Mesenchymal Hamartoma of the Liver in a Late-Term Equine Fetus

Mesenchymal hamartoma of the liver is a rare congenital disorder of biliary tract development. During the necropsy of a late-term equine fetus, a markedly enlarged liver of more than two times normal weight was found. Light microscopic review revealed that the normal hepatic parenchyma had been obliterated, replaced, and expanded by abnormal bile ducts surrounded by abundant, myxoid stroma. The lesion was diagnosed as a mesenchymal hamartoma. Small portions of the liver had bridging septa of fibrosis and proliferations of small-caliber abnormal bile ducts, resembling another congenital biliary abnormality termed congenital hepatic fibrosis.

Abstract P2-09-11: Consistency of pathogenicity determinations for hereditary cancer gene mutations

Background: As the number of laboratories offering genetic tests grows, the potential for inconsistent variant classifications increases. New resources can help address this: (a) ClinVar, a rapidly growing public database of clinical variants to which many (but not all) laboratories contribute; (b) the public release of thousands of BRCA1/2 reports from Myriad Genetics through the Sharing Clinical Reports Project (SCRP), the Free the Data (FTD) initiative, and recent publications; and (c) ExAC, a greatly improved database of population allele frequencies. These complement longstanding efforts, e.g. the ENIGMA consortium. In addition, the American College of Medical Genetics (ACMG) recently updated guidelines for the interpretation of sequence variants. Using these resources, we sought to investigate the consistency of variant classifications to help inform ongoing practice.

Methods: Pathogenicity assessments for variants in hereditary cancer genes were collected from multiple sources. Among these were 15,364 BRCA1/2 submissions to ClinVar, including 5416 submissions from SCRP and 1062 from our prior work [1]. When 3 or more submissions for a variant were available, we determined a consensus interpretation requiring 2 of 3 submitters to agree (or 3 of 4, etc.) to identify outliers. For our own classifications, we established a point-based system based on the 2015 ACMG guidelines, and independently applied it to publicly available evidence of pathogenicity without regard to other labs' classifications.

Results: Initially, discordance among ClinVar submissions appears high (20-30%). However, upon investigation much of this discordance is a result of (i) research submissions to ClinVar, (ii) differences in confidence (e.g. benign vs. likely benign), (iii) older data in ClinVar, (iv) single lab outliers, and (v) nuances in the detailed structure of the ClinVar database. A careful comparison using the consensus methodology of objectively filtered ClinVar data shows high concordance between our interpretations and consensus: 95% were identical and 99% were similar (e.g. benign and likely benign were considered similar). Where consensus was not achieved (8% of variants with 3 or more independent sources) or not possible (any variant with only 2 sources), pairwise comparisons showed that few of these remaining differences (5%) were clinically significant. Also, many variants with significant discordances appeared to be particularly rare in the human population, and thus would be present in few patients. The rate of discordances with SCRP/FTD data was similar with that of other ClinVar submitters.

Conclusions: Evaluations of inter-laboratory concordance need to be done carefully to avoid over-counting differences. Laboratories generally agree on the clinical significance of the vast majority of variants. Furthermore, the inter-laboratory consensus classification is often reached using a careful implementation of the ACMG guidelines and publicly available data. Thoroughly understanding the remaining differences is challenging when the evidence used by any laboratory is not available for peer review. Detailed data and methods from this study are available for review and alternate analyses.

[1] Lincoln et al. SABCS 2014; JMD 2015.

Citation Format: Lincoln S, Nykamp K, Kobayashi Y, Yang S, Powers M, Anderson M, Monzon F, Topper S. Consistency of pathogenicity determinations for hereditary cancer gene mutations. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-11.

Adverse effects of a 10-day course of ibuprofen in Holstein calves

Nonsteroidal anti-inflammatory drugs (NSAIDs) are recommended for various conditions in cattle. Ibuprofen is an inexpensive short-acting NSAID and is readily available in liquid formulation for administration to bottle-fed calves. We compared the adverse effects of a 10-day course of ibuprofen and placebo in 16 five- to six-week-old Holstein bull calves that were being treated for experimentally induced bovine respiratory syncytial virus infection. Ibuprofen was administered as a liquid in milk replacer at 30 mg/kg divided three times daily. We found an increased prevalence of abomasal ulceration 5 of 8 in the ibuprofen compared to placebo group 2 of 6 (P = NS). There was one (1 of 8) case of mild interstitial nephritis in the ibuprofen and none (0 of 8) in the placebo group (P = NS). Renal function as measured by serum BUN and creatinine levels was not different between groups; no animal demonstrated an increase in creatinine.

