tbuckley/cabot-search huggingface dataset:
Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae
Authors: Mathieu Piednoël, Andre J. Aberer, Gerald M. Schneeweiss, Jiri Macas, Petr Novak, Heidrun Gundlach, Eva M. Temsch, Susanne S. Renner
Journal: Molecular Biology and Evolution (2012)

We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%-28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%-22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types.
Conflicts in the Life of Thomas Jefferson
Authors: CARL BINGER
Journal: American Journal of Psychiatry (1969)

Thomas Jefferson achieved what the author considers an extraordinary mastery of his life, which was, however, not devoid of conflicts. Dr. Binger describes Jefferson's inner struggle relating to the separation of the colonies from Britain, his depressive withdrawal when his wife was seriously ill and their infant son died, his unhappiness and indignation following his censure by the Virginia legislature for failure to call out the militia during a period of emergency, and his and Alexander Hamilton's mutual hostility.
Eccentric and concentric isokinetic knee flexion and extension: a reliability study using the Cybex 6000 dynamometer.
Authors: R C Li, Y Wu, N Maffulli, K M Chan, J L Chan
Journal: British Journal of Sports Medicine (1996)

To determine the reliability of the Cybex 6000 isokinetic dynamometer in measuring the knee muscle performance concentrically and eccentrically.18 male and 12 female subjects with no previous knee injuries, who had not previously undergone any isokinetic testing, were studied. The flexor and extensor muscles groups of both knees were tested at 60 degrees s-1 and 120 degrees s-1 with the continuous concentric-eccentric cycle testing protocol. Variables studied included peak torque, total work, and average power. The interclass correlation coefficient (ICC 2,1) was used to determine the reliability with P < 0.05.Peak torque showed significantly greater ICC than the total work and average power, with test-retest reliability ranging from 0.82 to 0.91 for peak torque, from 0.76 to 0.89 for total work, and 0.71 to 0.88 for average power. Average variability for the three variables studied ranged from 9% to 14%. The ICCs for the three variables studied were significantly greater at 120 degrees s-1. The knee extensor muscle group showed greater test-retest reliability, and the results of isokinetic testing in the concentric contraction mode were more reproducible.The Cybex 6000 isokinetic dynamometer shows high reliability in measuring isokinetic concentric and eccentric variables. Some fluctuation should be allowed when evaluating variations of muscle performance between tests.
Serum Sex Steroids Depict a Nonlinear U-Shaped Association with High-Risk Prostate Cancer at Radical Prostatectomy
Authors: Andrea Salonia, Firas Abdollah, Umberto Capitanio, Nazareno Suardi, Alberto Briganti, Andrea Gallina, Renzo Colombo, Matteo Ferrari, Giulia Castagna, Patrizio Rigatti, Francesco Montorsi
Journal: Clinical Cancer Research (2012)

To assess the association between preoperative serum total testosterone (tT), 17β-estradiol (E(2)), sex hormone-binding globulin (SHBG), and tT-E(2) ratio values with high-risk prostate cancer (as defined by the National Comprehensive Cancer Network practice guidelines) at radical prostatectomy.Serum E(2), tT, and SHBG were dosed the day before surgery (7:00-11:00 am) in a cohort of 724 candidates to radical prostatectomy. Restricted cubic spline functions tested the association between predictors (i.e., model 1: age, body mass index, and serum tT, E(2), and SHBG levels; model 2: tT-E(2) values instead of tT and E(2) levels) and high-risk prostate cancer.Low-, intermediate-, or high-risk prostate cancer was found in 251 (34.7%), 318 (43.9%), and 155 (21.4%) patients, respectively. Patients in the high-risk class showed the lowest tT, E(2), and tT-E(2) ratio values (all P ≤ 0.02). At univariate analysis, only age, tT, E(2), and tT-E(2) ratio values were significantly associated with high-risk prostate cancer (all P ≤ 0.006). At multivariate analyses considering model 1 variables, age (P = 0.03), serum tT (all P < 0.001), and E(2) (all P ≤ 0.01) were associated with high-risk prostate cancer; only tT-E(2) ratios achieved independent predictor status for high-risk prostate cancer (all P < 0.001) when considering model 2. Both the lowest and the highest tT, E(2), and tT-E(2) values depicted a nonlinear U-shaped significant association with high-risk prostate cancer.These data showed that preoperative serum sex steroids are independent predictors of high-risk prostate cancer, depicting a nonlinear U-shaped association.
Information of Imminent Death or Not: Does It Make a Difference?
Authors: Gunilla Lundquist, Birgit H. Rasmussen, Bertil Axelsson
Journal: Journal of Clinical Oncology (2011)

