tbuckley/cabot-search huggingface dataset:
Morphometric and Visual Evaluation of Fibrosis in Renal Biopsies
Authors: Alton B. Farris, Catherine D. Adams, Nicole Brousaides, Patricia A. Della Pelle, A. Bernard Collins, Ellie Moradi, R. Neal Smith, Paul C. Grimm, Robert B. Colvin
Journal: Journal of the American Society of Nephrology (2010)

Interstitial fibrosis is an outcome measure of increasing importance in clinical trials of both renal transplantation and native disease, but data on the comparative advantages of fibrosis measurement methods are limited. We compared four morphometric techniques and contrasted these with two visual fibrosis-scoring methods on trichrome-stained slides. Two morphometric methods included whole-slide digital images: collagen III immunohistochemistry and a new technique using trichrome and periodic acid-Schiff subtraction morphometry; the other two methods included Sirius Red with and without polarization on multiple digital fields. We evaluated 10 serial sections from 15 renal biopsies with a range of fibrosis extent and diagnoses on duplicate sections with each method on separate days. Three pathologists performed visual scoring on whole-slide images. Visual and morphometric techniques had good to excellent interassay reproducibility (R(2) = 0.62 to 0.96) and interobserver reproducibility (R(2) = 0.75 to 0.99, all P < 0.001). Morphometry showed less variation between observers than visual assessment (mean of 1% to 5% versus 11% to 13%). Collagen III, Sirius Red unpolarized, and visual scores had the strongest correlations (R(2) = 0.78 to 0.89), the greatest dynamic range, and the best correlation with estimated GFR (R(2) = 0.38 to 0.50, P < 0.01 to 0.001). Considering efficiency, reproducibility, and functional correlation, two current techniques stand out as potentially the best for clinical trials: collagen III morphometry and visual assessment of trichrome-stained slides.
The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants
Authors: A. D. Wolfe, C. W. dePamphilis
Journal: Molecular Biology and Evolution (1998)

The photosynthetic gene rbcL has been lost or dramatically altered in some lineages of nonphotosynthetic parasitic plants, but the dynamics of these events following loss of photosynthesis and whether rbcL has sustained functionally significant changes in photosynthetic parasitic plants are unknown. To assess the changes to rbcL associated with the loss of functional constraints for photosynthesis, nucleotide sequences from nonparasitic and parasitic plants of Scrophulariales were used for phylogeny reconstruction and character analysis. Plants in this group display a broad range of parasitic abilities, from photosynthetic ("hemiparasites") to nonphotosynthetic ("holoparasites"). With the exception of Conopholis (Orobanchaceae), the rbcL locus is present in all parasitic plants of Scrophulariales examined. Several holoparasitic genera included in this study, including Boschniakia, Epifagus, Orobanche, and Hyobanche, have rbcL pseudogenes. However, the holoparasites Alectra orobanchoides, Harveya capensis, Harveya purpurea, Lathraea clandestina, Orobanche corymbosa, O. fasciculata, and Striga gesnerioides have intact open reading frames (ORFs) for the rbcL gene. Phylogenetic hypotheses based on rbcL are largely in agreement with those based on sequences of the nonphotosynthetic genes rps2 and matK and show a single origin of parasitism, and loss of photosynthesis and pseudogene formation have been independently derived several times in Scrophulariales. The mutations in rbcL in nonparasitic and hemiparasitic plants would result in largely conservative amino acid substitutions, supporting the hypothesis that functional proteins can experience only a limited range of changes, even in minimally photosynthetic plants. In contrast, ORFs in some holoparasites had many previously unobserved missense substitutions at functionally important amino acid residues, suggesting that rbcL genes in these plants have evolved under relaxed or altered functional constraints.
Value of chest radiography in phenotyping chronic obstructive pulmonary disease
Authors: M. Miniati, S. Monti, J. Stolk, G. Mirarchi, F. Falaschi, R. Rabinovich, C. Canapini, J. Roca, K. F. Rabe
Journal: European Respiratory Journal (2007)

