robust induction of mitochondrial biogenesis and increase of mitochondrial respiratory chain activities, including COX. No such effect was obtained by treating both Surf1(-/-) and Cox15(-/-) mice with the pan-PPAR agonist bezafibrate, which instead showed adverse effects in either model. Contrariwise, treatment with the AMPK agonist AICAR led to partial correction of COX deficiency in all three models, and, importantly, significant motor improvement up to normal in the Sco2(KO/KI) mouse. These results open new perspectives for therapy of mitochondrial disease.
Traffic related pollution and heart rate variability in a panel of elderly subjects
Authors: J Schwartz
Journal: Thorax (2005)

<b>Background:</b> Particulate air pollution has been associated with increased cardiovascular deaths and hospital admissions. To help understand the mechanisms, the types of particles most involved, and the types of persons most susceptible, the association between exposure to summertime air pollution and heart rate variability (HRV) was examined in a panel study of 28 elderly subjects. <b>Methods:</b> Subjects were seen once a week for up to 12 weeks and HRV (SDNN, r-MSSD, PNN<sub>50</sub>, low frequency/high frequency ratio (LFHFR)) was measured for approximately 30 minutes at each session using a defined protocol. Temperature, day of the week, and hour of the day were controlled, and dummy variables for each subject were controlled for subject specific risk factors. <b>Results:</b> PM<sub>2.5</sub> was associated with r-MSSD (−10.1% change for an interquartile range (IQR) increase in exposure (95% CI −2.8 to −16.9)) and PNN<sub>50</sub>, but stronger associations were seen with black carbon, an indicator of traffic particles, which was also associated with SDNN (−4.6% per IQR (95% CI −2.0 to −7.2)) and LFHFR. Secondary particles were more weakly associated with r-MSSD, as was ozone. No associations were seen with SO<sub>2</sub> or NO<sub>2</sub>. CO had similar patterns of association to black carbon, which disappeared after controlling for black carbon. Black carbon had a substantially higher effect on SDNN in subjects who had had a previous myocardial infarction (−12.7%, 95% CI −5.7 to −19.25). <b>Conclusions:</b> Particles, especially from traffic, are associated with disturbances of autonomic control of the heart.
Relations among questionnaire and laboratory measures of rhinovirus infection
Authors: B. Barrett
Journal: European Respiratory Journal (2006)

Due to high incidence and quality-of-life impact, upper respiratory infection substantially impacts on population health. To test or compare treatment effectiveness, a well-designed and validated illness-specific quality-of-life instrument is needed. Data reported in the current study were obtained from a trial testing echinacea for induced rhinovirus infection. Laboratory-assessed biomarkers included interleukin (IL)-8, nasal neutrophil count (polymorphonuclear neutrophils (PMN)), mucus weight, viral titre and seroconversion. The questionnaires used included the general health short form (SF)-8 (24-h recall version), the eight-item Jackson cold scale, and the 44-item Wisconsin Upper Respiratory Symptom Survey (WURSS). In total, 399 participants were inoculated with rhinovirus and monitored over 2,088 person-days. Statistically significant associations were found among nearly all variables. Between-questionnaire correlations were: WURSS–Jackson = 0.81; WURSS–SF-8 = 0.62; and Jackson–SF-8 = 0.60. Correlations with laboratory values were as follows: WURSS–mucus weight = 0.53; Jackson–mucus weight = 0.55; WURSS–viral titre = 0.37; Jackson–viral titre = 0.46; WURSS–IL-8 = 0.31; Jackson–IL-8 = 0.36; WURSS–PMN = 0.31; and Jackson–PMN = 0.28. Neither WURSS nor Jackson yielded satisfactory cut-off scores for diagnosis of infection. Symptomatic and biological outcomes of upper respiratory infection are highly variable, with only modest associations. While Wisconsin Upper Respiratory Symptom Survey and Jackson questionnaires both correlate with biomarkers, neither is a good predictor of induced infection. The inclusion of functional and quality-of-life items in the Wisconsin Upper Respiratory Symptom Survey does not significantly decrease the strength of association with laboratory-assessed biomarkers.
Quantitative assessment of WT1 expression by real time quantitative PCR may be a useful tool for monitoring minimal residual disease in acute leukemia patients
Authors: D Cilloni, E Gottardi, D De Micheli, A Serra, G Volpe, F Messa, G Rege-Cambrin, A Guerrasio, M Divona, F Lo Coco, G Saglio
Journal: Leukemia (2002)
Differentiation-Inducing Factor-1, a Morphogen of <i>Dictyostelium</i> , Induces G <sub>1</sub> Arrest and Differentiation of Vascular Smooth Muscle Cells
Authors: Yoshikazu Miwa, Toshiyuki Sasaguri, Chiya Kosaka, Yoji Taba, Akio Ishida, Takeo Abumiya, Yuzuru Kubohara
Journal: Circulation Research (2000)