This study examines whether end-of-life care for patients with cancer who were informed about imminent death differs from care for those patients with cancer who were not informed.This study included all cancer deaths between 2006 and 2008 for which the patient did not lose his or her decision-making capacities until hours or days before death (N=13,818). These patients were taken from a national quality register for end-of-life care. The majority of the patients-91% (n=12,609) -had been given information about imminent death; 9% (n=1,209) had not been informed. Because of the difference in sample size, a matching procedure was performed to minimize bias. This resulted in a comparison of 1,191 informed and 1,191 uniformed patients. Nonparametric methods were used for statistical analyses.Informed patients significantly more often had parenteral drugs prescribed as needed (ie, PRN), had his or her family informed, died in his or her preferred place, and had family who were offered bereavement support. There was no difference in symptom control (ie, pain, anxiety, confusion, nausea, and respiratory tract secretions) between the groups.Providing information of imminent death to a patient with cancer at the end of life does not seem to increase pain or anxiety, but it does seem to be associated with improved care and to increase the likelihood of fulfilling the principles of a good death.
FDA To Regulate Direct-to-Consumer Genetic Tests
Authors: V. Brower
Journal: JNCI Journal of the National Cancer Institute (2010)

began, genetic tests were available for about 100 diseases — most of them caused by just one faulty gene, such as the mutations that cause Tay-Sachs and cystic fi brosis. As genomic technologies matured and sequencing became less costly, companies began developing tests for a wider range of complex, multigenic, common diseases. These were initially offered by laboratories used by physicians, but more recently dozens of companies have begun marketing such tests on a DTC basis. The fi rst advertising campaign for a genetic test, Myriad Genetics’ BRACAnalysis, took place in the early 2000s. It included television ads for the test, which detects mutations in the BRCA1 and BRCA2 genes that raise the risk of breast and ovarian cancers. Myriad also advertised in the playbill of the Broadway play, Wit , which was about a professor dying of ovarian cancer.
Massive haemoptysis complicating exogenous lipid pneumonia
Authors: M Haro, I Murcia, A Nunez, E Julia, J Valer
Journal: European Respiratory Journal (1998)

Exogenous lipid pneumonia is an uncommon condition resulting from the aspiration or inhalation of fat or oil material. The prognosis in this entity is usually good and complications are rare. We report an unusual case of chronic lipid pneumonia complicated with massive haemoptysis who responded to steroid therapy after arterial embolization.
Opioids modulate the cholinergic contraction but not the nonadrenergic relaxation in guinea-pig airways in vitro
Authors: JL Pype, LJ Dupont, MG Demedts, GM Verleden
Journal: European Respiratory Journal (1996)

(D-ALa2, NMePhe4, Gly-ol5) encephalin (DAMGO), a selective mu-opioid receptor agonist, has previously been demonstrated to inhibit the cholinergic and the noncholinergic contraction in guinea-pig airways. In contrast, opioids had no inhibitory effect on cholinergic neurotransmission in the upper trachea when stimulated at 8 Hz. We investigated whether DAMGO, a selective mu-opioid receptor agonist, [D-Pen 2,5] encephalin (DPDPE), a selective delta-opioid receptor agonist, and U-69593, a selective kappa-opioid receptor agonist could modulate the cholinergic contraction in the upper trachea at different frequencies of stimulation. Moreover, we have investigated whether DAMGO, DPDPE and U-69593 could also modulate the iNANC relaxation. DAMGO (1-100 microM) inhibited the cholinergic contraction in the upper trachea with a maximum inhibition of 57+/-15% at 1 Hz (n=4; p&lt;0.05). On the other hand, DPDPE (10 microM) and U69593 (10 microM) did not produce any significant inhibition of the cholinergic contraction. Naloxone, an opioid receptor antagonist (100 microM), was able to antagonize the inhibitory effect of DAMGO (n=5; p&lt;0.01) on the cholinergic contraction at a frequency of 2 Hz. DAMGO (10 microM) did not displace the cumulative concentration-response relationship to acetylcholine (10 nM-10 mM), (n=4; NS). This provides evidence that prejunctional mu-opioid receptors (and not delta-opioid or kappa-opioid receptors) modulate cholinergic contraction in the upper trachea. In contrast, DAMGO (10 microM) had no significant inhibitory effect on the nonadrenergic relaxation (n=4; NS) in the upper trachea. Neither DPDPE nor U-69593 had any effect on the nonadrenergic relaxation. These findings suggest that DAMGO directly inhibits the cholinergic contraction and that the opioid receptor involved in the inhibition of the cholinergic contraction in the upper trachea is of the mu-opioid type. The finding that opioids inhibit cholinergic contraction without altering NANC relaxations suggests that distinct populations of nerves mediate these two effects.
A back-to-back comparison of white light video endoscopy with autofluorescence endoscopy for adenoma detection in high-risk subjects
Authors: D. Ramsoekh, J. Haringsma, J. W. Poley, P. van Putten, H. van Dekken, E. W. Steyerberg, M. E. van Leerdam, E. J. Kuipers
Journal: Gut (2010)