The objectives of the present study were to reappraise chest radiography for the diagnosis of emphysema, using computed tomography (CT) as the reference standard, and to establish whether or not chest radiography is useful for phenotyping chronic obstructive pulmonary disease (COPD). Patients (n = 154) who had undergone posteroanterior and lateral chest radiography and CT for diagnostic purposes were studied. CT data were scored for emphysema using the picture-grading method. Chest radiographs were examined independently by five raters using four criteria for emphysema that had been validated against lung pathology. These criteria were then used to assess the prevalence of emphysema in 458 COPD patients. Patients with and without evidence of emphysema were compared with regard to age, sex, smoking history, body mass index (BMI), forced expiratory volume in one second (FEV 1 ), diffusing capacity of the lung for carbon monoxide ( D L,CO ) and health status. Chest radiography yielded a sensitivity of 90% and a specificity of 98% for emphysema. Of the 458 COPD patients, 245 showed radiological evidence of emphysema. Emphysemic patients had a significantly lower BMI, FEV 1 and D L,CO , greater restriction of physical activity and worse quality of life than nonemphysemic patients. There was no difference across the two groups with regard to age, sex or smoking history. Chest radiography is a simple means of diagnosing moderate-to-severe emphysema. It is useful in phenotyping chronic obstructive pulmonary disease and may aid physicians in their choice of treatment.
Electrical Quiescence of Pulmonary Artery Smooth Muscle During Sympathomimetic Stimulation
Authors: CHE SU, JOHN A. BEVAN, RICHARD C. URSILLO
Journal: Circulation Research (1964)

Simultaneous recordings of isometric tension and muscle membrane potential have been made in the sympathetic nerve-pulmonary artery preparation of the rabbit. The mean resting membrane potential recorded intracellularly was 51.5 mv. Sympathetic nerve stimulation and l -norepinephrine caused contraction without change in the membrane potential and in the absence of action potentials. Increase in extracellular potassium initiated both depolarization and contraction, although these two processes exhibited different latencies and time courses. The significance of these findings is discussed in relation to recent findings of dissociation in smooth muscle between contraction and membrane potential changes.
Primary prevention of cardiovascular disease with pravastatin in Japan (MEGA Study): a prospective randomised controlled trial
Authors: Haruo Nakamura, Kikuo Arakawa, Hiroshige Itakura, Akira Kitabatake, Yoshio Goto, Takayoshi Toyota, Noriaki Nakaya, Shoji Nishimoto, Masaharu Muranaka, Akira Yamamoto, Kyoichi Mizuno, Yasuo Ohashi
Journal: The Lancet (2006)
Renal Transplantation Reversed Intractable Hypotension in a Diabetic Patient
Authors: Chiao-Yin Sun, Mai-Szu Wu
Journal: Diabetes Care (2007)

A small fraction of hemodialysis patients have chronic hypotension (1). Autonomic dysfunction, a product of diabetes and uremia, may be the most important cause that contributes to hypotension in dialysis patients (1). Unfortunately, there is no specific or effective therapy for them.

A 59-year-old female with hypertension and type 2 diabetes for >16 years received hemodialysis treatment 6 years ago, due to diabetic nephropathy. Chronic hypotension (80–100/50–60 …
Pathology and protection in nephrotoxic nephritis is determined by selective engagement of specific Fc receptors
Authors: Yoshikatsu Kaneko, Falk Nimmerjahn, Michael P. Madaio, Jeffrey V. Ravetch
Journal: The Journal of Experimental Medicine (2006)

Introduction of heterologous anti-glomerular basement membrane antiserum (nephrotoxic serum, NTS) into presensitized mice triggers the production of IgG anti-NTS antibodies that are predominantly IgG2b and the glomerular deposition of pathogenic immune complexes, leading to accelerated renal disease. The pathology observed in this model is determined by the effector cell activation threshold that is established by the coexpression on infiltrating macrophages of the IgG2a/2b restricted activation receptor FcgammaRIV and its inhibitory receptor counterpart, FcgammaRIIB. Blocking FcgammaRIV with a specific monoclonal antibody thereby preventing IgG2b engagement or treatment with high dose intravenous gamma-globulin (IVIG) to down-regulate FcgammaRIV while up-regulating FcgammaRIIB, protects mice from fatal disease. In the absence of FcgammaRIIB, IVIG is not protective; this indicates that reduced FcgammaRIV expression alone is insufficient to protect animals from pathogenic IgG2b immune complexes. These results establish the significance of specific IgG subclasses and their cognate FcgammaRs in renal disease.
Surgical Urology: A Handbook of Operative Surgery
Authors: C. B. Dawson
Journal: JAMA (1968)