Abstract —Differentiation-inducing factor-1 (DIF-1) is a morphogen that induces differentiation of Dictyostelium . Recently, DIF-1 has been shown to inhibit proliferation and induce differentiation in tumor cells, although the underlying mechanisms remain unknown. In this study, we examined the effects of DIF-1 on the proliferation and differentiation of vascular smooth muscle cells, to explore novel therapeutic strategies for atherosclerosis. DIF-1 nearly completely inhibited DNA synthesis and cell division in mitogen-stimulated cells. DIF-1 inhibited the phosphorylation of the retinoblastoma protein and the activities of cyclin-dependent kinase (Cdk) 4, Cdk6, and Cdk2, which phosphorylate the retinoblastoma protein. DIF-1 strongly suppressed the expression of cyclins D1, D2, and D3, as well as those of cyclins E and A, which normally began after that of the D-type cyclins. The mRNAs for the smooth muscle myosin heavy chains SM1 and SM2 were expressed in quiescent cells in primary culture, and these expression levels decreased after mitogenic stimulation. In the presence of DIF-1, the rate of the reduction was significantly decelerated. Moreover, the addition of DIF-1 to dedifferentiated cells induced the expressions of SM1 and SM2, accompanied by a reduction in the level of SMemb, a nonmuscle-type myosin heavy chain. Therefore, DIF-1 seemed to interrupt a very early stage of G 1 probably by suppressing the expressions of the D-type cyclins. Furthermore, this compound may prevent phenotypic modulation and induce differentiation of vascular smooth muscle cells.
Improved Vascular Endothelial Function After Oral B Vitamins
Authors: John C. Chambers, Per M. Ueland, Omar A. Obeid, Jane Wrigley, Helga Refsum, Jaspal S. Kooner
Journal: Circulation (2000)

Background —Hyperhomocysteinemia is an independent risk factor for coronary heart disease (CHD). Dietary supplementation with B vitamins lowers plasma homocysteine by up to 30%. However, little is known about the potential beneficial effects of homocysteine lowering on vascular function in patients with CHD. Methods and Results —We investigated 89 men with CHD (aged 56 [range 39 to 67] years). Brachial artery flow–mediated dilatation (endothelium dependent) and nitroglycerin-induced dilatation (endothelium independent) were measured before and 8 weeks after treatment with either (1) folic acid (5 mg) and vitamin B 12 (1 mg) daily (n=59) or (2) placebo (n=30). Total, protein-bound, and free plasma homocysteine, serum folate, and vitamin B 12 were measured at baseline and at 8 weeks. Flow-mediated dilatation improved after treatment with B vitamins (2.5±3.2% to 4.0±3.7%, P =0.002) but not placebo (2.3±2.6% to 1.9±2.6%, P =0.5). Vitamin therapy lowered plasma concentrations of total homocysteine (from 13.0±3.4 to 9.3±1.9 μmol/L, P &lt;0.001), protein-bound homocysteine (from 8.7±2.8 to 6.2±1.4 μmol/L, P &lt;0.001), and free homocysteine (from 4.3±1.2 to 3.0±0.6 μmol/L, P &lt;0.001) and raised concentrations of serum folate (from 10.3±4.3 to 31.2±10.8 ng/mL, P &lt;0.001) and vitamin B 12 (from 314±102 to 661±297 pg/mL, P &lt;0.001). In regression analysis, improved flow-mediated dilatation correlated closely with the reduction in free plasma homocysteine ( r =−0.26, P =0.001), independent of changes in protein-bound homocysteine, folate, and vitamin B 12 . Nitroglycerin-induced dilatation was unchanged after both B vitamins and placebo. Conclusions —Folic acid and vitamin B 12 supplementation improves vascular endothelial function in patients with CHD, and this effect is likely to be mediated through reduced concentrations of free plasma homocysteine concentrations. Our data support the view that lowering homocysteine, through B vitamin supplementation, may reduce cardiovascular risk.
Evaluation of Talking Parents, Healthy Teens, a new worksite based parenting programme to promote parent-adolescent communication about sexual health: randomised controlled trial
Authors: M. A Schuster, R. Corona, M. N Elliott, D. E Kanouse, K. L Eastman, A. J Zhou, D. J Klein
Journal: BMJ (2008)

