bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evans syndrome after autologous peripheral blood stem cell transplantation for recurrent Hodgkin lymphoma
Authors: Kato Ikuko , Okada Hitoshi , Nishida Tomoko , Konishi Yukihiko , Kondo Sonoko , Nishisho Sae , Iwase Takashi , Itoh Susumu , Kusaka Takashi 
Published: August 2016

AbstractThere have been a number of recent reports on the occurrence of autoimmune conditions after autologous hematopoietic stem cell transplantation. We describe a rare case of Evans syndrome (ES) that developed in a 16‐year‐old patient >1 year after autologous peripheral blood stem cell transplantation for recurrent Hodgkin lymphoma. ES is a rare and frequently refractory condition. No therapy for the condition has been established, and it can often be fatal. In the present case, i.v. cyclosporine A injection was significantly effective against the ES, which has not recurred.
Successful acute lymphoblastic leukemia‐type therapy in two children with mixed‐phenotype acute leukemia
Authors: Otsubo Keisuke , Yabe Miharu , Yabe Hiromasa , Fukumura Akiko , Morimoto Tsuyoshi , Kato Masahiko , Mochizuki Hiroyuki 
Published: August 2016

AbstractMixed‐phenotype acute leukemia (MPAL) is a rare type of leukemia expressing both myeloid and lymphoid markers. There is limited information, especially on pediatric cases. Therefore, the optimal therapeutic approach to pediatric MPAL has not been defined. Here, we report two pediatric cases of MPAL. According to the 2008 World Health Organization (WHO) classification and European Group for the Immunological Characterization of Leukemias (EGIL) criteria, patient 1 was diagnosed with overt MPAL positive for the myeloid marker myeloperoxidase (MPO), and B‐lymphoid markers. Patient 2 was diagnosed with T‐cell acute lymphoblastic leukemia (T‐ALL) using EGIL criteria. According to the 2008 WHO classification, however, patient 2 was diagnosed with overt MPAL positive for CD3, T‐lymphoid markers and MPO. We chose an ALL‐type therapy consisting of both lymphoid‐ and myeloid‐directed agents; these patients have maintained complete remission following treatment. Further information on pediatric MPAL is needed to establish an appropriate therapeutic strategy including stem cell transplantation for this rare condition.
Empirical Processes in Survey Sampling with (Conditional) Poisson Designs
Authors: Bertail Patrice , Chautru Emilie , Clémençon Stephan 
Published: August 2016

AbstractIt is the main purpose of this paper to study the asymptotics of certain variants of the empirical process in the context of survey data. Precisely, Functional Central Limit Theorems are established under usual conditions when the sample is drawn from a Poisson or a rejective sampling design. The framework we develop encompasses sampling designs with non‐uniform first order inclusion probabilities, which can be chosen so as to optimize estimation accuracy. Applications to Hadamard differentiable functionals are considered.
Catabolic response and phospholipid fatty acid profiles as microbial tools to assess soil functioning
Authors: Romaniuk R. , Costantini A. , Giuffré L. , Nannipieri P. 
Published: August 2016

AbstractMicrobial properties may help to provide an integrated view of changes in soil functioning associated with soil management or soil status. The fatty acid profiles of membrane phospholipids (PLFA) can give the composition of ecophysiological groups of soil microbial communities, while catabolic response profiles (CRP) estimate the heterotrophic functional diversity in soils, both relevant to the understanding of the role of micro‐organisms in the functioning of the soil. The objectives of this study were (i) to evaluate the CRP and PLFA as microbial tools to characterize changes in soil functioning and (ii) clarify the relation among these microbial measurements, with other physical, chemical and biochemical soil properties. We compare the same soil subjected to different managements and degrees of erosion. An undisturbed soil (UN), an old pasture soil (OP) and soils under continuous cultivation (NT) with four different depth of A horizon: 25 cm (NT 25), 23 cm (NT 23), 19 cm (NT 19) and 14 cm (NT 14) were tested. Substrate‐induced respiration of most substrates diminished when cropping pressure increased (UN > OP > NT), and soil catabolic evenness, as a diversity index, decreased by increasing production pressure and soil erosion. The correlation found among most of the measured physical, chemical and biochemical soil properties with the catabolic evenness showed the potential of this measurement to provide an integrated view of soil functioning. The PLFA analysis showed that the composition of microbial community denoting a partial recovery after 10 yr under grazed grassland. The stress indicators showed that farming practices increased microbial stress with the highest values found in the most eroded soils.
Retrospective evaluation ofCOX‐2 expression, histological and clinical factors as prognostic indicators in dogs with renal cell carcinomas undergoing nephrectomy
Authors: Carvalho S. , Stoll A. L. , Priestnall S. L. , Suarez‐Bonnet A. , Rassnick K. , Lynch S. , Schoepper I. , Romanelli G. , Buracco P. , Atherton M. , de Merlo E. M. , Lara‐Garcia A. 
Published: August 2016