Evaluation of bovine abortion cases and tissue suitability for identification of infectious agents in California diagnostic laboratory cases from 2007 to 2012

Establishing a definitive cause of bovine abortion is a challenging problem faced by veterinary practitioners and diagnosticians. Detection of an infectious or noninfectious source for abortion may facilitate interventions that mitigate future fetal loss in the herd. The purposes of this study were to identify the most common causes of bovine abortion in cases submitted to the California Animal Health and Food Safety Laboratory System, Davis (CAHFS) from 2007 to 2013 and to determine if detection of infectious pathogens differed with the fetal tissue evaluated. Records of 665 bovine abortion cases of 709 animals were reviewed for pathologic diagnoses, test methods used to identify causative conditions, and which tissues yielded successful identification of infectious agents associated with abortion. Over 58% of abortions were attributed to an infectious cause and 46.9% had an infectious agent identified. The most common infectious conditions were Epizootic Bovine Abortion (EBA) (16.2% of all fetuses), other fetal bacterial infections (14.7% of all fetuses), and Neospora caninum (9.3% of all fetuses.) The bacterium associated with EBA (currently named Pajaroellobacter abortibovis) was most commonly identified by immunohistochemistry (IHC) in lymphoid organs (thymus and spleen); N. caninum IHC was most frequently positive in brain, kidney, and placenta. In cases of pathogenic and opportunistic bacterial infections, abomasal samples yielded a significantly greater proportion of definitive aerobic culture results than lung or liver tissues. Direct fluorescent antibody test results for Bovine Viral Diarrhea Virus testing were identical between lung and kidney tissues and nearly identical (96.0%) for Bovine Herpesvirus I. Noninfectious abortive conditions included fetal stress (10.5%), dystocia (3.9%), congenital defects (3.3%), toxicological or mineral problems (1.8%), and death of the cow (1.1%). Just over 20% of the aborted fetuses had no gross or histopathological lesions to explain the abortion. This review highlights the need for submission of critical samples including abomasal contents, lymphoid tissues (thymus, spleen, and lymph nodes), and brain to maximize the diagnosticians' ability to identify causes of abortion.

Acute hepatitis C infection in HIV-negative men who have sex with men

Acute hepatitis C infection is recognized in HIV-infected men who have sex with men (MSM), but the risk in HIV-negative MSM remains unclear. We evaluated a population of MSM with acute hepatitis C. From January 2010 to May 2014, all cases of HCV antibody positive HIV-negative MSM were identified. European AIDS Network criteria were applied to determine acute infection, and 44 individuals fulfilled the criteria for acute hepatitis C. Ten were RNA negative at baseline and classed as prior spontaneous clearance. 15 (34.1%) had a previously negative HCV antibody within 1 year. 11 (25.0%) had significant elevation in ALT levels, and 18 (40.9%) were clinically diagnosed from risk exposure and history. Median age was 37 years (range 24-75). 41 (93.2%) individuals reported unprotected anal sex, 36 with (87.8%) both insertive and receptive intercourse, 4 (9.8%) with receptive intercourse, 1 (2.4%) with insertive intercourse, and no data were recorded for 3 (7.3%) patients. Individuals had an average of 7.3 reported (median 2, range 1-100) partners. 12 (27.3%) engaged in group sex, 11 (25.0%) practised fisting, 11 (25.0%) admitted using drugs during sexual activity, 16 (36.4%) reported nasal, and 9 (20.5%) reported injection drug use. 14 (31.8)% had unprotected sex whilst under the influence of recreational drugs. 29 individuals were aware of a partner's status. 2 (4.5%) individuals had sexual contact with a known HCV monoinfected partner, 13 (29.5%) with a HIV monoinfected partner and 6 (13.6%) with a HCV/HIV coinfected partner. 9 (20.5%) reported a partner/partners with no known infection. No data were available in 14 (31.8%) individuals. 13 (29.5%) individuals had a coexisting STI at the time of acute HCV diagnosis. 8 (18.2%) received HIV postexposure prophylaxis (PEP) within the 6 months prior to the HCV diagnosis (2 were participants in a HIV pre-exposure prophylaxis trial). 15 (34.1%) individuals achieved spontaneous clearance of HCV, and 11 patients received HCV treatment. Similar to the ongoing epidemic of acute HCV infection in HIV+ MSM, HIV-negative MSM remain at risk.

A procedural check list for pleural decompression and intercostal catheter insertion for adult major trauma

BACKGROUND

Intercostal catheter (ICC) insertion is the standard pleural decompression and drainage technique for blunt and penetrating traumatic injury. Potentially high complication rates are associated with the procedure, with the literature quoting over 20% in some cases (1-4). Empyema in particular is a serious complication. Risk adverse industries such as the airline industry and military services regularly employ checklists to standardise performance and decrease human errors. The use of checklists in medical practice is exemplified by introduction of the WHO Surgical Safety checklist.

METHODS

The Alfred Hospital in Melbourne, Australia is an Adult Level 1 Trauma Centre. In August 2009 The Alfred Trauma Service introduced an evidence-based checklist system for the insertion of ICCs, combined with standardised formal training for resident medical staff, in an attempt to minimise the incidence of ICC related empyema.

