tbuckley/cabot-search huggingface dataset:
MatchMiner: a tool for batch navigation among gene and gene product identifiers
Authors: Kimberly J Bussey, David Kane, Margot Sunshine, Sudar Narasimhan, Satoshi Nishizuka, William C Reinhold, Barry Zeeberg, None Ajay, John N Weinstein
Journal: Genome biology (2003)

MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research. The user inputs a list of gene identifiers and then uses the Merge function to find the overlap with a second list of identifiers of either the same or a different type or uses the LookUp function to find corresponding identifiers.
Establishment of an orthotopic tumour model for hepatocellular carcinoma and non-invasive in vivo tumour imaging by high resolution ultrasound in mice
Authors: Volker Schmitz, Lucia Tirado-Ledo, Klaus Tiemann, Esther Raskopf, Thomas Heinicke, Carsten Ziske, Maria A González-Carmona, Christian Rabe, Nicolas Wernert, Jesús Prieto, Cheng Qian, Tilman Sauerbruch, Wolfgang H Caselmann
Journal: Journal of Hepatology (2004)
Targeted Deletion of Angiotensin II Type 2 Receptor Caused Cardiac Rupture After Acute Myocardial Infarction
Authors: Sahoko Ichihara, Takaaki Senbonmatsu, Edward Price, Toshihiro Ichiki, F. Andrew Gaffney, Tadashi Inagami
Journal: Circulation (2002)

Background— Accumulating evidence has suggested that the cardiac renin-angiotensin system is activated during the remodeling process after myocardial infarction (MI). Although 2 types of angiotensin II receptors (AT 1 and AT 2 ) are upregulated in the infarcted tissue, the contribution of AT 2 to the subsequent fibrogenetic phase of wound healing is less certain. This study was conducted to evaluate the role of AT 2 in wound healing after MI using an in vivo intervention study in mice with MI. Methods and Results— We examined myocardial hypertrophy, cardiac fibrosis, and morphological evidence of fibrillar collagen accumulation at the infarcted and noninfarcted regions in male mice lacking the AT 2 receptor ( Agtr 2−/Y) and age-matched wild-type (WT) animals. Of the Agtr 2−/Y mice, 63.6% died of cardiac rupture, whereas 23.5% of the WT mice died of the same cause within 1 week. The extent of fibrosis and that of collagen gene expression in Agtr 2−/Y mice were significantly reduced compared with WT mice at 1 week after coronary ligation. Furthermore, MI resulted in a marked increase in the prostaglandin E 2 (PGE 2 ) level at 4 days after surgery in Agtr 2−/Y mice. In WT mice, the PGE 2 level was also elevated after MI but to a significantly lesser extent than in Agtr 2−/Y mice. Conclusions— A chronic loss of AT 2 by gene targeting prevented the collagen deposition and caused cardiac rupture. The markedly elevated PGE 2 may be a mechanism that inhibits collagen synthesis in the infarcted region of Agtr 2−/Y mice.
Inclusion of Educational Messages in Laboratory Reports Aids to Complete the Diagnostic Workup of Hyperglycemia
Authors: José Pérez-Jáuregui, Ana María González-Cardel, Gabriela Olay-Fuentes, Alfredo Reza-Albarrán, Roopa Mehta, Carlos A. Aguilar-Salinas
Journal: Diabetes Care (2008)

OBJECTIVE—To evaluate whether educational messages regarding oral glucose tolerance test (OGTT) indications in laboratory reports increase the number of OGTTs appropriately requested. RESEARCH DESIGN AND METHODS—The following message was printed on the lab reports of individuals with a fasting plasma glucose (FPG) concentration between 5.5 and 6.9 mmol/l: “A FPG between 5.5 and 6.9 mmol/l is considered abnormal by the American Diabetes Association (impaired fasting glucose). An OGTT is recommended if the patient does not have a diagnosis of diabetes and suffers from conditions associated with an increased risk for having type 2 diabetes (i.e., overweight, high blood pressure, abnormal plasma lipids or family history of diabetes).” The number of educational messages printed was 81,099. RESULTS—The intervention resulted in a significant increase in the number of OGTTs requested, from 78 ± 19 to 268 ± 48 tests per month. It also resulted in a greater proportion of case subjects that had an abnormal OGTT result. CONCLUSIONS—Educational messages in laboratory reports aid in the diagnostic workup of hyperglycemia.
Independent degeneration of photoreceptors and retinal pigment epithelium in conditional knockout mouse models of choroideremia
Authors: T. Tolmachova
Journal: Journal of Clinical Investigation (2006)