<h3>Objective</h3> To compare the sensitivity of autofluorescence endoscopy (AFE) and white light video endoscopy (WLE) for the detection of colorectal adenomas in high-risk patients belonging to Lynch syndrome (LS) or familial colorectal cancer (CRC) families. <h3>Methods</h3> This was a prospective single-centre study carried out in a tertiary referral centre. The subjects were 75 asymptomatic patients originating from LS or familial CRC families. Patients were examined with either WLE followed by AFE or AFE followed by WLE. Back-to-back colonoscopy was performed by two blinded endoscopists. All lesions were removed during the second endoscopic procedure. Lesions missed during the second procedure were identified and removed on third pass. The sensitivity calculations for colorectal adenomas were based on histology results. The main outcome measures were the difference in sensitivity between WLE and AFE for the detection of adenomas in patients with LS or familial CRC. <h3>Results</h3> At least one adenoma was detected in 41 (55%) patients. WLE identified adenomas in 28/41 patients and AFE in 37/41 patients, corresponding to a 32% increase. In total 95 adenomas were detected, 65 by WLE and 87 by AFE, resulting in a significantly higher sensitivity of AFE compared with WLE (92% vs 68%; p=0.001). The additionally detected adenomas with AFE were significantly smaller than the adenomas detected by WLE (mean 3.0 mm vs 4.9 mm, p&lt;0.01). <h3>Conclusions</h3> AFE improves the detection of colorectal adenomas in patients with LS or familial CRC. The results of this study suggest that AFE may be preferable for surveillance of these high-risk patients.
Teratoma of Testis
Authors: J. E. Schofield
Journal: BMJ (1947)

JURNAL411as a diagnosis in any case where chronic infiltration of the lung fails to respond to treatment.The pathology is that of a chronic response to irritation and is produced by animal or mineral cils.In the former case hydrolysis of the oil to fatty acids leads to more rapid development of fibrosis than in the latter.Similar appearances may be seen in the lymph nodes of this condition and of sprue, and it is suggested that they may be of similar origin.I have to thank Dr. W. Lindsay Locke for the radiographs,
Baby food industry lobbies WHO on breast feeding advice
Authors: G. Yamey
Journal: BMJ (2000)

In the existing WHO guidelines, complementary feeding at 4-6 months is advocated. However, many nutrition specialists believe that these guidelines lead to complementary foods being offered from the age of 3 months, or even earlier, subsequently suggesting that the WHO should change its recommendations to about 6 months. To this effect, the International Association of Infant Food Manufacturers lobbied the WHO to delay any change to its recommendations on the optimal length of exclusive breast-feeding. Their message states that any action dealing with Infant and Young Child Nutrition should be delayed until the World Health Assembly 2002. Supporting facts to justify the message argue the importance of an international study on infant growth being carried out by the WHO, which should be finished by 2002. Nevertheless, several nutrition specialists believe that the scientific evidence to support a change in the WHO policy already exists and that such a study was not set up to determine the optimal length of exclusive breast-feeding.
The utility of cardiac magnetic resonance imaging in the diagnosis of cardiac sarcoidosis
Authors: Kelly Stanton, Madhusudan Ganigara, Tamera Corte, Paul Torzillo, David Celermajer, Peter Corte, Raj Puranik
Journal: European Respiratory Journal (2014)

