tbuckley/cabot-search huggingface dataset:
Abstract 4851: A single-tube protocol for next gen library construction increases complexity and simplifies parallel sample handling
Authors: Kyusung Park, Xiaoping Duan, Rhonda Meredith, Jennifer M. Kilzer, Eric White, Delia Ye, Cisilya Duncan, Tanya Sokolsky, Adam N. Harris, Rob Bennett
Journal: Cancer Research (2011)

Abstract With the advent of second-generation sequencing technologies, exome- and transcriptome- and whole genome sequencing are tools of choice in studying cancer to detect alterations in the genome correlating with tumorigenesis. It is essential to compare genomic alterations in cancer with matched normal DNA from the same individual largely due to incomplete knowledge of the “normal” variations. There have been concerted efforts for targeted sequencing of cancer-related exomes in a high throughput manner. However, the needs to process multiple samples simultaneously while maintaining the complexity of libraries have not been addressed adequately. Fragment library generation for single- and paired-end reads is typically performed by a series of enzymatic steps following gDNA shearing by ultrasonication. These may include end-repair, A-tailing, and ligation, each followed by bead- or column-based purification. The clean-ups are necessary to prevent enzyme activity carryover from one step to another. We have developed a single-tube method to take sheared, bead size-selected DNA through end-repair, A-tailing, and ligation without intermittent purifications. The A-tailing is done by a thermophilic polymerase at a temperature sufficient to denature the end-repair enzymes. Ligation is performed by adding ligase and adaptors after cooling the reaction. A bead- or column-based purification is then performed after the ligation reaction to produce template for amplification. With the removal of the clean-up steps, the workflow is simplified, allowing faster processing of samples with less hands-on time. We also reduce loss of sample associated with the purifications, increasing the complexity of the output library or enabling a lower sample input concentration. Our method is well suited for labs which are producing multiple libraries each week but have not scaled up to full automation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4851. doi:10.1158/1538-7445.AM2011-4851
Retroversion of the Gravid Uterus
Authors: T. Skinner
Journal: BMJ (1860)

RETROVERSION OF THE GRAVID UTERUS.The subject of retroversion of the gravid uterus is ?ne of great importance, and one of sufficiently frequent occurrence to be of interest to all.The symptoms produced by this condition are not as a rule clearly marked until either abortion is threatened 0r retention of urine occurs.When abortion is threatened, or actually occurs, it is caused not so much by the uterine displacement as by an endo- metritis, which often accompanies backward dis- placements of the uterus.Moreover, abortion occurs 111 these cases as a rule within the first two months,
Insulin resistance and depression
Authors: Markku Timonen, Ulla Rajala, Mauri Laakso, Jari Jokelainen
Journal: BMJ (2005)

Managing chronic diseases Palliative care spectrum starts early onEditor-Palliative care does not start when a patient is dying. 1 A whole spectrum of palliation begins from the day of diagnosis of a potentially terminal disease, such as soft tissue sarcoma.Palliation, in the sense of needing to absorb what this means for the patient, becomes even then a medical imperative.The "How long have I got, Doc?" question may not be articulated, but it will be there and needs an empathetic response.Curative treatment is sought, but-with sarcoma-lung metastases signal the end of that phase and the beginning of palliative treatment.The doctor and the patient know the dragon can be disabled but never slain.Palliation is then partnership, working to decide what may be gained at what cost.(This may apply during curative treatment: to take chemotherapy drugs now "just in case," or to keep them for later?)Palliative treatment can be long (in sarcoma up to 20 years or more), or it can be brief.Its ending is not solely a medical judgment.Doctors may decide they can do no more, but active patients use online support groups, seeking new treatment options across the world.Patients may decide to end palliative treatment.Grown weary of painful chemotherapy offering diminishing returns, they may prefer a shorter but better life.Making that choice together is an aspect of palliation.When death is near, palliative care becomes terminal care.If throughout doctors and patients have aligned their understanding of the disease, and have taken decisions jointly, have explored the holistic meaning of disease in life and death, the palliative spectrum may offer healing if not cure.If, however, being palliative begins only when the patient is dying doctors cannot then meet patients, where they are most needed, in the ground of their being and their not being.
Muscle Pain After Administration of Succinylcholine
Authors: W. Curtis Pearcy
Journal: JAMA (1960)