RESULTS

Between January 2003 and July 2009 the incidence of empyema was 1.44% (29 in 2009 insertions). This decreased to 0.57% between August 2009 and December 2011 (6 in 1060 insertions) when the measures described above were introduced [p=0.038 Fisher's exact test, 2-tailed].

CONCLUSION

Quality control checklists - such as the ICC checklist described - are a sensible and functional means to standardise practice, to decrease procedural error and to reduce complication rates during trauma resuscitation.

Aleutian Disease: An Emerging Disease in Free-Ranging Striped Skunks (Mephitis mephitis) From California

Aleutian disease virus (ADV, Amdovirus, Parvoviridae) primarily infects farmed mustelids (mink and ferrets) but also other fur-bearing animals and humans. Three Aleutian disease (AD) cases have been described in captive striped skunks; however, little is known about the relevance of AD in free-ranging carnivores. This work describes the pathological findings and temporospatial distribution in 7 cases of AD in free-ranging striped skunks. All cases showed neurologic disease and were found in a 46-month period (2010-2013) within a localized geographical region in California. Lesions included multisystemic plasmacytic and lymphocytic inflammation (ie, interstitial nephritis, myocarditis, hepatitis, meningoencephalitis, pneumonia, and splenitis), glomerulonephritis, arteritis with or without fibrinoid necrosis in several organs (ie, kidney, heart, brain, and spleen), splenomegaly, ascites/hydrothorax, and/or encephalomalacia with cerebral microangiopathy. ADV infection was confirmed in all cases by specific polymerase chain reaction and/or in situ hybridization. The results suggest that AD is an emerging disease in free-ranging striped skunks in California.

Organic cleanliness of the Mars Science Laboratory sample transfer chain

One of the primary science goals of the Mars Science Laboratory (MSL) Rover, Curiosity, is the detection of organics in Mars rock and regolith. To achieve this, the Curiosity rover includes a robotic sampling system that acquires rock and regolith samples and delivers it to the Sample Analysis at Mars (SAM) instrument on board the rover. In order to provide confidence that any significant organics detection result was Martian and not terrestrial in origin, a requirement was levied on the flight system (i.e., all sources minus the SAM instrument) to impart no more than 36 parts per billion (ppb by weight) of total reduced carbon terrestrial contamination to any sample transferred to the SAM instrument. This very clean level was achieved by a combination of a rigorous contamination control program on the project, and then using the first collected samples for a "dilution cleaning" campaign of the sample chain prior to delivering a sample to the SAM instrument. Direct cleanliness assays of the sample-contacting and other Flight System surfaces during pre-launch processing were used as inputs to determine the number of dilution cleaning samples needed once on Mars, to enable delivery of suitably clean samples to the SAM experiment. Taking into account contaminant redistribution during launch thorough landing of the MSL on Mars, the amount of residue present on the sampling hardware prior to the time of first dilution cleaning sample acquisition was estimated to be 60 ng/cm(2) on exposed outer surfaces of the sampling hardware and 20 ng/cm(2) on internal sample contacting surfaces; residues consisting mainly of aliphatic hydrocarbons and esters. After three dilution cleaning samples, estimated in-sample contamination level for the first regolith sample delivered to the SAM instrument at the Gale Crater "Rocknest" site was bounded at ≤10 ppb total organic carbon. A Project decision to forego ejecting the dilution cleaning sample and instead transfer the first drill-acquired sample at the "John Klein" site to SAM resulted in an estimated level of terrestrial contamination of ≤430 ppb. The estimated terrestrial contamination for portions from the second drill-acquired sample, at Cumberland, was ≤69 ppb; the estimate for a future, third, drilled sample is ≤38 ppb. These levels are comparable in magnitude to the SAM instrument blanks at the nanomole level (as chlorohydrocarbon).

Measurement of inclusive W and Z boson production cross sections in pp collisions at sqrt[s] = 8 TeV

A measurement of total and fiducial inclusive W and Z boson production cross sections in pp collisions at sqrt[s] = 8 TeV is presented. Electron and muon final states are analyzed in a data sample collected with the CMS detector corresponding to an integrated luminosity of 18.2 ± 0.5 pb(-1). The measured total inclusive cross sections times branching fractions are σ(pp → WX)×B(W → ℓν) = 12.21 ± 0.03(stat) ± 0.24(syst) ± 0.32(lum) nb and σ(pp → ZX) × B(Z → ℓ+ℓ-) = 1.15 ± 0.01(stat) ± 0.02(syst) ± 0.03(lum) nb for the dilepton mass in the range of 60-120 GeV. The measured values agree with next-to-next-to-leading-order QCD cross section calculations. Ratios of cross sections are reported with a precision of 2%. This is the first measurement of inclusive W and Z boson production in proton-proton collisions at sqrt[s] = 8 TeV.