problems of orality affect the capacity to learn.Pearson does mention these in passing, but it is striking how little attention is paid to these fundamental aspects of the child's early experiences and what we have learned is the effect of these experiences on learning and creativity.In this sense the book is disappointing.It is also of interest that the focus of the book is on the individual child and his problems rather than the family and its problems since most educators and persons concerned with mental hygiene in recent years have begun to shift their attention to the total situation from which the learning problems stem.There are also some prescriptions of helpful attitudes for teachers which contain the usual pitfalls of any prescriptions about how someone should behave for someone else's benefit.Despite these shortcomings, this is a valuable book which should be read by those interested in education and the psychology of learning.
Risk for Valvular Heart Disease After Treatment for Hodgkin Lymphoma
Authors: David J. Cutter, Michael Schaapveld, Sarah C. Darby, Michael Hauptmann, Frederika A. van Nimwegen, Augustinus D. G. Krol, Cecile P. M. Janus, Flora E. van Leeuwen, Berthe M. P. Aleman
Journal: JNCI Journal of the National Cancer Institute (2015)

Background:Hodgkin lymphoma (HL) survivors are at increased risk for developing valvular heart disease (VHD). We evaluated the determinants of the risk and the radiation dose-response.
The Janus Kinases Inhibitor AZD1480 Attenuates Growth of Small Cell Lung Cancers <i>In Vitro</i> and <i>In Vivo</i>
Authors: Jih-Hsiang Lee, Kang-Seo Park, Anna Teresa Alberobello, Bhaskar Kallakury, Meng-Tzu Weng, Yisong Wang, Giuseppe Giaccone
Journal: Clinical Cancer Research (2013)

The prognosis of small cell lung cancer (SCLC) is poor, and there has been very little progress in the medical treatment of SCLC in the past two decades. We investigated the potential of Janus-activated kinases (JAK) inhibitor, AZD1480, for treatment of SCLC in vitro and in vivo.
An unusual cause of left lower lobe collapse
Authors: Omendra Narayan, Warren Lenney, Michael Singh, M. Kalkat, Francis Gilchrist
Journal: European Respiratory Journal (2014)

Introduction:   Lobar collapse is common and has many varied aetiologies.   Methods:   A 15 year old girl reported increasing exercise induced shortness of breath for the last two years. She had an obstructive spirometry (FEV1 1.71 L - 56%) but an inadequate response to the asthma medications. Subsequently she became acutely unwell with cough and pyrexia and a chest X-ray confirmed a diagnosis of left lower lobe pneumonia with collapse. This did not reinflate with physiotherapy, oral antibiotics and prednisolone. At bronchoscopy a large soft tissue mass was seen on left main bronchus just below the level of carina (figure A). A CT scan was undertaken to elucidate this mass further (figure B).   Management:   A biopsy was done by thoracic surgeons that confirmed the diagnosis of a typical bronchial carcinoid. Initially this was treated by laser obliteration and subsequently she had resection and re-anastomosis of the left main bronchus. She is currently well and is symptom free.   Conclusion:   Bronchial carcinoids are very rare in children and hence there can be a delay in diagnosis and treatment. The long-term outcome is strictly related with the histological subtype and the lymph node status.
Evidence-Based Clinical Practice Guideline for the Prevention of Ventilator-Associated Pneumonia
Authors: Peter Dodek, Sean Keenan, Deborah Cook, Daren Heyland, Michael Jacka, Lori Hand, John Muscedere, Debra Foster, Nav Mehta, Richard Hall, Christian Brun-Buisson
Journal: Annals of Internal Medicine (2004)