Autopsy reports suggest that cardiac sarcoidosis (CS) occurs in up to 30% of patients with pulmonary sarcoidosis yet the clinical diagnosis is made in only 5% of cases. Current diagnostic algorithms lack sensitivity and specificity. Cardiac MRI (CMR) provides a unique opportunity to diagnose myocardial inflammation/scar.   Aim:  To determine the prevalence and clinical significance of Late Gadolinium Enhancement (LGE) detected on CMR at 1.5T in patients with biopsy proven sarcoidosis.   Methods:  Consecutive patients referred for CMR to evaluate for CS were retrospectively reviewed. Review of medical records, ECGs, echocardiograms, myocardial scintigraphy and PET scans was conducted and correlated with CMR findings. Comparison was made to the Japanese Ministry of Health (JMH) diagnostic criteria.   Results:  34 patients (51+/-10 years; 17 Male) were reviewed. A mid-wall pattern of LGE, consistent with LV inflammation/scar, was detected in 8 patients (24%). Of those with LGE, 88% had a hyper-intense myocardial signal on T2 imaging indicating active inflammation. Only 1 of the 9 LGE positive patients met the JMH diagnostic criteria.  LGE was associated with the presence of clinically significant arrhythmia (p=0.04); however, there was a non significant association between LGE and LV dysfunction (EF≤55%; p=0.07). There was no association with pulmonary stage and LGE on CMR (p=0.21).   Conclusion:  LGE identified on CMR in patients with sarcoidosis was associated with clinically significant arrhythmias and may represent a more sensitive diagnostic tool for CS. As cardiac manifestations of sarcoidosis have important prognostic implications, further prospective evaluation of CMR is warranted.
Results of the ATAC (Arimidex, Tamoxifen, Alone or in Combination) trial after completion of 5 years' adjuvant treatment for breast cancer
Authors: A Howell, J Cuzick, M Baum, A Buzdar, M Dowsett, J F Forbes, G Hoctin-Boes, J Houghton, G Y Locker, J S Tobias
Journal: The Lancet (2005)
A new era in idiopathic pulmonary fibrosis: considerations for future clinical trials
Authors: Harold R. Collard, Williamson Z. Bradford, Vincent Cottin, Kevin R. Flaherty, Talmadge E. King, Gary G. Koch, Martin Kolb, Fernando J. Martinez, Bruce Montgomery, Ganesh Raghu, Luca Richeldi, Dan Rose, Athol U. Wells, Kevin K. Brown
Journal: European Respiratory Journal (2015)

The past decade has seen substantial progress in understanding the pathobiology, natural history, and clinical significance of idiopathic pulmonary fibrosis (IPF), culminating in the establishment of two effective medical therapies. Now seems an important time to reconsider the design and conduct of future IPF clinical trials. Building on lessons learned over the past decade, we use this perspective to lay out four key considerations for moving forward effectively and efficiently with the next generation of clinical trials in IPF. These are: development of a coordinated IPF clinical trials network; establishment of expectations for early phase proof of concept studies; adaptation of late-phase efficacy trial designs to the emergence of approved therapies, and; agreement on primary end-points for late phase clinical trials. Continued progress in the field of IPF will require creativity and collaboration on the part of all stakeholders. We believe that addressing these four considerations will encourage and enable investment in this new era of drug development in IPF, and will lead to more rapid development of effective therapies.
Response to Letter Regarding Article, “Attained Educational Level and Incident Atherothrombotic Events in Low- and Middle-Income Compared With High-Income Countries”
Authors: Abhinav Goyal, Deepak L. Bhatt, P. Gabriel Steg, Bernard J. Gersh, Mark J. Alberts, E. Magnus Ohman, Robert M. Califf, Ramón Corbalán, Kim A. Eagle, Efrain Gaxiola, Runlin Gao, Shinya Goto, Ralph B. D'Agostino, Sidney C. Smith, Peter W.F. Wilson
Journal: Circulation (2011)