An incidence of muscle pain as high as 90% has been reported after the use of succinylcholine as a relaxant in surgical patients. In the present study the incidence was determined in a total of more than 400 patients. The succinylcholine was administered intravenously, usually in a single rapid injection. Doses ranged from 10 to 100 mg. A statistically significant, though small, incidence of 6% was observed. The incidence was not significantly higher among patients receiving the larger doses. The difficulty of distinguishing muscle pain that might be induced by the relaxant from other types of postoperative pain was recognized. It is concluded that the use of succinylcholine is associated with a small but definite incidence of postoperative muscle pain.
Bovine spongiform encephalopathy: is it an autoimmune disease due to bacteria showing molecular mimicry with brain antigens?
Authors: A Ebringer, C Thorpe, J Pirt, C Wilson, P Cunningham, C Ettelaie
Journal: Environmental Health Perspectives (1997)

Bovine spongiform encephalopathy (BSE) could be an autoimmune disease produced following exposure of cattle to feedstuffs containing bacteria showing molecular mimicry between bacterial components and bovine tissue. Analysis of molecular sequence databases (Genbank and SwissProt) shows that three bacteria (Acinetobacter calcoaceticus,Ruminococcus albus, and Agrobacter tumefaciens) share sequences with the encephalitogenic peptide of bovine myelin, while three molecules in Escherichia coli show molecular mimicry with host-encoded prion protein. Immune responses against these bacteria at both T and B cell levels may cause neurological tissue injury resembling BSE. The role of these bacteria in BSE, if any, merits further investigation.
The Anti-apoptotic and pro-proliferative p53-related DN-p73 protein is expressed in human HCC
Authors: Emanuele Palescandolo, Antonio Costanzo, Stefania Vossio, Natalia Pediconi, Paola Merlo, Cristiana Almerighi, Marcella Fulco, Elisabetta Cariani, Clara Balsano, Massimo Levrero
Journal: Journal of Hepatology (2002)
Human immunodeficiency virus among people who inject drugs: Is risk increasing in Europe?
Authors: D Hedrich, E Kalamara, O Sfetcu, A Pharris, A Noor, L Wiessing, V Hope, M Van de Laar
Journal: Eurosurveillance (2013)

In most European Union (EU)/European Economic Area (EEA) countries, between 2010 and 2012, reports of new human immunodeficiency virus (HIV) diagnoses among people who inject drugs have been stable or declining. HIV outbreaks in Greece and Romania, first reported in 2011, continue and economic conditions hinder provision of effective response coverage. When measured against some established thresholds, prevention coverage remains inadequate in at least one-third of EU/EEA countries. Urgent consideration to scale up prevention efforts is merited.
Technical Assault and Battery
Authors: Neil L. Chayet
Journal: New England Journal of Medicine (1967)

THE two most prevalent legal actions brought against physicians are those in which the issue is negligence (malpractice) and those involving the question of consent.In the negligence or malpractice case the issue is whether or not the physician acted with less skill than the prudent physician practicing in the same or a similar community. In most cases this means that another physician must testify that the defendant did in fact practice below that standard of care.When the physician proceeds without proper consent, the law terms his action "technical assault and battery." All that the patient need prove is . . .
Long-Term (52-Week) Treatment With Beclomethasone Dipropionate Hydrofluoroalkane Nasal Aerosol (320 mcg Once Daily) Is Safe and Effective in Adult and Adolescent Subjects With Perennial Allergic Rhinitis
Authors: A.S. Nayak, C.P. Andrews, D.I. Bernstein, P.M. Dorinsky, A. Tankelevich, Y. Ding, S.K. Tantry
Journal: Journal of Allergy and Clinical Immunology (2012)
Two doctors die from Ebola and lives of others under threat in West Africa
Authors: I. Torjesen
Journal: BMJ (2014)

The risks to doctors while caring for patients in the outbreak of Ebola virus disease in west Africa became increasingly apparent this week when it was confirmed that a second doctor had died from the virus in a month and that at least two others had been infected.

