tbuckley/cabot-search huggingface dataset:
Molecular evolution at subzero temperatures: mitochondrial and nuclear phylogenies of fishes from Antarctica (suborder Notothenioidei), and the evolution of antifreeze glycopeptides.
Authors: L Bargelloni, P A Ritchie, T Patarnello, B Battaglia, D M Lambert, A Meyer
Journal: Molecular Biology and Evolution (1994)

Most fishes of the perciform suborder Notothenioidei are endemic to the subzero marine waters of Antarctica. A number of remarkable physiological attributes allow them to inhabit this extreme environment; for example, the blood of almost all notothenioid species contains antifreeze glycopeptides. To establish a molecular phylogenetic hypothesis for these fishes, DNA sequences from two mitochondrial genes, portions of the 12S and 16S ribosomal genes (928 base pairs [bp]), were determined for 18 species. These belong to 15 genera in five families of the suborder. The DNA data suggest that two of these families are unnatural groups and consequently that the classification and phylogeny of this suborder is in need of revision. In terms of DNA variation, the Bovichtidae are a distantly related sister group to the other families of the suborder that includes the icefishes, the only vertebrates without hemoglobin. The fishes of the suborder (except the Bovichtidae) seem to have speciated rapidly, forming an adaptive radiation in the Antarctic waters. A phylogenetic analysis of published hemoglobin amino acid sequences for other notothenioid fishes supports these results from mtDNA. On the basis of molecular phylogeny, the evolution of antifreeze glycopeptides was studied. The age of the radiation of notothenioid fishes had been estimated to be at least 38 Mya. However, the level of mtDNA variation detected in notothenioid fishes appears to be too low to agree with this date of origin and might instead suggest a younger age (10-15 Mya). Alternatively, the low level of detected mtDNA variation would agree with the traditional old-age estimate if an extremely slow rate of mtDNA evolution is postulated for this group. This slow-rate hypothesis, if true, could be explained by decreased metabolic rates slowing down the tempo of molecular evolution.
Response 1 to pharmacogenetic screening to prevent carbamazepine-induced toxic epidermal necrolysis and Stevens-Johnson syndrome: a critical appraisal
Authors: C.Y. Shen, Y.T. Chen
Journal: British Journal of Dermatology (2011)

Wu and Reynolds1 have written a critical review of our study,2 a large multicentre trial that aims at showing that personalized medicine and pharmacogenomics could be useful in the right clinical setting. Because the risk of carbamazepine‐induced Stevens–Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is strikingly higher among persons who carry the HLA‐B*1502 allele than among those who do not carry the allele (odds ratio 1375), for ethical reasons this study could not be designed as a randomized controlled study. Instead, we used the estimated historical incidence for comparison. Our estimation of historical incidence was based on the data from the National Health Insurance Research Database (NHIRD) which was established in Taiwan when the Government launched the National Health Insurance (NHI) in 1995. This mandatory single‐payer social health insurance system provides universal healthcare for almost all people in Taiwan, with an enrolment rate of 99·48% as of 2008. Furthermore, 92·47% of all healthcare facilities in the country have been contracted by the NHI system. Therefore, the NHIRD data are representative and comprehensive, and have been used by many investigators, resulting in much high‐quality research and many publications (see website http://w3.nhri.org.tw/nhird/talk_07.htm).
Positional obstructive sleep apnea (OSA) and automatic positive airway pressure (APAP) therapy
Authors: Ana Rita Dias, Cristina Martinho, Ana Marta Silva, Catarina Leitão, Liliana Almeida, Marta Escaleira, Vanessa Cardoso, Rita Pinto Basto, Paula Pinto, Cristina Bárbara
Journal: European Respiratory Journal (2012)

Introduction:  Recent studies have shown that respiratory events that occur during sleep in supine position have a high prevalence in mild and moderate OSA patients.   Objectives : To determine the prevalence of positional OSA in patients with mild to moderate OSA; Compare biometric characteristics and response to APAP between positional and nonpositional OSA patients.   Methods:  404 polysomnographies (Embla S7000) were analyzed by an experienced technician.  Positional OSA was considered when AHI normalized in the nonsupine position (AHI ≤ 5 events per hour of sleep). Patients who adapted APAP were evaluated one month after starting treatment.   Results:  We studied 126 patients, 65% male, with a mean age of 53 ± 11.7 years and a mean RDI of 14.3±6.1 respiratory events/hour.  Prevalence of positional OSA was 53.2% in the total group (56.8% in mild patients and 48% in moderate patients).  Thirty four out of 66 patients with positional OSA adapted APAP, 22 (64.7%) had no compliance to therapy and 12 (35.3%) had a mean compliance rate of more than 4.5 hours.  Concerning APAP parameters, the 95-percentile pressure (P95) was lower in patients with positional OSA (p=0.003). Leaks and residual AHI were not different between the two groups.   Conclusion:  We found a high prevalence of positional OSA in patients with mild to moderate OSA.  Most patients with positional OSA were not compliant to therapy with APAP (64.7%). So, despite continuous positive airway pressure is considered the gold standard treatment of OSA, patients who did not have compliance should be encouraged for positional therapy.   Keywords:  Positional OSA, Polysomnography, APAP.
The Role of Iron Chelation Therapy for Patients With Myelodysplastic Syndromes
Authors: David P. Steensma
Journal: Journal of the National Comprehensive Cancer Network (2011)