Immune deficiency in Ataxia-Telangiectasia: a longitudinal study of 44 patients

Ataxia-Telangiectasia (A-T) is a genetic condition leading to neurological defects and immune deficiency. The nature of the immune deficiency is highly variable, and in some cases causes significant morbidity and mortality due to recurrent sinopulmonary infections. Although the neurological defects in A-T are progressive, the natural history of the immune deficiency in A-T has not been evaluated formally. In this study we analyse the clinical history and immunological data in 44 patients with A-T who attended the National Ataxia-Telangiectasia clinic in Nottingham between 2001 and 2011. Using patient medical records and Nottingham University Hospitals (NUH) National Health Service Trust medical IT systems, data regarding clinical history, use of immunoglobulin replacement therapy, total immunoglobulin levels, specific antibody levels and lymphocyte subset counts were obtained. T cell receptor spectratyping results in some patients were already available and, where possible, repeat blood samples were collected for analysis. This study shows that subtle quantitative changes in certain immunological parameters such as lymphocyte subset counts may occur in patients with A-T over time. However, in general, for the majority of patients the severity of immune deficiency (both clinically and in terms of immunological blood markers) does not seem to deteriorate significantly with time. This finding serves to inform the long-term management of this cohort of patients because, if recurrent respiratory tract infections present later in life, then other contributory factors (e.g. cough/swallowing difficulties, underlying lung disease) should be investigated aggressively. Our findings also offer some form of reassurance for parents of children with A-T, which is otherwise a progressively severely debilitating condition.

Long-term outcome of anti-tumor necrosis factor alpha blockade in the treatment of juvenile spondyloarthritis

OBJECTIVES

A significant proportion of patients with juvenile spondyloarthritis (JSpA) are refractory to treatment with established medications. The objective of this study was to assess long-term efficacy of treatment with anti-TNF agents in patients with JSpA.

METHODS

An observational study of 16 patients with JSpA from 3 centres treated with infliximab (n=10) and etanercept (n=6) was performed, with a median follow-up period of 7.2 years. Prospective data was collected according to a standardized protocol. Outcomes examined were TEC, TAJC, markers of inflammation (ESR, CRP), functional assessments (C-HAQ, BASDAI, BASFI), and ongoing requirement for anti-TNF treatment.

RESULTS

13/16 patients (83%) had achieved clinical remission 6 months into the treatment. Improvement was sustained over time, with a median TAJC and TEC of 0 at any time point after 6 weeks. 6/16 patients (38%) showed a flare of arthritis after a median of 3.5 years. Two patients with hip disease prior to treatment required an arthroplasty 3 and 8 years post anti-TNF initiation. Patients showed progression of sacroiliitis with median modified New York score of 1 (range 0-3) at time of diagnosis and 3 (range 0-4) at last follow-up (p=0.002). Median BASDAI at last follow up was 1.6, median BASFI 3.1. Two patients developed transient reactions (one generalised, one local); no patient developed other adverse effects during the study.

CONCLUSIONS

Anti-TNF treatment in JSpA refractory to standard treatment results in good long-term disease control except for pre-existing hip disease. However, radiographic evidence suggests inferior efficacy for control of sacroiliac joint disease.