We thank Dr Nabi for his comments regarding our publication that related attained educational level to cardiovascular disease outcomes in the REduction of Atherothrombosis for Continued Health (REACH) Registry experience. 1 Dr Nabi correctly interprets Table 3 of our report, which indicates that in women from low-and middle-income countries (LMICs), there was no gradient in the rate of cardiovascular events across education groups.We believe that these data are fairly interpreted by our statement, "higher AEL may not be protective against cardiovascular events in LMICs, particularly in women."Dr Nabi also questions our suggestion that the promotion of education in women in LMICs may be insufficient to reduce their cardiovascular risk, and that other interventions may be necessary, such as ensuring that women of all educational backgrounds have adequate access to health care.We agree that this area requires further study, and we hope that our findings are investigated more fully in other analyses in the future.We believe that the most important conclusion of our work is that studies conducted in high-income countries that link socioeconomic status (including educational attainment) to cardiovascular outcomes cannot be extrapolated to LMIC settings.It is essential to conduct separate studies in LMIC settings, which bear most of the global burden of cardiovascular disease.
TNF and IP-10 drive inflammation into hyperinflammation in the murine lung
Authors: Lucy Kathleen Reiss, Stefan Uhlig
Journal: European Respiratory Journal (2013)

The lung is prone to injurious stimuli from two sides: directly via the airways or indirectly via the capillary network. Once the alveolar-capillary barrier is disrupted, pulmonary inflammation is ongoing. Inflammation may proceed without tissue damage until the stressor is removed or may aggravate leading to organ dysfunction as in acute respiratory distress syndrome. We propose that salutary and destructive inflammation (hyperinflammtion) are two distinct modules, activated depending on the severity of injury. This study was designed to examine our hypothesis that TNF and IP-10 drive inflammation into hyperinflammation.

C57/BL6 mice were instilled with 50μL HCl pH=2 or saline and then ventilated for 1 hour, before 5μg TNF + 5μg IP-10 in 50μL PBS were aerosolized into the lungs. Control groups received 50μL PBS. Mice were ventilated for a further 6 hours. Lung mechanics, oxygenation and cardiovascular parameters were monitored during ventilation. Pro-inflammatory mediators, leukocyte recruitment, microvascular permeability and histology were examined in the lungs.

There was no significant difference between mice instilled with acid pH=2 or saline alone. Inflammatory mediators and neutrophils were found in all ventilated lungs, but oxygenation and lung functions were not impaired. Additional application of TNF+IP-10 led to critical physiological dysfunction only in mice pre-treated with acid pH=2, not in those treated with saline. This indicates that acid pH=2 initiates inflammation and makes the lungs susceptible to hyperinflammation triggered by TNF+IP-10.

We conclude that a certain set of mediators, including TNF and IP-10, may be responsible for turning mild inflammation into full-blown hyperinflammation.
Detection of Prostate Cancer with a Blood-Based Assay for Early Prostate Cancer Antigen
Authors: Barbara Paul, Rajiv Dhir, Douglas Landsittel, Moira R. Hitchens, Robert H. Getzenberg
Journal: Cancer Research (2005)

Abstract Prostate-specific antigen lacks specificity for prostate cancer, so the identification and characterization of a unique blood-based marker for the disease would provide for a more accurate diagnosis, reducing both unnecessary biopsies and patient uncertainty. We previously identified a novel biomarker for prostate cancer, early prostate cancer antigen (EPCA). EPCA antibodies positively stained the negative biopsies of men who, as much as 5 years later, were diagnosed with prostate cancer. The goal of this study was to determine whether EPCA antibodies could be used in a clinically applicable plasma-based immunoassay to specifically detect prostate cancer. Using an EPCA-based ELISA, the protein was measured in the plasma of 46 individuals, including prostate cancer patients, healthy individuals, other cancer patients, spinal cord injury victims, and patients with prostatitis. With a predetermined cutoff value of 1.7 absorbance at 450 nm, only the prostate cancer population, as a whole, expressed plasma-EPCA levels above the cutoff. Statistical analysis showed a significant difference in EPCA levels between the prostate cancer population and each of the other groups, specifically the healthy donors (P &amp;lt; 0.0001), bladder cancer patients (P = 0.03), and spinal cord injury patients (P = 0.001). Sensitivity of the EPCA assay for prostate cancer patients was 92% whereas the overall specificity was 94%. Specificity for the healthy donors was 100%. Although larger trials are required, this initial study shows the potential of EPCA to serve as a highly specific blood-based marker for prostate cancer. EPCA, when coupled with prostate-specific antigen, may help reduce the number of both unnecessary biopsies and undetected prostate tumors.