The appropriate role of iron chelation therapy in the management of patients with myelodysplastic syndromes (MDS) is currently controversial. Some investigators interpret data to indicate that careful attention to iron parameters, with early initiation of iron chelation in patients with evidence suggesting transfusion-associated iron overload, is an important component of high-quality MDS patient care. Other physicians are more skeptical, noting that chelation can be cumbersome or costly, has associated risks, and has not yet been shown to reduce morbidity or mortality in the MDS setting. This article reviews the extent to which iron chelation therapy might be either an important clinical intervention in MDS or a distraction from more pressing clinical concerns.
Lymphocyte Fluorescence Polarization Changes After Phytohemagglutinin Stimulation in the Diagnosis of Colorectal Carcinoma&lt;xref ref-type="fn" rid="fn2"&gt;2&lt;/xref&gt;&lt;xref ref-type="fn" rid="fn3"&gt;3&lt;/xref&gt;
Authors: G R Hocking, J M Rolland, R C Nairn, E Pihl, A M Cuthbertson, E S Hughes, W R Johnson
Journal: JNCI Journal of the National Cancer Institute (1982)

A lymphocyte fluorescence polarization test that measures reactivity to phytohemagglutinin (PHA) has permitted discrimination of a majority of patients with colorectal carcinoma from noncancer individuals. The test involves separation of two lymphocyte fractions from 20 ml venous blood on a modified leukocyte separation gradient, incubation with PHA for 45 minutes, addition of fluorescein diacetate, and analysis of change in fluorescence polarization. Of 19 colorectal patients tested preoperatively, 13 had a positive stimulation index, 3 a zero index, and 3 a negative index. Of 7 patients with other malignant neoplasms, a positive value was obtained in 6 and a negative value in 1. Of 14 patients with other diseases, a negative value was obtained in 9, zero in 3, and positive in 2. Of 31 normal donors a negative value was obtained in 27, zero in 2, and weak positive in 2. This rapid test promises to develop into a useful cancer-diagnostic method, and elucidation of its biological basis should identify a new cancer marker.
Joint Action of West Nile Virus and Chemical Carcinogens in Production of Papillomas in Mice&lt;xref ref-type="fn" rid="fn1"&gt;2&lt;/xref&gt;
Authors: Satoshi Tanaka, Chester M. Southam
Journal: JNCI Journal of the National Cancer Institute (1962)

Skin papillomas occurred with greater frequency in mice given West Nile virus intraperitoneally during a 10-day course of skin painting with 3-methyl-cholanthrene or henzo[a]pyrene than in mice given the chemical carcinogens alone. Carcinoma incidence was also increased, but only in proportion to the increased incidence of papillomas; the frequency with which carcinoma developed in papillomatous skin was not influenced by the virus infection. Papillomatosis was not increased when virus administration was delayed until after the course of methylcholanthrene applications. Ancillary studies provide evidence against the possibilities that virus-caused deaths eliminated papil-loma-resistant mice, or that mice most susceptible to papillomatosis are less susceptible to the virus infection. The virus was demonstrated in the skin of both control and carcinogen-treated mice at 3 and 4 days after intraperitoneal virus administration. Chi-square analysis indicates that the observed differences would rarely occur by chance.
Lipodystrophia centrifugalis abdominalis infantilis in a 4-year-old caucasian girl: association with partial IgA deficiency and autoantibodies
Authors: None Müller, None Beissert, None Metze, None Luger, None Bonsmann
Journal: British Journal of Dermatology (1999)