John J, Sulak L, Alimena J, Bhattacharya S, Christopher G, Cutts D, Demiragli Z, Ferapontov A, Garabedian A, Heintz U, Jabeen S, Kukartsev G, Laird E, Landsberg G, Luk M, Narain M, Segala M, Sinthuprasith T, Speer T, Breedon R, Breto G, Calderon De La Barca Sanchez M, Chauhan S, Chertok M, Conway J, Conway R, Cox PT, Erbacher R, Gardner M, Houtz R, Ko W, Kopecky A, Lander R, Mall O, Miceli T, Nelson R, Pellett D, Ricci-Tam F, Rutherford B, Searle M, Smith J, Squires M, Tripathi M, Wilbur S, Yohay R, Andreev V, Cline D, Cousins R, Erhan S, Everaerts P, Farrell C, Felcini M, Hauser J, Ignatenko M, Jarvis C, Rakness G, Schlein P, Takasugi E, Traczyk P, Valuev V, Weber M, Babb J, Clare R, Dinardo ME, Ellison J, Gary JW, Hanson G, Liu H, Long OR, Luthra A, Nguyen H, Paramesvaran S, Sturdy J, Sumowidagdo S, Wilken R, Wimpenny S, Andrews W, Branson JG, Cerati GB, Cittolin S, Evans D, Holzner A, Kelley R, Lebourgeois M, Letts J, Macneill I, Mangano B, Padhi S, Palmer C, Petrucciani G, Pieri M, Sani M, Sharma V, Simon S, Sudano E, Tadel M, Tu Y, Vartak A, Wasserbaech S, Würthwein F, Yagil A, Yoo J, Barge D, Bellan R, Campagnari C, D’Alfonso M, Danielson T, Flowers K, Geffert P, George C, Golf F, Incandela J, Justus C, Kalavase P, Kovalskyi D, Krutelyov V, Lowette S, naVillalba RM, Mccoll N, Pavlunin V, Ribnik J, Richman J, Rossin R, Stuart D, To W, West C, Apresyan A, Bornheim A, Bunn J, Chen Y, Di Marco E, Duarte J, Kcira D, Ma Y, Mott A, Newman HB, Rogan C, Spiropulu M, Timciuc V, Veverka J, Wilkinson R, Xie S, Yang Y, Zhu RY, Azzolini V, Calamba A, Carroll R, Ferguson T, Iiyama Y, Jang DW, Liu YF, Paulini M, Russ J, Vogel H, Vorobiev I, Cumalat JP, Drell BR, Ford WT, Gaz A, Luiggi Lopez E, Nauenberg U, Smith JG, Stenson K, Ulmer KA, Wagner SR, Alexander J, Chatterjee A, Eggert N, Gibbons LK, Hopkins W, Khukhunaishvili A, Kreis B, Mirman N, Nicolas Kaufman G, Patterson JR, Ryd A, Salvati E, Sun W, Teo WD, Thom J, Thompson J, Tucker J, Weng Y, Winstrom L, Wittich P, Winn D, Abdullin S, Albrow M, Anderson J, Apollinari G, Bauerdick LAT, Beretvas A, Berryhill J, Bhat PC, Burkett K, Butler JN, Chetluru V, Cheung HWK, Chlebana F, Cihangir S, Elvira VD, Fisk I, Freeman J, Gao Y, Gottschalk E, Gray L, Green D, Gutsche O, Hare D, Harris RM, Hirschauer J, Hooberman B, Jindariani S, Johnson M, Joshi U, Klima B, Kunori S, Kwan S, Leonidopoulos C, Linacre J, Lincoln D, Lipton R, Lykken J, Maeshima K, Marraffino JM, Martinez Outschoorn VI, Maruyama S, Mason D, McBride P, Mishra K, Mrenna S, Musienko Y, Newman-Holmes C, O’Dell V, Prokofyev O, Ratnikova N, Sexton-Kennedy E, Sharma S, Spalding WJ, Spiegel L, Taylor L, Tkaczyk S, Tran NV, Uplegger L, Vaandering EW, Vidal R, Whitmore J, Wu W, Yang F, Yun JC, Acosta D, Avery P, Bourilkov D, Chen M, Cheng T, Das S, De Gruttola M, Di Giovanni GP, Dobur D, Drozdetskiy A, Field RD, Fisher M, Fu Y, Furic IK, Hugon J, Kim B, Konigsberg J, Korytov A, Kropivnitskaya A, Kypreos T, Low JF, Matchev K, Milenovic P, Mitselmakher G, Muniz L, Remington R, Rinkevicius A, Skhirtladze N, Snowball M, Yelton J, Zakaria M, Gaultney V, Hewamanage S, Lebolo LM, Linn S, Markowitz P, Martinez G, Rodriguez JL, Adams T, Askew A, Bochenek J, Chen J, Diamond B, Gleyzer SV, Haas J, Hagopian S, Hagopian V, Johnson KF, Prosper H, Veeraraghavan V, Weinberg M, Baarmand MM, Dorney B, Hohlmann M, Kalakhety H, Yumiceva F, Adams MR, Apanasevich L, Bazterra VE, Betts RR, Bucinskaite I, Callner J, Cavanaugh R, Evdokimov O, Gauthier L, Gerber CE, Hofman DJ, Khalatyan S, Kurt P, Lacroix F, Moon DH, O’Brien C, Silkworth C, Strom D, Turner P, Varelas N, Akgun U, Albayrak EA, Bilki B, Clarida W, Dilsiz K, Duru F, Griffiths S, Merlo JP, Mermerkaya H, Mestvirishvili A, Moeller A, Nachtman J, Newsom CR, Ogul H, Onel Y, Ozok F, Sen S, Tan P, Tiras E, Wetzel J, Yetkin T, Yi K, Barnett BA, Blumenfeld B, Bolognesi S, Fehling D, Giurgiu G, Gritsan AV, Guo ZJ, Hu G, Maksimovic P, Swartz M, Whitbeck A, Baringer P, Bean A, Benelli