AbstractLimited veterinary literature is available regarding prognostic markers for canine renal cell carcinoma (CRCC). We retrospectively evaluatedCOX‐2 expression, histological and clinical features associated with prognosis ofCRCC. Sixty‐four cases post‐nephrectomy were included, 54 had histopathological assessment and 30 hadCOX‐2 immunostaining performed. Eight dogs (13%) had metastatic disease at initial diagnosis. Twenty‐seven dogs (42%) received adjuvant therapy after nephrectomy. On univariate analysis,COX‐2 expression, mitotic index (MI), histologic type, vascular invasion, neoplastic invasiveness and metastasis at diagnosis were significantly associated with overall median survival time (MST).COX‐2 score (COX‐2 score > 3MST420 days versus 1176 days ifCOX‐2 score <3;P = 0.011) andMI(MI> 30MST120 days versus 540 days forMI < 30;P = 0.003) were the only variables associated withCRCCoutcome on multivariate analysis. The addition ofMIandCOX‐2 immunostaining to standard histopathological evaluation would help predicting outcome inCRCCpatients.
Contractile function recovery in severely injured gastrocnemius muscle of rats treated with either oleic or linoleic acid
Authors: Abreu Phablo , Pinheiro Carlos H. J. , Vitzel Kaio F. , Vasconcelos Diogo A. A. , Torres Rosângela P. , Fortes Marco S. , Marzuca‐Nassr Gabriel N. , Mancini‐Filho Jorge , Hirabara Sandro M. , Curi Rui 
Published: August 2016

New Findings
What is the central question of this study?
Oleic and linoleic acids modulate fibroblast proliferation and myogenic differentiation in vitro. However, their in vivo effects on muscle regeneration have not yet been examined. We investigated the effects of either oleic or linoleic acid on a well‐established model of muscle regeneration after severe laceration.

What is the main finding and its importance?
We found that linoleic acid increases fibrous tissue deposition and impairs muscle regeneration and recovery of contractile function, whereas oleic acid has the opposite effects in severely injured gastrocnemius muscle, suggesting that linoleic acid has a harmful effect and oleic acid a potential therapeutic effect on muscle regeneration.

Oleic and linoleic acids control fibroblast proliferation and myogenic differentiation in vitro; however, there was no study in skeletal muscle in vivo. The aim of this study was to evaluate the effects of either oleic or linoleic acid on the fibrous tissue content (collagen deposition) of muscle and recovery of contractile function in rat gastrocnemius muscle after being severely injured by laceration. Rats were supplemented with either oleic or linoleic acid for 4 weeks after laceration [0.44 g (kg body weight)−1 day−1]. Muscle injury led to an increase in oleic‐to‐stearic acid and palmitoleic‐to‐palmitic acid ratios, suggesting an increase in Δ9 desaturase activity. Increased fibrous tissue deposition and reduced isotonic and tetanic specific forces and resistance to fatigue were observed in the injured muscle. Supplementation with linoleic acid increased the content of eicosadienoic (20:2, n−6) and arachidonic (20:4, n−6) acids, reduced muscle mass and fibre cross‐sectional areas, increased fibrous tissue deposition and further reduced the isotonic and tetanic specific forces and resistance to fatigue induced by laceration. Supplementation with oleic acid increased the content of docosahexaenoic acid (22:6, n−3) and abolished the increase in fibrous tissue area and the decrease in isotonic and tetanic specific forces and resistance to fatigue induced by muscle injury. We concluded that supplementation with linoleic acid impairs muscle regeneration and increases fibrous tissue deposition, resulting in impaired recovery of contractile function. Oleic acid supplementation reduced fibrous tissue deposition and improved recovery of contractile function, attenuating the tissue damage caused by muscle injury.
Preliminary results on the feasibility of using ultrasound to monitor intrafractional motion during radiation therapy for pancreatic cancer
Authors: Omari Eenas A. , Erickson Beth , Ehlers Christopher , Quiroz Francisco , Noid George , Cooper David T. , Lachaine Martin , Li X. Allen 
Published: August 2016