We report the third case of lipodystrophia centrifugalis abdominalis outside East Asia. A 4-year-old Caucasian girl developed an area of bluish erythema on the left side of the lower abdomen which spread centrifugally to the umbilical and inguinal areas with depression of the skin resulting from the loss of subcutaneous fat, surrounded by an erythematous border. This unusual skin disease was characterized by clinical and histological examination. Laboratory tests revealed a partial IgA deficiency, antinuclear antibodies and IgG antibodies against gliadin.
Diagnostic Yield and Complications of Bronchoscopy for Peripheral Lung Lesions. Results of the AQuIRE Registry
Authors: David E. Ost, Armin Ernst, Xiudong Lei, Kevin L. Kovitz, Sadia Benzaquen, Javier Diaz-Mendoza, Sara Greenhill, Jennifer Toth, David Feller-Kopman, Jonathan Puchalski, Daniel Baram, Raj Karunakara, Carlos A. Jimenez, Joshua J. Filner, Rodolfo C. Morice, George A. Eapen, Gaetane C. Michaud, Rosa M. Estrada-Y-Martin, Samaan Rafeq, Horiana B. Grosu, Cynthia Ray, Christopher R. Gilbert, Lonny B. Yarmus, Michael Simoff
Journal: American Journal of Respiratory and Critical Care Medicine (2015)

Advanced bronchoscopy techniques such as electromagnetic navigation (EMN) have been studied in clinical trials, but there are no randomized studies comparing EMN with standard bronchoscopy.To measure and identify the determinants of diagnostic yield for bronchoscopy in patients with peripheral lung lesions. Secondary outcomes included diagnostic yield of different sampling techniques, complications, and practice pattern variations.We used the AQuIRE (ACCP Quality Improvement Registry, Evaluation, and Education) registry to conduct a multicenter study of consecutive patients who underwent transbronchial biopsy (TBBx) for evaluation of peripheral lesions.Fifteen centers with 22 physicians enrolled 581 patients. Of the 581 patients, 312 (53.7%) had a diagnostic bronchoscopy. Unadjusted for other factors, the diagnostic yield was 63.7% when no radial endobronchial ultrasound (r-EBUS) and no EMN were used, 57.0% with r-EBUS alone, 38.5% with EMN alone, and 47.1% with EMN combined with r-EBUS. In multivariate analysis, peripheral transbronchial needle aspiration (TBNA), larger lesion size, nonupper lobe location, and tobacco use were associated with increased diagnostic yield, whereas EMN was associated with lower diagnostic yield. Peripheral TBNA was used in 16.4% of cases. TBNA was diagnostic, whereas TBBx was nondiagnostic in 9.5% of cases in which both were performed. Complications occurred in 13 (2.2%) patients, and pneumothorax occurred in 10 (1.7%) patients. There were significant differences between centers and physicians in terms of case selection, sampling methods, and anesthesia. Medical center diagnostic yields ranged from 33 to 73% (P = 0.16).Peripheral TBNA improved diagnostic yield for peripheral lesions but was underused. The diagnostic yields of EMN and r-EBUS were lower than expected, even after adjustment.
Long-Pentraxin 3 Derivative as a Small-Molecule FGF Trap for Cancer Therapy
Authors: Roberto Ronca, Arianna Giacomini, Emanuela Di Salle, Daniela Coltrini, Katiuscia Pagano, Laura Ragona, Sara Matarazzo, Sara Rezzola, Daniele Maiolo, Rubben Torella, Elisabetta Moroni, Roberta Mazzieri, Giulia Escobar, Marco Mor, Giorgio Colombo, Marco Presta
Journal: Cancer Cell (2015)
Immunogenicity of Guinea Pig Cells Transformed in Culture by Chemical Carcinogens&lt;xref ref-type="fn" rid="fn2"&gt;2&lt;/xref&gt;
Authors: S H Ohanian, R P McCabe, C H Evans
Journal: JNCI Journal of the National Cancer Institute (1981)

The immunogenicity of inbred strain 2/N guinea pig fibroblasts transformed to the malignant state in vitro by chemical carcinogens was evaluated with the use of a variety of in vivo and in vitro methods including delayed-type hypersensitivity skin and tumor transplantation tests and analysis of antibody production by immunofluorescence, complement fixation, and staphylococcal protein A binding tests. Neoplastic transformation was induced by direct treatment of cells in culture with benzo[a]pyrene, 3-methylcholanthrene, or N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) or by the host-mediated method by which fetuses were exposed to diethylnitrosamine or MNNG in vivo prior to cell culture. Rabbits and syngeneic guinea pigs were inoculated with unirradiated and X-irradiated clonally derived cells. Delayed hypersensitivity skin reactions to immunizing or other cells were equivalent in immunized or control guinea pigs, and no protection to tumor outgrowth from a challenge inoculum of immunizing cells was observed. Antibody activity induced in the sera of immunized guinea pigs was cross-reactive and removed by absorption with nontumorigenic cells. Rabbit antisera after absorption with fetal guinea pig cells were nonreactive with the specific immunizing or other culture cells. Chemical carcinogen-induced neoplastic transformation of guinea pig cells can, therefore, occur without formation of detectable, individually distinct cell surface tumor-specific neoantigens.
Correction of acidosis in hemodialysis decreases whole-body protein degradation.
Authors: K A Graham, D Reaich, S M Channon, S Downie, T H Goodship
Journal: Journal of the American Society of Nephrology (1997)