G, Kenny III RP, Murray M, Noonan D, Sanders S, Stringer R, Wood JS, Barfuss AF, Chakaberia I, Ivanov A, Khalil S, Makouski M, Maravin Y, Shrestha S, Svintradze I, Gronberg J, Lange D, Rebassoo F, Wright D, Baden A, Calvert B, Eno SC, Gomez JA, Hadley NJ, Kellogg RG, Kolberg T, Lu Y, Marionneau M, Mignerey AC, Pedro K, Peterman A, Skuja A, Temple J, Tonjes MB, Tonwar SC, Apyan A, Bauer G, Busza W, Butz E, Cali IA, Chan M, Dutta V, Gomez Ceballos G, Goncharov M, Kim Y, Klute M, Lai YS, Levin A, Luckey PD, Ma T, Nahn S, Paus C, Ralph D, Roland C, Roland G, Stephans GSF, Stöckli F, Sumorok K, Sung K, Velicanu D, Wolf R, Wyslouch B, Yang M, Yilmaz Y, Yoon AS, Zanetti M, Zhukova V, Dahmes B, De Benedetti A, Franzoni G, Gude A, Haupt J, Kao SC, Klapoetke K, Kubota Y, Mans J, Pastika N, Rusack R, Sasseville M, Singovsky A, Tambe N, Turkewitz J, Cremaldi LM, Kroeger R, Perera L, Rahmat R, Sanders DA, Summers D, Avdeeva E, Bloom K, Bose S, Claes DR, Dominguez A, Eads M, Gonzalez Suarez R, Keller J, Kravchenko I, Lazo-Flores J, Malik S, Meier F, Snow GR, Dolen J, Godshalk A, Iashvili I, Jain S, Kharchilava A, Kumar A, Rappoccio S, Wan Z, Alverson G, Barberis E, Baumgartel D, Chasco M, Haley J, Massironi A, Nash D, Orimoto T, Trocino D, Wood D, Zhang J, Anastassov A, Hahn KA, Kubik A, Lusito L, Mucia N, Odell N, Pollack B, Pozdnyakov A, Schmitt M, Stoynev S, Velasco M, Won S, Berry D, Brinkerhoff A, Chan KM, Hildreth M, Jessop C, Karmgard DJ, Kolb J, Lannon K, Luo W, Lynch S, Marinelli N, Morse DM, Pearson T, Planer M, Ruchti R, Slaunwhite J, Valls N, Wayne M, Wolf M, Antonelli L, Bylsma B, Durkin LS, Hill C, Hughes R, Kotov K, Ling TY, Puigh D, Rodenburg M, Smith G, Vuosalo C, Williams G, Winer BL, Wolfe H, Berry E, Elmer P, Halyo V, Hebda P, Hegeman J, Hunt A, Jindal P, Koay SA, Lopes Pegna D, Lujan P, Marlow D, Medvedeva T, Mooney M, Olsen J, Piroué P, Quan X, Raval A, Saka H, Stickland D, Tully C, Werner JS, Zenz SC, Zuranski A, Brownson E, Lopez A, Mendez H, Ramirez Vargas JE, Alagoz E, Benedetti D, Bolla G, Bortoletto D, De Mattia M, Everett A, Hu Z, Jones M, Jung K, Koybasi O, Kress M, Leonardo N, Maroussov V, Merkel P, Miller DH, Neumeister N, Shipsey I, Silvers D, Svyatkovskiy A, Vidal Marono M, Wang F, Xu L, Yoo HD, Zablocki J, Zheng Y, Guragain S, Parashar N, Adair A, Akgun B, Ecklund KM, Geurts FJM, Li W, Padley BP, Redjimi R, Roberts J, Zabel J, Betchart B, Bodek A, Covarelli R, De Barbaro P, Demina R, Eshaq Y, Ferbel T, Garcia-Bellido A, Goldenzweig P, Han J, Harel A, Miner DC, Petrillo G, Vishnevskiy D, Zielinski M, Bhatti A, Ciesielski R, Demortier L, Goulianos K, Lungu G, Malik S, Mesropian C, Arora S, Barker A, Chou JP, Contreras-Campana C, Contreras-Campana E, Duggan D, Ferencek D, Gershtein Y, Gray R, Halkiadakis E, Hidas D, Lath A, Panwalkar S, Park M, Patel R, Rekovic V, Robles J, Rose K, Salur S, Schnetzer S, Seitz C, Somalwar S, Stone R, Thomas S, Walker M, Cerizza G, Hollingsworth M, Spanier S, Yang ZC, York A, Bouhali O, Eusebi R, Flanagan W, Gilmore J, Kamon T, Khotilovich V, Montalvo R, Osipenkov I, Pakhotin Y, Perloff A, Roe J, Safonov A, Sakuma T, Suarez I, Tatarinov A, Toback D, Akchurin N, Damgov J, Dragoiu C, Dudero PR, Jeong C, Kovitanggoon K, Lee SW, Libeiro T, Volobouev I, Appelt E, Delannoy AG, Greene S, Gurrola A, Johns W, Maguire C, Mao Y, Melo A, Sharma M, Sheldon P, Snook B, Tuo S, Velkovska J, Arenton MW, Boutle S, Cox B, Francis B, Goodell J, Hirosky R, Ledovskoy A, Lin C, Neu C, Wood J, Gollapinni S, Harr R, Karchin PE, Kottachchi Kankanamge Don C, Lamichhane P, Sakharov A, Anderson M, Belknap DA, Borrello L, Carlsmith D, Cepeda M, Dasu S, Friis E, Grogg KS, Grothe M, Hall-Wilton R, Herndon M, Hervé A, Kaadze K, Klabbers P, Klukas J, Lanaro A, Lazaridis C, Loveless R, Mohapatra A, Mozer MU, Ojalvo I, Pierro GA, Ross I, Savin A, Smith WH, Swanson J. Measurement of the top-quark mass in all-jets [Formula: see text] events in pp collisions at [Formula: see text] TeV