To evaluate a worksite based parenting programme-Talking Parents, Healthy Teens-designed to help parents learn to address sexual health with their adolescent children.Randomised controlled trial (April 2002-December 2005).13 worksites in southern California.569 parents completed baseline surveys at work, gave permission for confidential surveys to be posted to their adolescent children, and were randomised to intervention or control groups. Parents and adolescents completed follow-up surveys at one week, three months, and nine months after the programme.Talking Parents, Healthy Teens consists of eight weekly one hour sessions at worksites for parents of adolescent children in 6th-10th grade (about ages 11-16 years).Parent-adolescent communication about a list of sexual topics; whether parent taught adolescent how to use a condom; ability to communicate with parent/adolescent about sex; openness of parent-adolescent communication about sex.Differences between intervention and control groups were significant for the mean number of new sexual topics that parents and adolescents reported discussing between baseline and each follow-up (P<0.001 for each); intervention parents were less likely than controls to discuss no new topics (8% v 29%, 95% confidence interval for difference 16% to 24%) and more likely to discuss seven or more new topics (38% v 8%, 19% to 41%) at nine months. Some differences increased after completion of the programme: at one week after the programme, 18% of adolescents in the intervention group and 3% in the control group (6% to 30%) said that their parents had reviewed how to use a condom since baseline (P<0.001); this grew to 29% v 5% (13% to 36%) at nine months (P<0.001). Compared with controls at nine months, parents and adolescents in the intervention group reported greater ability to communicate with each other about sex (P<0.001) and more openness in communication about sex (P<0.001).A worksite based programme can have substantial effects on communication between parents and adolescents about sexual health.Clinical Trials NCT00465010.
THE SURFACE COMPOSITION OF THE TUBERCLE BACILLUS AND OTHER ACID-FAST BACTERIA
Authors: Stuart Mudd, Emily B. H. Mudd
Journal: The Journal of Experimental Medicine (1927)

Acid-fast bacteria in the boundary surface between salt solution and a test oil (tricaprylin) are spontaneously wet and enveloped by the oil. This behavior contrasts with that of all other cells studied by the interfacial tension method. Four strains of human tubercle bacillus and an atypical bovine strain are an exception to the first statement above. These have possessed stability in the saline-oil interface; this stability is slight, however, and not comparable with that of non-acid-fast bacteria. Acid-fast bacteria subjected to prolonged extraction with alcohol show resistance to wetting by oil comparable to that of non-acid-fast bacteria. These "defatted" bacteria nevertheless retain their acid-fast staining properties. Acid fastness cannot then depend on the integrity of a surface membrane. Study of the cataphoresis of acid-fast bacteria by Freund has rendered the presence of protein in the surface highly probable. We are forced then to regard the surface of acid-fast bacteria as complex, containing at least lipoid and protein. Not improbably also carbohydrate is present.
Randomized, prospective trial of noninvasive positive pressure ventilation in acute respiratory failure.
Authors: N Kramer, T J Meyer, J Meharg, R D Cece, N S Hill
Journal: American Journal of Respiratory and Critical Care Medicine (1995)