Correction of acidosis in hemodialysis (HD) decreases protein degradation. The effect of the correction of chronic metabolic acidosis in chronic renal failure patients treated with HD was determined from the kinetics of infused L-[1-(13)C]leucine. Six HD patients were studied before (acid) and after (bicarbonate) correction of acidosis (pH: acid 7.36 +/- 0.01, bicarbonate 7.40 +/- 0.01, P < 0.005). Leucine appearance from body protein (PD) and leucine disappearance into body protein (PS) decreased significantly with correction of acidosis (PD: acid 180.6 +/- 7.3, bicarbonate 130.9 +/- 7.2 mumol.kg-1.h-1, P < 0.005; PS: acid 172.3 +/- 6.8, bicarbonate 122.0 +/- 6.8 mumol.kg-1.h-1, P < 0.005). There was no significant change in leucine oxidation or plasma amino acid concentrations. These results demonstrate that optimal correction of acidosis in HD is beneficial in terms of protein turnover and may improve long-term nutritional status in HD.
Esophagogastroduodenal anastomosis (EGDA), a rat surgical model of Barrett’s esophagus and esophageal adenocarcinoma
Authors: Xiaoxin Chen, Yinghao Su, Raj K. Goyal, Chung S. Yang
Journal: Cancer Research (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

1984 

In rats, esophagogastroduodenal anastomosis (EGDA) without concomitant chemical carcinogen treatment can lead to esophagitis, intestinal metaplasia, dysplasia, and esophageal adenocarcinoma (EAC). This study describes the morphology and phenotypic features of the rat model and compares the model with the corresponding lesions in human Barrett’s esophagus (BE). We observe several types of intestinal metaplasia in the rat esophagus, scattered mucinous cells (SMC), multi-layered epithelium (MLE), partially metaplastic epithelium (PME) and columnar-lined esophagus (CLE). SMCs are mucin-secreting columnar cells in the squamous epithelium of the rat esophagus, suggesting multi-clonality and epithelial origin of intestinal metaplasia. MLE is identified as an island of mucinous cells interspersed in squamous epithelium, with the columnar and goblet cells on the top, in the middle, or at the bottom of the squamous cell component. It frequently occurs at the neo-squamocolumnar junction and occasionally in the mid-esophagus in isolated foci. PME is identified as a sheet of esophageal epithelium, part of which has become columnar epithelium and the remaining is still squamous epithelium. It only occurs at the neo-squamocolumnar junction. On serial sections, we have clearly observed the transition of PME to CLE, which had features of specialized intestinal metaplasia at the neo-squamocolumnar junction. Rat CLE resembles human BE in morphology, mucin features and expression of differentiation markers (CK7, CK20, Das-1, villin, and pS2/TFF1). Invasive EAC in EGDA rat is of well-differentiated mucinous type, which is in contrast to the variably differentiated glandular type of human EAC. These studies indicate that intestinal metaplasia induced in EGDA rats may develop through a process from SMC, MLE, PME to CLE. Histopathologically, rat CLE and EAC are similar to the corresponding lesions in humans. EGDA rats may serve as a useful model to study the molecular mechanism and chemopreventive interventions of human BE and EAC. (Supported by NIH DK031092, DK63650 and CA75683)
Core beliefs and psychological distress in patients with psoriasis and atopic eczema attending secondary care: the role of schemas in chronic skin disease
Authors: A. Mizara, L. Papadopoulos, S.R. McBride
Journal: British Journal of Dermatology (2011)