The World Medical Association has warned that poor care practices were putting doctors’ lives at risk in what has become the world’s worst recorded outbreak of the disease. Reports have also emerged that doctors and officials trying to get to some villages in affected areas have been threatened by frightened local people doing all they can to keep outsiders and potential carriers of the virus out. Some communities are blaming aid agencies for spreading the virus and turning to traditional medicine rather than sending people with suspected cases to official Ebola clinics.

The present outbreak began in Guinea in February and spread to neighbouring Liberia and Sierra Leone. As at 23 July at least 1200 people were …
Christmas with the Millstones
Authors: N. Sharp
Journal: BMJ (2003)

![][1] 

“It has not been a good year,” said Martha Millstone. “Nothing has gone right since that man from CHI found a dead body in the evidence base room.”

“We're trying to have a nice family Christmas, dear,” said David Millstone. He pushed a purple paper crown on to his head.

“Then tell me what that woman is doing here.” Martha pointed at Janet Pringle.

“I know when I'm not wanted.” Janet got up and took off her silver paper hat. It caught on one of her snowman earrings.

“I invited Janet because she is Douglas's friend,” said David, “and I want her to stay.”

“She is a floozy and a topless model,” said Martha.

“I've given up the topless modelling, now that I've paid off my student loan,” said Janet.

“Have you?” asked Douglas Millstone. He sounded pleased.

“She's a full time GP trainee now,” said David, “and we're very pleased to have her at Murkton Moor.”

“I wouldn't have invited him.” Martha pointed at Douglas.

“Douglas is our son,” said David.

“I knew I shouldn't have come,” said Douglas.

“Everyone sit down and eat,” said David. “The turkey's getting cold.”

“The third person I didn't invite is you.” Martha pointed her fork at James Fatterley. “You're not even family.”

“James is a family friend and valued colleague,” said David.

“He's a lousy chief executive. He suspended me, and he's trying to close down the hospital,” said Martha. “Now he's given me the impossible choice: save the hospital or return to work.”

   ![][2] 

Janet Pringle

“He's only doing his job,” said David. “I think we should all eat, drink, and be merry. It is Christmas.”

“Something is wrong,” said Martha.

“Nonsense, dear, the turkey looks fine. There are roast potato, mashed potato, sausages, bacon, sprouts, carrots, parsnips, stuffing—”

“We're all here,” …

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 [2]: /embed/graphic-2.gif
The lack of long-range negative correlations in glucose dynamics is associated with worse glucose control in patients with diabetes mellitus
Authors: Hitomi Ogata, Kumpei Tokuyama, Shoichiro Nagasaka, Takeshi Tsuchita, Ikuyo Kusaka, Shun Ishibashi, Hiroaki Suzuki, Nobuhiro Yamada, Kumiko Hamano, Ken Kiyono, Zbigniew R. Struzik, Yoshiharu Yamamoto
Journal: Metabolism (2012)
Relationship between the increase in Ca2+ transient and contractile force induced by angiotensin II in aequorin-loaded rabbit ventricular myocardium
Authors: A Watanabe
Journal: Cardiovascular Research (1998)

Objectives: Pieces of evidence have been accumulating that imply a crucial role of angiotensin II (Ang II) in initiation and progress of heart failure, but the signalling processes subsequent to Ang II receptor activation in cardiac myocytes are complex and still controversial. We examined the effects of Ang II on the relationship between the intracellular Ca2+ transient and isometric contraction in mammalian ventricular myocardium. Methods: Isolated rabbit ventricular papillary muscle was loaded with the Ca2+ sensitive bioluminescent protein aequorin and electrically stimulated at a rate of 0.5 Hz at 37°C. Results: Ang II (10−8–10−6 M), in the presence of bupranolol (3×10−7 M) and prazosin (10−7 M), elicited a positive inotropic effect (PIE) in association with an increase in the peak Ca2+ transient. The maximal PIE of Ang II was about 30% of the isoproterenol-induced maximum (ISOmax), while the maximal increase in the peak Ca2+ transient induced by Ang II was only 7% of ISOmax. Ang II tended to prolong the duration of contraction (both time to peak force and relaxation time) but did not produce a discernible change in the duration of Ca2+ transient. The relationship between the amplitude of Ca2+ transient and peak force was shifted to the left by Ang II, as compared with the relationship for elevation of [Ca2+]o (2.5–15.0 mM). The PIE and the increase in the amplitude of Ca2+ transient induced by Ang II were abolished by a selective angiotensin type 1 (AT1) receptor antagonist losartan (10−5 M) but were not affected by a selective AT2 receptor antagonist PD123319 (10−6 M). Conclusions: These results indicate that Ang II elicits a PIE through a dual mechanism via activation of AT1 receptors in rabbit ventricular myocardium: by an increase in the amplitude of Ca2+ transient; and in addition by an increase in the myofilament Ca2+ sensitivity.
Interrelationship of blood transfusion, non-A, non-B hepatitis and hepatocellular carcinoma: Analysis by detection of antibody to hepatitis C virus
Authors: Kendo Kiyosawa, Takeshi Sodeyama, Eiji Tanaka, Yukio Gibo, Kaname Yoshizawa, Yoshiyuki Nakano, Seiichi Furuta, Yoshihiro Akahane, Kusuya Nishioka, Robert H. Purcell, Harvey J. Alter
Journal: Hepatology (1990)