Ventilator-associated pneumonia (VAP) is an important patient safety issue in critically ill patients.To develop an evidence-based guideline for the prevention of VAP.MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews.The authors systematically searched for relevant randomized, controlled trials and systematic reviews that involved mechanically ventilated adults and were published before 1 April 2003.Physical, positional, and pharmacologic interventions that may influence the development of VAP were considered. Independently and in duplicate, the authors scored the validity of trials; the effect size and confidence intervals; the homogeneity of results; and safety, feasibility, and economic issues.Recommended: The orotracheal route of intubation, changes of ventilator circuits only for each new patient and if the circuits are soiled, use of closed endotracheal suction systems that are changed for each new patient and as clinically indicated, heat and moisture exchangers in the absence of contraindications, weekly changes of heat and moisture exchangers, and semi-recumbent positioning in the absence of contraindications. Consider subglottic secretion drainage and kinetic beds. Not recommended: Sucralfate to prevent VAP in patients at high risk for gastrointestinal bleeding and topical antibiotics to prevent VAP. Because of insufficient or conflicting evidence, no recommendations were made about systematically searching for maxillary sinusitis, chest physiotherapy, the timing of tracheostomy, prone positioning, prophylactic intravenous antibiotics, or intravenous plus topical antibiotics.No formal economic analysis was performed, and patient perspectives were not considered.If effectively implemented, this guideline may decrease the morbidity, mortality, and costs of VAP in mechanically ventilated patients.
Neural respiratory drive and breathlessness in COPD
Authors: Caroline J. Jolley, Yuanming M. Luo, Joerg Steier, Gerrard F. Rafferty, Michael I. Polkey, John Moxham
Journal: European Respiratory Journal (2014)

The aim of this study was to test the hypothesis that neural respiratory drive, measured using diaphragm electromyogram (EMGdi) activity expressed as a percentage of maximum (EMGdi%max), is closely related to breathlessness in chronic obstructive pulmonary disease. We also investigated whether neuroventilatory uncoupling contributes significantly to breathlessness intensity over an awareness of levels of neural respiratory drive alone. EMGdi and ventilation were measured continuously during incremental cycle and treadmill exercise in 12 chronic obstructive pulmonary disease patients (forced expiratory volume in 1 s±sd was 38.7±14.5 % pred). EMGdi was expressed both as EMGdi%max and relative to tidal volume expressed as a percentage of predicted vital capacity to quantify neuroventilatory uncoupling. EMGdi%max was closely related to Borg breathlessness in both cycle (r=0.98, p=0.0001) and treadmill exercise (r=0.94, p=0.005), this relationship being similar to that between neuroventilatory uncoupling and breathlessness (cycling r=0.94, p=0.005; treadmill r=0.91, p=0.01). The relationship between breathlessness and ventilation was poor when expansion of tidal volume became limited. In chronic obstructive pulmonary disease the intensity of exertional breathlessness is closely related to EMGdi%max. These data suggest that breathlessness in chronic obstructive pulmonary disease can be largely explained by an awareness of levels of neural respiratory drive, rather than the degree of neuroventilatory uncoupling. EMGdi%max could provide a useful physiological biomarker for breathlessness in chronic obstructive pulmonary disease.
The Relationship Between Childhood Physical Abuse and Suicidality Among Depressed Women: Results From a Community Sample
Authors: Angela E. McHolm, Harriet L. MacMillan, Ellen Jamieson
Journal: American Journal of Psychiatry (2003)

OBJECTIVE: The aim of this study was to examine the distribution and determinants of suicidal ideation and suicide attempts in a community sample of women with major depressive disorder. Variables of interest included childhood physical abuse, individual and familial psychiatric history, and sociodemographic factors. METHOD: Women (age 15 to 64 years) from a community sample who met criteria for major depressive disorder (lifetime prevalence) (N=347) were assessed with a modified version of the Composite International Diagnostic Interview. Childhood physical abuse history was collected through a self-administered questionnaire. RESULTS: Approximately one-quarter (23.9%, N=83) of the women with major depressive disorder reported that they had made a suicide attempt, and more than half (55.6%, N=193) had experienced suicidal ideation. A history of suicide attempt was most strongly related to the number of comorbid psychiatric disorders (odds ratio=2.04, 95% confidence interval [CI]=1.21–3.43). Suicidal ideation was most strongly associated with a history of childhood physical abuse (odds ratio=2.77, 95% CI=1.26–6.12). CONCLUSIONS: Suicidal ideation and suicide attempts were reported frequently by women with a history of major depressive disorder. Correlates for suicide attempts showed some differences from those for ideation. This finding is of clinical importance, since it relates to the identification of individuals at risk for suicidal behavior.
Systemic lupus erythematosus (SLE) in childhood: analysis of clinical and immunological findings in 34 patients and comparison with SLE characteristics in adults
Authors: J. Font, R. Cervera, G. Espinosa, L. Pallares, M. Ramos-Casals, S. Jimenez, M. Garcia-Carrasco, L. Seisdedos, M. Ingelmo
Journal: Annals of the Rheumatic Diseases (1998)