Purpose:Substantial intrafraction organ motion during radiation therapy (RT) for pancreatic cancer is well recognized as a major limiting factor for accurate delivery of RT. The aim of this work is to determine the feasibility of monitoring the intrafractional motion of the pancreas or surrounding structures using ultrasound for RT delivery.Methods:Transabdominal ultrasound (TAUS) and 4DCT data were acquired on ten pancreatic cancer patients during radiation therapy process in a prospective study. In addition, TAUS and MRI were collected for five healthy volunteers. The portal vein (PV) and the head of the pancreas (HP) along with other structures were contoured on these images. Volume changes, distance between the HP and PV, and motion difference between the HP and PV were measured to examine whether PV can be used as a motion surrogate for HP. TAUS images were acquired and processed using a research version of the Clarity autoscan ultrasound system (CAUS). Motion monitoring was performed with the ultrasound probe mounted on an arm fixed to the couch. Video segments of the monitoring sessions were captured.Results:On TAUS, PV is better visualized than HP. The measured mean volume deviation for all patients for the HP and PV was 1.4 and 0.6 ml, respectively. The distance between the HP and PV was close to a constant with 0.22 mm mean deviation throughout the ten breathing phases. The mean of the absolute motion difference for all patients was 1.7 ± 0.8 mm in LR, 1.5 ± 0.5 mm in AP, and 2.3 ± 0.7 mm in SI, suggesting that the PV is a good surrogate for HP motion estimation. By using this surrogate, the HP motion tracking using TAUS was demonstrated.Conclusions:Large intrafractional organ motion due to respiratory and/or bowel motion is a limiting factor in administering curative radiation doses to pancreatic tumors. The authors investigate the use of real‐time ultrasound to track pancreas motion. Due to the poor visibility of the pancreas head on an ultrasound image, the portal vein is identified as a surrogate. The authors have demonstrated the feasibility of tracking HP motion through the localization of the PV using TAUS. This will potentially allow real‐time tracking of intrafractional motion to justify small PTV‐margins and to account for unusual motions, thus, improving normal tissue sparing.
Molecular Basis for Lytic Bacteriophage Resistance in Enterococci
Authors: Duerkop Breck A. , Huo Wenwen , Bhardwaj Pooja , Palmer Kelli L. , Hooper Lora V. 
Published: August 2016

ABSTRACT

The human intestine harbors diverse communities of bacteria and bacteriophages. Given the specificity of phages for their bacterial hosts, there is growing interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. A significant barrier to such therapies is the rapid development of phage-resistant bacteria, highlighting the need to understand how bacteria acquire phage resistance
in vivo
. Here we identify novel lytic phages in municipal raw sewage that kill
Enterococcus faecalis
, a Gram-positive opportunistic pathogen that resides in the human intestine. We show that phage infection of
E. faecalis
requires a predicted integral membrane protein that we have named PIP
EF
(for phage infection protein from
E. faecalis
). We find that PIP
EF
is conserved in
E. faecalis
and harbors a 160-amino-acid hypervariable region that determines phage tropism for distinct enterococcal strains. Finally, we use a gnotobiotic mouse model of
in vivo
phage predation to show that the sewage phages temporarily reduce
E. faecalis
colonization of the intestine but that
E. faecalis
acquires phage resistance through mutations in PIP
EF
. Our findings define the molecular basis for an evolutionary arms race between
E. faecalis
and the lytic phages that prey on them. They also suggest approaches for engineering
E. faecalis
phages that have altered host specificity and that can subvert phage resistance in the host bacteria.