To clarify the relationship between hepatitis C virus infection and the development of hepatocellular carcinoma as sequelae of non-A, non-B posttransfusion hepatitis, 231 patients with chronic non-A, non-B hepatitis (96 with chronic hepatitis, 81 with cirrhosis and 54 with hepatocellular carcinoma) were analyzed for antibody to hepatitis C virus and were compared with 125 patients with chronic hepatitis B (50 with chronic hepatitis, 46 with cirrhosis and 29 with hepatocellular carcinoma). Antibody to hepatitis C virus was detected in 89.6%, 86.4% and 94.4% of patients with non-A, non-B hepatitis-related chronic hepatitis, cirrhosis and hepatocellular carcinoma, respectively, compared with 6%, 17.4% and 34.5% with similar diseases related to hepatitis B. A history of transfusion was documented in 52%, 33% and 42% of anti-hepatitis C virus-positive cases of chronic hepatitis, cirrhosis and hepatocellular carcinoma. The mean intervals between the date of transfusion and the date of diagnosis of anti-hepatitis C virus-positive chronic hepatitis, cirrhosis and hepatocellular carcinoma were 10, 21.2 and 29 yr, respectively. In 21 patients with transfusion-associated hepatocellular carcinoma, anti-hepatitis C virus was present in each serial sample available for testing, including samples obtained up to 14 yr before the diagnosis of hepatocellular carcinoma. These data suggest the slow, sequential progression from acute hepatitis C virus-related non-A, non-B hepatitis through chronic hepatitis and cirrhosis to hepatocellular carcinoma and support a causal association between hepatitis C virus and hepatocellular carcinoma.
Cancer mortality in agricultural regions of Minnesota.
Authors: D M Schreinemachers, J P Creason, V F Garry
Journal: Environmental Health Perspectives (1999)

Because of its unique geology, Minnesota can be divided into four agricultural regions: south-central region one (corn, soybeans); west-central region two (wheat, corn, soybeans); northwest region three (wheat, sugar beets, potatoes); and northeast region four (forested and urban in character). Cancer mortality (1980-1989) in agricultural regions one, two, and three was compared to region four. Using data compiled by the National Center for Health Statistics, cancer mortality was summarized by 5-year age groups, sex, race, and county. Age-standardized mortality rate ratios were calculated for white males and females for all ages combined, and for children aged 0-14. Increased mortality rate ratios and 95% confidence intervals (CIs) were observed for the following cancer sites: region one--lip (men), standardized rate ratio (SRR) = 2.70 (CI, 1.08-6.71); nasopharynx (women), SRR = 3.35 (CI, 1.20-9.31); region two--non-Hodgkin's lymphoma (women), SRR = 1.35 (CI, 1.09-1.66); and region three--prostate (men), SRR = 1.12 (CI, 1.00-1.26); thyroid (men), SRR = 2.95 (CI, 1.35-6.44); bone (men), SRR = 2.09 (CI, 1. 00-4.34); eye (women), SRR = 5.77 (CI, 1.90-17.50). Deficits of smoking-related cancers were noted. Excess cancers reported are consistent with earlier reports of agriculturally related cancers in the midwestern United States. However, reports on thyroid and bone cancer in association with agricultural pesticides are few in number. The highest use of fungicides occurs in region three. Ethylenebisdithiocarbamates, whose metabolite is a known cause of thyroid cancer in rats, are frequently applied. This report provides a rationale for evaluation of the carcinogenic potential of this suspect agent in humans.
Iliac Fossa Mass Syndrome In Hemophilia
Authors: Anthony F.H. Britten
Journal: JAMA (1970)