<h3>OBJECTIVE</h3> To define the pattern of disease expression in patients with childhood onset systemic lupus erythematosus (SLE). <h3>METHODS</h3> Prospective analysis of clinical manifestations and immunological features of 34 patients in whom the first manifestations appeared in childhood from a series of 430 unselected patients with SLE. <h3>RESULTS</h3> Thirty one (91%) patients from the childhood onset group were female and three male (9%) (ratio female/male, 10/1, with no difference compared with the adult onset group). Mean age of this group at disease onset was 11 years (range 5–14) compared with 32 years (15–48) for the remaining patients. The childhood onset patients more often had nephropathy (20%<i>v</i> 9% in adult onset SLE, p=0.04; OR:2.7; 95%CI:1.1, 7), fever (41% <i>v</i> 21%, p=0.006; OR:2.6, 95%CI:1.2, 5.7), and lymphadenopathy (6%<i>v</i> 0.5%, p=0.03, OR: 12.3, 95%CI: 1.2, 127.6), as presenting clinical manifestations. During the evolution of the disease, the childhood onset patients had an increased prevalence of malar rash (79% <i>v</i> 51%, p=0.002; OR:3.7; 95%CI:1.5, 9.5) and chorea (9% <i>v</i> 0%, p&lt;0.0001). This group exhibited a higher prevalence of anticardiolipin antibodies (aCL) of the IgG isotype when compared with the remaining patients (29% <i>v</i> 13%, p=0.017; OR:2.9, 95%CI:1.2, 6.8). No significant differences were found among the other antibodies between the two groups. Childhood onset patients more often received azathioprine (15% <i>v</i> 6%, p=0.00004; OR:11.2; 95%CI:2.8, 44.9) but no differences were detected between the groups concerning side effects or drug toxicity. <h3>CONCLUSIONS</h3> The presentation and the clinical course of SLE varied in this series of 430 patients depending on their age at disease onset. Nephropathy, fever, and lymphadenopathy were more common in childhood onset patients as presenting clinical manifestations, while malar rash, chorea, and detection of IgG aCL were more common during the evolution of the disease.
Abstract P1-02-10: Variation in HER2 positive rates in California by geographic region: Implications for setting pathology laboratory benchmarks
Authors: KH Allison, KC Jensen, RB West, CA Clarke, SL Gomez, AW Kurian
Journal: Cancer Research (2013)

Abstract Background: It is unclear how much regional variation there is for HER2 positive rates in breast cancer. By looking at regional variation, we can begin to examine the impact of both demographic variation and pathology laboratory practice on HER2 positive rates so that valid laboratory benchmarks can be established. Methods: Utilizing data from the California Cancer Registry (CCR), we examined the HER2 positive rates sorted by 58 California counties. Counties were grouped into 10 geographic regions for analysis. Stage at presentation and total numbers of breast cancer cases were studied at as variables. Results: 97,248 breast cancer cases were included in the CCR data. Overall, the HER2 positive rate was 16.5%. HER2 positive rates increased with increasing stage at presentation both overall and by region. Overall they were 12.9% for stage 1, 17.4% for stage 2, 23.2% for stage 3, 25.9% for stage 4 and 25.2% for unstaged cases. There was significant regional variation in overall HER2 positive rates ranging from 13.2-18.9%. 4 regions had overall rates within 0.5% of each other, 3 regions had rates &amp;gt; 0.5% below average and 3 regions had rates &amp;gt;0.5% above average. In the regions with overall rates below the average, one region (region 4, N = 4,636) had lower rates across all stages, and two regions (region 7, N = 8,623 and region 8, N = 14,152) had lower rates only for stages 1-2. Of regions with overall rates higher than the average, one region had increased rates across all stages (region 9, N = 24,279) and two regions had increased rates only in stages 1-3 (region 5, N = 9,176 and region 6, N = 4,888). Conclusions: In California, there is significant variation in HER2 positive rates by geographic region, even when controlling for stage. The possible influence of differences in regional population characteristics versus differences in laboratory practices to explain this variation should be further examined so that valid regional laboratory benchmarks can be established. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-02-10.