IMPORTANCE
Bacteriophage therapy has received renewed attention as a potential solution to the rise in antibiotic-resistant bacterial infections. However, bacteria can acquire phage resistance, posing a major barrier to phage therapy. To overcome this problem, it is necessary to understand phage resistance mechanisms in bacteria. We have unraveled one such resistance mechanism in
Enterococcus faecalis
, a Gram-positive natural resident of the human intestine that has acquired antibiotic resistance and can cause opportunistic infections. We have identified a cell wall protein hypervariable region that specifies phage tropism in
E. faecalis
. Using a gnotobiotic mouse model of
in vivo
phage predation, we show that
E. faecalis
acquires phage resistance through mutations in this cell wall protein. Our findings define the molecular basis for lytic phage resistance in
E. faecalis
. They also suggest opportunities for engineering
E. faecalis
phages that circumvent the problem of bacterial phage resistance.
Moonshot Science—Risks and Benefits
Authors: Casadevall Arturo , Fang Ferric C. 
Published: August 2016

ABSTRACT
Ever since the successful Apollo 11 Moon landing in 1969, a “moonshot” has come to signify a bold effort to achieve a seemingly impossible task. The Obama administration recently called for a moonshot to cure cancer, an initiative that has elicited mixed responses from researchers who welcome additional funding but worry about raising expectations. We suggest that a successful moonshot requires a sufficient understanding of the basic science underlying a problem in question so that efforts can be focused on engineering a solution. Current gaps in our basic knowledge of cancer biology make the cancer moonshot a uniquely challenging endeavor. Nevertheless, history has shown that intensive research efforts have frequently yielded conceptual and technological breakthroughs with unanticipated benefits for society. We expect that this effort will be no different.
Rapid spread ofNeisseria gonorrhoeaeciprofloxacin resistance due to a newly introduced resistant strain in Nuuk, Greenland, 2012–2015: a community-based prospective cohort study
Authors: Pedersen Michael Lynge , Poulsen Peter , Berthelsen Lene , Nørgaard Christina , Hoffmann Steen , Jensen Jørgen Skov 
Published: August 2016

ObjectivesTo determine the antimicrobial susceptibility and genotype distribution ofNeisseria gonorrhoeaestrains isolated from a cohort of patients in Nuuk, Greenland in order to assess the risk of rapid spread in the event of introduction of new strains.MethodsGonococcal isolates (n=102) obtained from a prospective cohort study of ciprofloxacin resistance were collected between March 2012 and February 2013. Etest minimal inhibitory concentrations (MICs) were determined for ciprofloxacin, azithromycin, ceftriaxone, penicillin, tetracycline, spectinomycin and gentamicin. All isolates were subjected to molecular typing usingN. gonorrhoeaemultiantigen sequence typing (NG-MAST). After the introduction of a ciprofloxacin-resistant strain in early 2014, an additional 18 isolates were characterised.ResultsDuring the study period, all 102 isolates were fully susceptible to ciprofloxacin (≤0.03 mg/L), azithromycin, spectinomycin, gentamicin and ceftriaxone. 10 different NG-MAST types circulated in Nuuk but 7 were found as single isolates, and 3 of the 7 belonged to 1 of the 3 major genogroups (G210, G9816 and G9817) together comprising 96% of the 102 isolates. ST210 accounted for 55% of the 102 strains. The newly introduced ciprofloxacin resistant strain belonged to ST2400 and dominated the population with 59% resistant strains within 6 months after its introduction. All G2400 strains had MICs≥2 mg/L.ConclusionsIntroduction of a ciprofloxacin-resistant strain into a very homogeneousN. gonorrhoeaepopulation led to an explosive spread of the resistant clone, probably as a result of large sexual networks suggested by the strain homogeneity. Careful surveillance of antimicrobial susceptibility is essential to avoid widespread treatment failure in closed populations.
Suspected anaphylaxis from intravenous cefazolin during general anaesthesia in a dog
Authors: Pang Daniel S J , Prebble Melanie 
Published: August 2016

A six‐year‐old female Shetland Sheepdog with a history of cardiorespiratory compromise during general anaesthesia was referred for ovariohysterectomy surgery. Clinical examination was unremarkable at presentation and physiological parameters under general anaesthesia were within expected ranges during preparation for surgery. Shortly after injecting intravenous cefazolin, the audible signal from the Doppler ultrasound unit stopped. Rapid survey of the patient revealed tachycardia with weak femoral pulses, tachypnoea, hyperpnoea and substantially increased resistance to manual positive pressure ventilation. Stopping inhalant anaesthesia, administering salbutamol, corticosteroids and diphenhydramine were associated with resolution of clinical signs. However, marked hypotension and resistance to ventilation recurred approximately 25 minutes later. Low dose intravenous adrenaline (5 mcg/kg) was effective at increasing arterial blood pressure and reversing respiratory dysfunction. Surgery was completed and the patient recovered uneventfully. Initial reliance on second‐line therapy and delay in administering adrenaline, the recommended treatment for anaphylaxis, may have slowed resolution of clinical signs.
Regex-based entity extraction with active learning and genetic programming
Authors: Bartoli Alberto , De Lorenzo Andrea , Medvet Eric , Tarlao Fabiano 
Published: August 2016