Choroideremia (CHM) is an X-linked degeneration of the retinal pigment epithelium (RPE), photoreceptors, and choroid, caused by loss of function of the CHM/REP1 gene. REP1 is involved in lipid modification (prenylation) of Rab GTPases, key regulators of intracellular vesicular transport and organelle dynamics. To study the pathogenesis of CHM and to develop a model for assessing gene therapy, we have created a conditional mouse knockout of the Chm gene. Heterozygous-null females exhibit characteristic hallmarks of CHM: progressive degeneration of the photoreceptors, patchy depigmentation of the RPE, and Rab prenylation defects. Using tamoxifen-inducible and tissue-specific Cre expression in combination with floxed Chm alleles, we show that CHM pathogenesis involves independently triggered degeneration of photoreceptors and the RPE, associated with different subsets of defective Rabs.
School Bullying: Development and Some Important Challenges
Authors: Dan Olweus
Journal: Annual Review of Clinical Psychology (2013)

After sketching how my own interest and research into bullying problems began, I address a number of potentially controversial issues related to the definition and measurement of such problems. The importance of maintaining the distinctions between bullying victimization and general victimization and between bullying perpetration and general aggression is strongly emphasized. There are particular problems with the common method of peer nominations for purposes of prevalence estimation, comparisons of such estimates and mean levels across groups and time, and measurement of change. Two large-scale projects with time series data show that several recent claims about cyber bullying made in the media and by some researchers are greatly exaggerated and lack scientific support. Recent meta-analyses of the long-term outcomes for former bullies and victims provide convincing evidence that being involved in such problems is not just a harmless and passing school problem but something that has serious adjustment and public health consequences that also entail great costs to society. Another section presents my view of why the theme of bullying took quite some time to reach the peer relations research community in the United States and the role of a dominant research tradition focusing on "likeability" in this account. In a final section, I summarize some reasons why it may be considered important and interesting to focus both research and intervention on bully/victim problems.
Single embryo transfer and IVF/ICSI outcome: a balanced appraisal
Authors: Jan M.R. Gerris
Journal: Human Reproduction Update (2004)

This review considers the value of single embryo transfer (SET) to prevent multiple pregnancies (MP) after IVF/ICSI. The incidence of MP (twins and higher order pregnancies) after IVF/ICSI is much higher (approximately 30%) than after natural conception (approximately 1%). Approximately half of all the neonates are multiples. The obstetric, neonatal and long-term consequences for the health of these children are enormous and costs incurred extremely high. Judicious SET is the only method to decrease this epidemic of iatrogenic multiple gestations. Clinical trials have shown that programmes with >50% of SET maintain high overall ongoing pregnancy rates ( approximately 30% per started cycle) while reducing the MP rate to <10%. Experience with SET remains largely European although the need to reduce MP is accepted worldwide. An important issue is how to select patients suitable for SET and embryos with a high putative implantation potential. The typical patient suitable for SET is young (aged <36 years) and in her first or second IVF/ICSI trial. Embryo selection is performed using one or a combination of embryo characteristics. Available evidence suggests that, for the overall population, day 3 and day 5 selection yield similar results but better than zygote selection results. Prospective studies correlating embryo characteristics with documented implantation potential, utilizing databases of individual embryos, are needed. The application of SET should be supported by other measures: reimbursement of IVF/ICSI (earned back by reducing costs), optimized cryopreservation to augment cumulative pregnancy rates per oocyte harvest and a standardized format for reporting results. To make SET the standard of care in the appropriate target group, there is a need for more clinical studies, for intensive counselling of patients, and for an increased sense of responsibility in patients, health care providers and health insurers.
Efficacy of the World Health Organization Analgesic Ladder to Treat Pain in End-Stage Renal Disease
Authors: Ahmad S. Barakzoy, Alvin H. Moss
Journal: Journal of the American Society of Nephrology (2006)