The role of ingrained cognitive and emotional patterns (schemas) in patients with psoriasis and eczema has not previously been investigated. High levels of psychiatric morbidity and psychological distress observed in these populations suggest the presence of maladaptive schemas and therefore a possible target for future successful psychological intervention.To investigate the presence of early maladaptive schemas (EMS) in patients with psoriasis and eczema and to explore their links with psychological distress.A sample of 185 adults (psoriasis n = 55, atopic eczema n = 54, chronic disease control n = 23, normal control n = 53) completed validated, self-administered questionnaires.Differences were found between dermatology patients and control groups. Patients with psoriasis differed on seven EMS from the normal control group: emotional deprivation (P = 0·011), social isolation (P < 0·001), defectiveness (P < 0·001), failure (P < 0·001), vulnerability to harm (P < 0·001), subjugation (P = 0·009) and emotional inhibition (P = 0·002). They differed from the chronic disease group on vulnerability to harm (P = 0·002) only. Patients with eczema differed from the normal control group on eight EMS: emotional deprivation (P < 0·001), social isolation (P < 0·001), defectiveness (P < 0·001), failure (P < 0·001), dependence (P = 0·010), vulnerability to harm (P = 0·002), subjugation (P = 0·006) and insufficient self-control (P = 0·010). EMS were strongly positively related to psychological distress experienced by dermatology patients. Hierarchical regressions demonstrated two schemas, vulnerability to harm (P < 0·001) and defectiveness (P = 0·029), to be predictive of anxiety, and social isolation (P = 0·012) and vulnerability to harm (P = 0·018) to be predictive of depression, irrespective of age and years of coping for dermatology patients.The findings have important theoretical and clinical implications for psychological management of patients with psoriasis and eczema. Treatment protocols may benefit by targeting schemas. Further studies are needed to investigate the benefits of schema-focused therapy in patients with skin disease.
Selective Sex-Related Modification of Diethylnitrosamine-lnduced Carcinogenesis in BALB/c Mice by Concomitant Administration of Butylated Hydroxytoluene2
Authors: Neal K. Clapp, Richard L. Tyndall, Lou C. Satterfield, William C. Klima, Norman D. Bowles
Journal: JNCI Journal of the National Cancer Institute (1978)

Tumor induction in BALB/c mice by diethylnitrosamine (DENA) was shown to be sex related. Female mice killed 13.5 months after DENA exposure generally had higher incidences of forestomach and lung tumors than did males and also had higher numbers of lung tumors per tumor-bearing mouse. Although neither sex developed stomach tumors spontaneously, males had higher incidences of spontaneous lung tumors than did females (45 vs. 26%). When butylated hydroxytoluene (BHT) was given concomitantly with DENA treatment, females had an increased survival (68 vs. 43%) and a reduced incidence of forestomach squamous cell carcinomas (77 vs. 100%) compared with females given DENA alone. No such protective effect on survival or on the occurrence of stomach tumors was seen in males given BHT and DENA or on lung tumorigenesis in either sex. In males, BHT given alone increased survival of treated mice over that of untreated controls, but it had no such effect on the females. The results of this study suggested an as yet unexplained hormonal influence and/or dependence for this BHT modification of DENA tumorigenesis.
Asthma control, symptoms and exacerbations across treatment levels in patients with asthma
Authors: Thys van der Molen, Monica Fletcher, David Price
Journal: European Respiratory Journal (2013)

Introduction:  Asthma therapies are widely available in Europe, but exacerbations remain common. We report on asthma control and symptoms across different treatment levels in the largest European survey of patient attitudes to asthma management.   Methods:  Online surveys were conducted with 8000 patients with asthma (aged 18–50 years, ≥2 prescriptions in the past 2 years) recruited via validated consumer panels from 11 European countries. Only those on identified treatment were included here (N=4330).   Results:  GINA-defined asthma control levels were low and the incidence of acute exacerbations (oral steroid use for asthma) was high with all treatments (Table). Many respondents on maintenance treatment had night-time awakenings on ≥1 day (46–51%) or used their reliever inhaler ≥3 times (41–48%) in the week before the survey. Half of all respondents using single or combination inhalers reported that their symptoms interfered with normal activities on ≥1 day in the previous week.   Conclusions:  Asthma symptoms and exacerbations were common across all treatments, despite matching therapy to severity. This highlights the continuing need to close the gap between efficacy in clinical trials and real-world outcomes.
Expedience of Maintenance Treatment for Patients with Acute Myeloid Leukemia Younger Than 65 Years According to a Retrospective Analysis of the Efficacy of Two Protocols
Authors: S. Semochkin, T. Tolstykh, V. Ivanova, V. Lunin, S. Kulikova, N. Huazheva, S. Chernysh, E. Arshanskaya, M. Pochtar, A. Tlevtsezheva, S. Minenko, I. Lasarev, O. Kudriavtseva, L. Rybkina, E. Tihonova, A. Rumiantsev
Journal: Annals of Oncology (2014)