The mass of the top quark is measured using a sample of [Formula: see text] candidate events with at least six jets in the final state. The sample is selected from data collected with the CMS detector in pp collisions at [Formula: see text] TeV in 2011 and corresponds to an integrated luminosity of 3.54 [Formula: see text]. The mass is reconstructed for each event employing a kinematic fit of the jets to a [Formula: see text] hypothesis. The top-quark mass is measured to be [Formula: see text] GeV. A combination with previously published measurements in other decay modes by CMS yields a mass of [Formula: see text] GeV.

Changes in hematocrit following a blood transfusion does not influence the risk for necrotizing enterocolitis: A case-control study

OBJECTIVE

Transfusion Associated Necrotizing Enterocolitis (TANEC) is defined as the onset of necrotizing enterocolitis (NEC) within 48 hours of receiving a blood transfusion in preterm neonates. We wanted to determine if hematocrit changes following blood transfusions were associated with disease development.

PATIENTS AND METHODS

This is a case-control analysis of inborn neonates ≤32 weeks' gestational age, from January 1, 2007 and December 31, 2010, who were diagnosed with Bell stage II or greater NEC. Those meeting TANEC criteria were identified and an analysis completed to determine if beginning or ending hematocrit values were associated with an increased risk for disease development.

RESULTS

Nineteen of forty-nine (39%) infants with NEC met the criteria for TANEC. We found no differences in gestational age at birth or birth weight in our experimental groups. The degree of illness including PDA, IVH, central line use, and respiratory support 48 hours prior to disease onset was also similar between groups. Those with TANEC had higher modified Bell staging of NEC and were more likely to be receiving full enteric feeds at the time of NEC onset. No statistically significant differences were found in hematocrit levels prior to or following the blood transfusion closest to NEC onset in the TANEC group, as compared to classic NEC (CNEC) or control infants.

CONCLUSION

The onset of NEC following transfusion occurs with a frequency that invites investigation regarding causation. Our data indicates no association between the beginning and ending hematocrit values and TANEC in our patient population.

EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk

In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.

Fatty Liver Hemorrhagic Syndrome in the Backyard Chicken

Fatty liver hemorrhagic syndrome, characterized by sudden death in overconditioned hens due to hepatic rupture and hemorrhage, is one of the leading noninfectious idiopathic causes of mortality in backyard chickens. Nutritional, genetic, environmental, and hormonal factors, or combinations of these, have been proposed yet not proven as the underlying cause. In an attempt to characterize the hepatic changes leading to the syndrome, this retrospective case study examined 76 backyard chickens that were diagnosed with fatty liver hemorrhagic syndrome between January 2007 and September 2012 and presented for necropsy to the diagnostic laboratory of the California Animal Health and Food Safety Laboratory System. A majority of the birds were female (99%), obese (97.5%), and in active lay (69.7%). Livers were examined histologically, and the degree of hepatocellular vacuolation (lipidosis), the reticular stromal architecture, the presence of collagenous connective tissue, and vascular wall changes were evaluated and graded using hematoxylin and eosin, Gomori’s reticulin, oil red O, Masson’s trichrome, and Verhoeff-Van Gieson stains. Interestingly, there was no correlation between lipidosis and reticulin grades; hepatocellular lipidosis was absent in 22% of the cases and mild in 26% of the cases. Additionally, there was evidence of repeated bouts of intraparenchymal hemorrhage before the acute “bleed-out” in 35.5% of the cases. These data are not supportive of the previously proposed causes and provide a framework for future studies to elucidate the pathogenesis of this condition. Furthermore, the data shown in this study support hemorrhagic liver syndrome as a more accurate name, as hepatic lipidosis is absent in a significant proportion of ruptured livers.

Search for supersymmetry in hadronic final states with missing transverse energy using the variables αT and b-quark multiplicity in pp collisions at [Formula: see text]

An inclusive search for supersymmetric processes that produce final states with jets and missing transverse energy is performed in pp collisions at a centre-of-mass energy of 8 TeV. The data sample corresponds to an integrated luminosity of 11.7 fb-1 collected by the CMS experiment at the LHC. In this search, a dimensionless kinematic variable, αT, is used to discriminate between events with genuine and misreconstructed missing transverse energy. The search is based on an examination of the number of reconstructed jets per event, the scalar sum of transverse energies of these jets, and the number of these jets identified as originating from bottom quarks. No significant excess of events over the standard model expectation is found. Exclusion limits are set in the parameter space of simplified models, with a special emphasis on both compressed-spectrum scenarios and direct or gluino-induced production of third-generation squarks. For the case of gluino-mediated squark production, gluino masses up to 950-1125 GeV are excluded depending on the assumed model. For the direct pair-production of squarks, masses up to 450 GeV are excluded for a single light first- or second-generation squark, increasing to 600 GeV for bottom squarks.