Pain is the one of the most common symptoms experienced by patients with ESRD; it impairs their quality of life and is undertreated. Most pain clinicians believe that the pain management approach of the World Health Organization (WHO) three-step analgesic ladder is applicable to the treatment of patients with ESRD, but this approach has not been validated for them. A cohort of 45 hemodialysis patients were assessed for type and severity of pain using the Short-Form McGill Pain Questionnaire and then treated during a 4-wk period according to the WHO analgesic ladder. Mean age was 65 +/- 12.5 yr, and 22 (49%) patients had diabetic nephropathy as the cause of ESRD. Initial pain was rated severe by 34 (76%) patients. There was no difference in initial pain rating by gender, age, race, or type of pain. Forty percent of patients reported nociceptive pain, 31% neuropathic, and 29% both. Adequate analgesia was achieved in 43 (96%) of 45 patients. The mean pain score decreased from 7.8 +/- 1.2 to 1.6 +/- 1.3 (P < 0.001). Patients who were 65 yr and older had higher posttreatment scores than those who were younger than 65 (2.1 +/- 1.4 versus 0.94 +/- 0.93; P = 0.002) and more medication adverse effects. It is concluded that the use of the WHO three-step analgesic ladder leads to effective pain relief in hemodialysis patients. Older patients will need more careful pain management to achieve the same results as younger patients. Further studies are needed to confirm these results in a larger, more diverse dialysis population.
Physical activity promotion in primary care has a sustained influence on activity levels of sedentary adults: Table 1
Authors: Christopher M Williams, Nicole Nathan, Luke Wolfenden
Journal: British Journal of Sports Medicine (2013)

▸ Orrow G, Kinmonth A, Sanderson S, Sutton S. Effectiveness of physical activity promotion based in primary care: systematic review and meta-analysis of randomised controlled trials. BMJ 2012;344:e1389

Despite the well-established benefits of physical activity (PA) a large proportion of people in developed countries still lead sedentary lifestyles.1 Community-based interventions can improve PA levels of sedentary individuals, but improvements are inconsistently sustained.2–4 Primary care may play an important role in facilitating sustained regular PA through direct intervention or via referral to other programmes as many people routinely access primary care.

This systematic review aimed to determine whether the promotion of PA in primary care had a sustained effect on PA or fitness levels in sedentary adults; and whether referral interventions were more effective than other interventions.

Studies were identified through searches of seven electronic databases, reference lists of relevant articles and previous systematic reviews, and contact with an independent expert. Eligible studies were randomised controlled trials recruiting adult patients (16 years and above) through primary care for any PA promotion intervention with a goal to increase activity or fitness level (or both) in patients. The minimum follow-up was 12 months after randomisation. Studies of multifactorial …
Breast Cancer After Treatment of Hodgkin's Disease
Authors: S. L. Hancock, M. A. Tucker, R. T. Hoppe
Journal: JNCI Journal of the National Cancer Institute (1993)

Most studies of survivors of Hodgkin's disease have shown a low risk for subsequent breast cancer, even though much lower doses of radiation than those used for Hodgkin's disease have been shown to induce breast cancer in other settings.This study quantifies the risk of breast cancer following Hodgkin's disease treatment according to age at treatment and type of treatment.To evaluate the risk of breast cancer from irradiation, we reviewed records of 885 women treated for Hodgkin's disease between 1961 and 1990 (mean follow-up, 10 years). Risks for breast cancer incidence and mortality were calculated by comparison with expected rates for a general female population matched by age and race.Twenty-five patients have developed invasive breast cancer, yielding a relative risk (RR) of 4.1 (95% confidence interval [CI] = 2.5-5.7). An additional patient developed multifocal carcinoma in situ. Age at irradiation strongly influenced risk: RR was 136 for women treated before 15 years of age (95% CI = 34-371). RR declined with age at irradiation (P for trend < .0001), but the elevation remained statistically significant for subjects less than 30 years old at the time of irradiation (for those 15-24, RR = 19 [95% CI = 10.3-32]; for those 24-29, RR = 7 [95% CI = 3.2-14.4]). In women above 30 years of age, the risk was not elevated (RR = 0.7; 95% CI = 0.2-1.8). Risk of breast cancer increased significantly with time since treatment (P for trend < .0001). The RR was 2.0 (95% CI = 1.0-3.5) with follow-up under 15 years and 13.6 (95% CI = 7.9-18.2) with follow-up equal to or exceeding 15 years. The addition of mechlorethamine, vincristine, procarbazine, and prednisone chemotherapy to irradiation increased the risk within the first 15 years. Most breast cancers (22 of 26) arose within or at the margin of the radiation field and were infiltrating ductal carcinomas. Stage distribution and outcome suggest that the increased incidence was not solely attributable to vigilant screening. RR of death from breast cancer was 5.1 (95% CI = 2.2-10.0).Women treated for Hodgkin's disease with radiation before 30 years of age are at markedly increased risk for breast cancer, with risk increasing dramatically more than 15 years after therapy.The high RR for development of breast cancer in women exposed to therapeutic radiation under 30 years of age raises important issues about optimal treatment strategies for patients with Hodgkin's disease, breast cancer, and other cancers.
Conditional Expression of the CTCF-Paralogous Transcriptional Factor BORIS in Normal Cells Results in Demethylation and Derepression of MAGE-A1 and Reactivation of Other Cancer-Testis Genes
Authors: Sergei Vatolin, Ziedulla Abdullaev, Svetlana D. Pack, Patrick T. Flanagan, Mary Custer, Dmitri I. Loukinov, Elena Pugacheva, Julie A. Hong, Herbert Morse, David S. Schrump, John I. Risinger, J. Carl Barrett, Victor V. Lobanenkov
Journal: Cancer Research (2005)