Recent studies suggest that noninvasive positive pressure ventilation (NPPV) administered by nasal or oronasal mask avoids the need for endotracheal intubation, rapidly improves vital signs, gas exchange, and sense of dyspnea, and may reduce mortality in selected patients with acute respiratory failure, but few controlled trials have been done. The present study used a randomized prospective design to evaluate the possible benefits of NPPV plus standard therapy versus standard therapy alone in patients with acute respiratory failure. Patients to receive NPPV were comfortably fitted with a standard nasal mask connected to a BiPAP ventilatory assist device (Respironics, Inc., Murrysville, PA) in the patient flow-triggered/time-triggered (S/T) mode, and standard therapy consisted of all other treatments deemed necessary by the primary physician, including endotracheal intubation. The need for intubation was reduced from 73% in the standard therapy group (11 of 15 patients) to 31% in the NPPV group (5 of 16 patients, p < 0.05). Among chronic obstructive pulmonary disease (COPD) patients, the reduction was even more striking, with 8 of 12 (67%) control patients requiring intubation compared with 1 of 11 (9%) NPPV patients (p < 0.05). Heart and respiratory rates were significantly lower in the NPPV group than in control patients within 1 h, and PaO2 was significantly improved in the NPPV group for the first 6 h. Dyspnea scores and maximal inspiratory pressures were better in the NPPV than in control patients at 6 h, and nurses and therapists spent similar amounts of time at the bedside for both groups.(ABSTRACT TRUNCATED AT 250 WORDS)
Dissembled DJ-1 high molecular weight complex in cortex mitochondria from Parkinson's disease patients
Authors: Hikmet Nural, Ping He, Thomas Beach, Lucia Sue, Weiming Xia, Yong Shen
Journal: Molecular Neurodegeneration (2009)

Abstract The PARK7 gene encodes a protein, DJ-1, with several functions such as protection of cells from oxidative stress, sperm maturation and fertilization, and chaperone activity. Mutations in the PARK7 gene are associated with autosomal recessive early-onset Parkinson's disease (PD). DJ-1 has been reported to be expressed in multiple cells in the central nerve system. Here, by using both native and denatured Western blots, we examined levels of total DJ-1 and high molecular weight complexes of DJ-1 (HMW) in both the substantia nigra and cortex from rapidly autopsied 18 PD and 9 non-pathological control (NPC) brains. We have discovered that the level of total DJ-1 protein is significantly reduced in the substantia nigra in brains of sporadic PD patients. Moreover, in the PD cortex mitochondria fraction, the HMW DJ-1 complex is significantly lower than in the NPC. These results suggest abnormal DJ-1 expression levels and DJ-1 complex changes may contribute to PD pathogenesis.
Analysis of 1p, 19q, 9p, and 10q as prognostic markers for high-grade astrocytomas using fluorescence in situ hybridization on tissue microarrays from Radiation Therapy Oncology Group trials
Authors: Daniel J Brat, Wendy F Seiferheld, Arie Perry, Elizabeth H Hammond, Kevin J Murray, Alan R Schulsinger, Minesh P Mehta, Walter J Curran
Journal: Neuro-Oncology (2004)

Survival periods vary considerably for patients with high-grade astrocytomas, and reliable prognostic markers are not currently available. We therefore investigated whether genetic losses from chromosomes 1p, 19q, 9p, or 10q were associated with survival in 89 high-grade astrocytomas using tissue microarrays (TMAs) derived from Radiation Therapy Oncology Group clinical trials. Cases included 15 anaplastic astrocytomas (AAs) and 74 glioblastomas (GBMs) selected on the basis of survival times significantly shorter or longer than the expected median. Genetic analysis was performed by TMA-fluorescence in situ hybridization (FISH) on array sections using 8 DNA probes, including those directed at 1p32, 19q13.4, 9p21 (p16/CDKN2A), and 10q (PTEN and DMBT1). Genetic status for each locus was correlated with patient survival group, and data were analyzed by using Fisher's exact test of association (adjusted P = 0.025). Losses of chromosome 1p, either alone or in combination with 19q, were encountered in only 2 cases, both AAs. This contrasts with oligodendrogliomas, in which combined 1p and 19q losses are frequent and predictive of prolonged survival. Solitary 19q loss was noted in 3/15 AAs and in 7/70 GBMs and was more frequent in the long-term survival group (P = 0.041, AA and GBM combined). Chromosome 9p loss was seen in 5/8 AAs and 39/57 GBMs, whereas chromosome 10q loss was detected in 4/15 AAs and 48/68 GBMs. The 9p and 10q deletions were slightly more frequent in short-term survivors, though none of the comparisons achieved statistical significance. Long-term and short-term survival groups of high-grade astrocytomas appear to have dissimilar frequencies of 19q, 9p, and 10q deletions. TMA-FISH is a rapid and efficient way of evaluating genetic alterations in such tumors.