ABSTRACT To the Editor.— The communication by Cianci and Piscatelli (210:1100, 1969) and letter by Gilbert (211: 501, 1970) describe the complication of femoral neuropathy and retroperitoneal hemorrhage in patients taking anticoagulant drugs.Neither communication makes mention of the fact that this syndrome (inguinal pain, flexion contracture at hip, femoral nerve palsy, mass in the iliac fossa) is a common complication of hemophilia, frequently described in the medical literature. We saw five cases in 1969 amongst a group of 65 patients with hemophilia observed at this hospital. The anatomy and pathology of this interesting lesion have been fully and beautifully described by Goodfellow et al (J Bone Joint Surg49B: 748, 1967 ), a study strongly recommended to all those interested in this problem.
Cancer patients need better preparation to access good quality care in a crisis
Authors: Z. Kmietowicz
Journal: BMJ (2012)

More needs to be done to improve the care given to patients with cancer who become acutely ill, a new report concludes.

A joint working party of the Royal College of Physicians and Royal College of Radiologists said that cancer patients who became unexpectedly unwell too often received fragmented care.1 Often they were not told what to expect in terms of their illness and did not know whom to contact when their condition worsened and they needed medical attention. If they did need to be admitted to hospital, they were often seen by several healthcare professionals in many medical specialties and were often given confusing …
How to avoid complications of potent diuretics
Authors: R. H. Maffly
Journal: JAMA (1976)

EFFECTIVE use of diuretic drugs requires an understanding of the principles involved in their action. I have found that posing the following questions often will in turn clarify questions and problems raised by physicians consulting me. <h3>1. What is the goal of treating a patient with a diuretic drug?</h3> Clearly, the practical goal is improved health of your patient, but the drug itself cannot guarantee this goal. The drugs included in the term "diuretic"—as the term is ordinarily used today—directly accomplish one thing only, a decrease in the amount of sodium in the body. This decrease in total-body sodium will usually lead to decrease in the amount of water associated with sodium throughout the body and thus in loss of accumulations of extracellular fluids such as edema, ascites, and pleural effusion. The obvious corollary of this statement is that if you<i>do not</i>want to reduce the total body sodium
Changes in Bariatric Surgery Procedure Use in Michigan, 2006-2013
Authors: Bradley N. Reames, Jonathan F. Finks, Daniel Bacal, Arthur M. Carlin, Justin B. Dimick
Journal: JAMA (2014)

Bariatric surgery is the most effective therapy available for significant and sustainable weight loss in patients with morbid obesity. 1,2As a result of the increasing prevalence of obesity, improvements in perioperative safety, and expanded insurance coverage, bariatric surgery use has increased during the last decade. 3,4hanges in procedure use over time reflect emerging evidence regarding the comparative safety and effectiveness of available procedures. 1,2,5 An understanding of current trends in bariatric procedure use can inform primary care physicians counseling patients with morbid obesity who are considering surgical intervention.Although recent reports have documented an increased use of sleeve gastrectomy (SG) in certain populations, 4,6 the extent to which this procedure has supplanted other procedures, such as Roux-en-Y gastric bypass (RYGB) or laparoscopic adjustable gastric banding (LAGB), is poorly understood.Moreover, it is unclear if relative use differs within clinical subgroups that might be predicted to have better outcomes with a specific procedure.To better understand current trends in bariatric surgery use, we examined procedure rates in patients undergoing bariatric surgery in Michigan between June 2006 and
ALTERED DISTRIBUTION OF B AND T LYMPHOCYTES IN LYMPH-NODES FROM HOMOSEXUAL MEN WITH KAPOSI'S SARCOMA
Authors: RobertL. Modlin, PaulR. Meyer, ArthurJ. Ammann, ThomasH. Rea, FlorenceM. Hofman, SethA. Vaccaro, MarcusA. Conant, CliveR. Taylor
Journal: The Lancet (1983)