Brother of the Regulator of Imprinted Sites (BORIS) is a mammalian CTCF paralog with the same central 11Zn fingers (11ZF) that mediate specific interactions with varying approximately 50-bp target sites. Regulated in vivo occupancy of such sites may yield structurally and functionally distinct CTCF/DNA complexes involved in various aspects of gene regulation, including epigenetic control of gene imprinting and X chromosome inactivation. The latter functions are mediated by meCpG-sensitive 11ZF binding. Because CTCF is normally present in all somatic cells, whereas BORIS is active only in CTCF- and 5-methylcytosine-deficient adult male germ cells, switching DNA occupancy from CTCF to BORIS was suggested to regulate site specificity and timing of epigenetic reprogramming. In addition to 11ZF-binding paternal imprinting control regions, cancer-testis gene promoters also undergo remethylation during CTCF/BORIS switching in germ cells. Only promoters of cancer testis genes are normally silenced in all somatic cells but activated during spermatogenesis when demethylated in BORIS-positive germ cells and are found aberrantly derepressed in various tumors. We show here that BORIS is also expressed in multiple cancers and is thus itself a cancer-testis gene and that conditional expression of BORIS in normal fibroblasts activates cancer-testis genes selectively. We tested if replacement of CTCF by BORIS on regulatory DNA occurs in vivo on activation of a prototype cancer-testis gene, MAGE-A1. Transition from a hypermethylated/silenced to a hypomethylated/activated status induced in normal cells by 5-aza-2'-deoxycytidine (5-azadC) was mimicked by conditional input of BORIS and is associated with complete switching from CTCF to BORIS occupancy at a single 11ZF target. This site manifested a novel type of CTCF/BORIS 11ZF binding insensitive to CpG methylation. Whereas 5-azadC induction of BORIS takes only few hours, derepression of MAGE-A1 occurred 1 to 2 days later, suggesting that BORIS mediates cancer-testis gene activation by 5-azadC. Indeed, infection of normal fibroblasts with anti-BORIS short hairpin RNA retroviruses before treatment with 5-azadC blocked reactivation of MAGE-A1. We suggest that BORIS is likely tethering epigenetic machinery to a novel class of CTCF/BORIS 11ZF target sequences that mediate induction of cancer-testis genes.
Intramyocardial VEGF-B <sub>167</sub> Gene Delivery Delays the Progression Towards Congestive Failure in Dogs With Pacing-Induced Dilated Cardiomyopathy
Authors: Martino Pepe, Mohammed Mamdani, Lorena Zentilin, Anna Csiszar, Khaled Qanud, Serena Zacchigna, Zoltan Ungvari, Uday Puligadda, Silvia Moimas, Xiaobin Xu, John G. Edwards, Thomas H. Hintze, Mauro Giacca, Fabio A. Recchia
Journal: Circulation Research (2010)