Inclusive search for supersymmetry using razor variables in pp collisions at √s=7 TeV

An inclusive search is presented for new heavy particle pairs produced in √s=7 TeV proton-proton collisions at the LHC using 4.7±0.1 fb(-1) of integrated luminosity. The selected events are analyzed in the 2D razor space of M(R), an event-by-event indicator of the heavy particle mass scale, and R, a dimensionless variable related to the missing transverse energy. The third-generation sector is probed using the event heavy-flavor content. The search is sensitive to generic supersymmetry models with minimal assumptions about the superpartner decay chains. No excess is observed in the number of events beyond that predicted by the standard model. Exclusion limits are derived in the CMSSM framework as well as for simplified models. Within the CMSSM parameter space considered, gluino masses up to 800 GeV and squark masses up to 1.35 TeV are excluded at 95% confidence level depending on the model parameters. The direct production of pairs of top or bottom squarks is excluded for masses as high as 400 GeV.

Search for physics beyond the standard model in events with τ leptons, jets, and large transverse momentum imbalance in pp collisions at [Formula: see text]

A search for physics beyond the standard model is performed with events having one or more hadronically decaying τ leptons, highly energetic jets, and large transverse momentum imbalance. The data sample corresponds to an integrated luminosity of 4.98 fb-1 of proton-proton collisions at [Formula: see text] collected with the CMS detector at the LHC in 2011. The number of observed events is consistent with predictions for standard model processes. Lower limits on the mass of the gluino in supersymmetric models are determined.

Measurement of masses in the [Formula: see text] system by kinematic endpoints in pp collisions at [Formula: see text]

A simultaneous measurement of the top-quark, W-boson, and neutrino masses is reported for [Formula: see text] events selected in the dilepton final state from a data sample corresponding to an integrated luminosity of 5.0 fb-1 collected by the CMS experiment in pp collisions at [Formula: see text]. The analysis is based on endpoint determinations in kinematic distributions. When the neutrino and W-boson masses are constrained to their world-average values, a top-quark mass value of [Formula: see text] is obtained. When such constraints are not used, the three particle masses are obtained in a simultaneous fit. In this unconstrained mode the study serves as a test of mass determination methods that may be used in beyond standard model physics scenarios where several masses in a decay chain may be unknown and undetected particles lead to underconstrained kinematics.

Search for a standard-model-like Higgs boson with a mass in the range 145 to 1000 GeV at the LHC

A search for a standard-model-like Higgs boson in the H→WW and H→ZZ decay channels is reported, for Higgs boson masses in the range 145 Collapse

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Search for supersymmetry in pp collisions at [Formula: see text] TeV in events with a single lepton, jets, and missing transverse momentum

Results are reported from a search for new physics processes in events containing a single isolated high-transverse-momentum lepton (electron or muon), energetic jets, and large missing transverse momentum. The analysis is based on a 4.98 fb-1 sample of proton-proton collisions at a center-of-mass energy of 7 TeV, obtained with the CMS detector at the LHC. Three separate background estimation methods, each relying primarily on control samples in the data, are applied to a range of signal regions, providing complementary approaches for estimating the background yields. The observed yields are consistent with the predicted standard model backgrounds. The results are interpreted in terms of limits on the parameter space for the constrained minimal supersymmetric extension of the standard model, as well as on cross sections for simplified models, which provide a generic description of the production and decay of new particles in specific, topology based final states.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1140/epjc/s10052-013-2404-z) contains supplementary material, which is available to authorized users.

Measurement of associated production of vector bosons and top quark-antiquark pairs in pp collisions at sqrt[s]=7 TeV

The first measurement of vector-boson production associated with a top quark-antiquark pair in proton-proton collisions at sqrt[s] = 7  TeV is presented. The results are based on a data set corresponding to an integrated luminosity of 5.0  fb(-1), recorded by the CMS detector at the LHC in 2011. The measurement is performed in two independent channels through a trilepton analysis of ttZ events and a same-sign dilepton analysis of ttV (V = W or Z) events. In the trilepton channel a direct measurement of the ttZ cross section σ(ttZ) = 0.28(-0.11)(+0.14) (stat)(-0.03)(+0.06) (syst)  pb is obtained. In the dilepton channel a measurement of the ttV cross section yields σ(ttV) = 0.43(-0.15)(+0.17) (stat)(-0.07)(+0.09) (syst)  pb. These measurements have a significance, respectively, of 3.3 and 3.0 standard deviations from the background hypotheses and are compatible, within uncertainties, with the corresponding next-to-leading order predictions of 0.137(-0.016)(+0.012) and 0.306(-0.053)(+0.031)  pb.