We consider the long-standing problem of the automatic generation of regular expressions for text extraction, based solely on examples of the desired behavior. We investigate several active learning approaches in which the user annotates only one desired extraction and then merely answers extraction queries generated by the system.
The resulting framework is attractive because it is the system, not the user, which digs out the data in search of the samples most suitable to the specific learning task. We tailor our proposals to a state-of-the-art learner based on Genetic Programming and we assess them experimentally on a number of challenging tasks of realistic complexity. The results indicate that active learning is indeed a viable framework in this application domain and may thus significantly decrease the amount of costly annotation effort required.
We consider the long-standing problem of the automatic generation of regular expressions for text extraction, based solely on examples of the desired behavior. We investigate several active learning approaches in which the user anno- tates only one desired extraction and then merely answers extraction queries generated by the system.
The resulting framework is attractive because it is the sys- tem, not the user, which digs out the data in search of the samples most suitable to the specific learning task. We tailor our proposals to a state-of-the-art learner based on Genetic Programming and we assess them experimentally on a num- ber of challenging tasks of realistic complexity. The results indicate that active learning is indeed a viable framework in this application domain and may thus significantly decrease the amount of costly annotation effort required.
MNX1 Is Oncogenically Upregulated in African-American Prostate Cancer
Authors: Zhang Li , Wang Jianghua , Wang Yongquan , Zhang Yiqun , Castro Patricia , Shao Longjiang , Sreekumar Arun , Putluri Nagireddy , Guha Nilanjan , Deepak Saligrama , Padmanaban Arunkumar , Creighton Chad J. , Ittmann Michael 
Published: August 2016

Abstract
Incidence and mortality rates for prostate cancer are higher in African-American (AA) men than in European-American (EA) men, but the biologic basis for this disparity is unclear. We carried out a detailed analysis of gene expression changes in prostate cancer compared with their matched benign tissues in a cohort of AA men and compared them with existing data from EA men. In this manner, we identified MNX1 as a novel oncogene upregulated to a relatively greater degree in prostate cancer from AA men. Androgen and AKT signaling play a central role in the pathogenesis of prostate cancer and we found that both of these signaling pathways increased MNX1 expression. MNX1 in turn upregulated lipid synthesis by stimulating expression of SREBP1 and fatty acid synthetase. Our results define MNX1 as a novel targetable oncogene increased in AA prostate cancer that is associated with aggressive disease. Cancer Res; 76(21); 6290–8. ©2016 AACR.
Histone H3K27 Trimethylation Modulates 5-Fluorouracil Resistance by Inhibiting PU.1 Binding to the DPYD Promoter
Authors: Wu Rentian , Nie Qian , Tapper Erin E. , Jerde Calvin R. , Dunlap Garrett S. , Shrestha Shikshya , Elraiyah Tarig A. , Offer Steven M. , Diasio Robert B. 
Published: August 2016

Abstract
The antimetabolite 5-fluorouracil (5-FU) is one of the most widely used chemotherapy drugs. Dihydropyrimidine dehydrogenase (DPD) is a major determinant of 5-FU response and toxicity. Although DPYD variants may affect 5-FU metabolism, they do not completely explain the reported variability in DPD function or the resultant differences in treatment response. Here, we report that H3K27 trimethylation (H3K27me3) at the DPYD promoter regulated by Ezh2 and UTX suppresses DPYD expression by inhibiting transcription factor PU.1 binding, leading to increased resistance to 5-FU. Enrichment of H3K27me3 at the DPYD promoter was negatively correlated with both DPYD expression and DPD enzyme activity in peripheral blood specimens from healthy volunteers. Lastly, tumor expression data suggest that DPYD repression by Ezh2 predicts poor survival in 5-FU–treated cancers. Collectively, the findings of the present article suggest that a previously uncharacterized mechanism regulates DPD expression and may contribute to tumor resistance to 5-FU. Cancer Res; 76(21); 6362–73. ©2016 AACR.