Vascular endothelial growth factor (VEGF)-B selectively binds VEGF receptor (VEGFR)-1, a receptor that does not mediate angiogenesis, and is emerging as a major cytoprotective factor.To test the hypothesis that VEGF-B exerts non-angiogenesis-related cardioprotective effects in nonischemic dilated cardiomyopathy.AAV-9-carried VEGF-B(167) cDNA (10(12) genome copies) was injected into the myocardium of chronically instrumented dogs developing tachypacing-induced dilated cardiomyopathy. After 4 weeks of pacing, green fluorescent protein-transduced dogs (AAV-control, n=8) were in overt congestive heart failure, whereas the VEGF-B-transduced (AAV-VEGF-B, n=8) were still in a well-compensated state, with physiological arterial Po(2). Left ventricular (LV) end-diastolic pressure in AAV-VEGF-B and AAV-control was, respectively, 15.0+/-1.5 versus 26.7+/-1.8 mm Hg and LV regional fractional shortening was 9.4+/-1.6% versus 3.0+/-0.6% (all P<0.05). VEGF-B prevented LV wall thinning but did not induce cardiac hypertrophy and did not affect the density of alpha-smooth muscle actin-positive microvessels, whereas it normalized TUNEL-positive cardiomyocytes and caspase-9 and -3 activation. Consistently, activated Akt, a major negative regulator of apoptosis, was superphysiological in AAV-VEGF-B, whereas the proapoptotic intracellular mediators glycogen synthase kinase (GSK)-3beta and FoxO3a (Akt targets) were activated in AAV-control, but not in AAV-VEGF-B. Cardiac VEGFR-1 expression was reduced 4-fold in all paced dogs, suggesting that exogenous VEGF-B(167) exerted a compensatory receptor stimulation. The cytoprotective effects of VEGF-B(167) were further elucidated in cultured rat neonatal cardiomyocytes exposed to 10(-8) mol/L angiotensin II: VEGF-B(167) prevented oxidative stress, loss of mitochondrial membrane potential, and, consequently, apoptosis.We determined a novel, angiogenesis-unrelated cardioprotective effect of VEGF-B(167) in nonischemic dilated cardiomyopathy, which limits apoptotic cell loss and delays the progression toward failure.
Increased Shear Rate Resistance and Fastest Kinetics of Erythrocyte Aggregation in Diabetes Measured With Ultrasound
Authors: Guy Cloutier, Audrey Zimmer, François T.H. Yu, Jean-Louis Chiasson
Journal: Diabetes Care (2008)

To measure with ultrasound the increased erythrocyte aggregation (EA) kinetics and adhesion energy between erythrocytes in patients with type 2 diabetes and poor metabolic control.Blood samples were analyzed in a Couette rheometer at 32 MHz following shear rate reductions from 500 s(-1) to residual shears of 0 (stasis), 1, 2, 10, 50, 100, and 200 s(-1). The increase in EA was determined with the integrated backscatter coefficient as a function of time and shear rate.The time required to form aggregates was shorter in diabetic patients at shear rates below 200 s(-1) (P < 0.01). Erythrocytes formed larger aggregates in diabetic patients than in control subjects (P < 0.05 at 2 to 100 s(-1)).Ultrasound can potentially noninvasively demonstrate, in vivo and in situ, the impact of local abnormal EA on arteriovenous flow disorders in diabetes.
Predictors of Viridans Streptococcal Shock Syndrome in Bacteremic Children With Cancer and Stem-Cell Transplant Recipients
Authors: Adam Gassas, Ronald Grant, Susan Richardson, L. Lee Dupuis, John Doyle, Upton Allen, Oussama Abla, Lillian Sung
Journal: Journal of Clinical Oncology (2004)

To describe episodes of viridans streptococcal bacteremia (VSB) in a cohort of children with cancer and stem-cell transplant (SCT) recipients and to determine predictors of viridans streptococcal shock syndrome (VSSS) in this group of children.For this retrospective review, we included episodes of VSB isolated between March 1997 and September 2002, in children (<or= 18 years) with a diagnosis of cancer or SCT patients. The primary outcome was VSSS, defined as hypotension requiring intravascular volume expansion or inotropic support and/or respiratory insufficiency necessitating assisted ventilation.Eighty-eight episodes of VSB occurred in 79 children. The mean age of the children was 6.7 years (range, 0.6 to 18.0 years). The most common underlying diagnosis was acute myelogenous leukemia (AML) in 31 (35%) of 88 episodes, and 38 (43%) of 88 had undergone SCT. VSSS occurred in 16 (18%) of 88 episodes, and two children died from VSSS. Two variables were predictive of VSSS, namely peak temperature at presentation (odds ratio [OR], 6.3; 95% CI, 2.1 to 19.0; P =.001) and inpatient status (OR, 5.9; 95% CI, 1.3 to 28.0; P =.02). Diagnosis of AML (OR, 1.1; 95% CI, 0.4 to 3.5; P =.8), receipt of SCT (OR, 1.9; 95% CI, 0.6 to 5.7; P =.2), high-dose cytarabine (OR, 0.6; 95% CI, 0.1 to 3.2; P =.6), and mucositis (OR, 0.8; 95% CI, 0.3 to 2.6; P =.7) were not predictive of VSSS.VSSS occurred in 18% of episodes of VSB in children with cancer or SCT recipients. Peak temperature before antibiotic therapy and inpatient status were predictive of VSSS.