bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlating mammographic and pathologic findings in clinical decision support using natural language processing and data mining methods
Authors: Patel Tejal A. , Puppala Mamta , Ogunti Richard O. , Ensor Joe E. , He Tiancheng , Shewale Jitesh B. , Ankerst Donna P. , Kaklamani Virginia G. , Rodriguez Angel A. , Wong Stephen T. C. , Chang Jenny C. 
Published: August 2016

BACKGROUNDA key challenge to mining electronic health records for mammography research is the preponderance of unstructured narrative text, which strikingly limits usable output. The imaging characteristics of breast cancer subtypes have been described previously, but without standardization of parameters for data mining.METHODSThe authors searched the enterprise‐wide data warehouse at the Houston Methodist Hospital, the Methodist Environment for Translational Enhancement and Outcomes Research (METEOR), for patients with Breast Imaging Reporting and Data System (BI‐RADS) category 5 mammogram readings performed between January 2006 and May 2015 and an available pathology report. The authors developed natural language processing (NLP) software algorithms to automatically extract mammographic and pathologic findings from free text mammogram and pathology reports. The correlation between mammographic imaging features and breast cancer subtype was analyzed using one‐way analysis of variance and the Fisher exact test.RESULTSThe NLP algorithm was able to obtain key characteristics for 543 patients who met the inclusion criteria. Patients with estrogen receptor‐positive tumors were more likely to have spiculated margins (P = .0008), and those with tumors that overexpressed human epidermal growth factor receptor 2 (HER2) were more likely to have heterogeneous and pleomorphic calcifications (P = .0078 and P = .0002, respectively).CONCLUSIONSMammographic imaging characteristics, obtained from an automated text search and the extraction of mammogram reports using NLP techniques, correlated with pathologic breast cancer subtype. The results of the current study validate previously reported trends assessed by manual data collection. Furthermore, NLP provides an automated means with which to scale up data extraction and analysis for clinical decision support. Cancer 2017;114–121. © 2016 American Cancer Society.
Impact of country of birth on age at the time of diagnosis of hepatocellular carcinoma in the United States
Authors: Yang Ju Dong , Altekruse Sean F. , Nguyen Mindie H. , Gores Gregory J. , Roberts Lewis R. 
Published: August 2016

BACKGROUNDThere is global variation in the onset of hepatocellular carcinoma (HCC). The objective of the current study was to investigate the impact of country of birth on age at the time of HCC diagnosis in the United States.METHODSIncident HCC cases diagnosed between 2000 and 2012 in the Surveillance, Epidemiology, and End Results program 18 registry were included. Factors associated with very early onset (age at diagnosis < 40 years) and early onset (age at diagnosis < 50 years) were identified by logistic regression.RESULTSA total of 59,907 patients were included. The median age at the time of diagnosis of HCC was 62 years and 76% of the patients were male. Of the 75% of patients for whom information regarding birth country was available, 29% were foreign born. In multivariate logistic regression, birth in West Africa (adjusted odds ratio [AOR], 16.3; 95% confidence interval [95% CI], 9.2‐27.9 [P<.01]), Central/South/other Africa (AOR, 11.0; 95% CI, 4.5‐23.7 [P<.01]), Oceania (AOR, 4.9; 95% CI, 2.9‐8.0 [P<.01]), and East Africa (AOR, 3.5; 95% CI, 1.5‐6.8 [P<.01]) was found to have the strongest association with very early‐onset HCC after adjusting for sex and race/ethnicity. Birth in West Africa, Central/South/other Africa, Oceania, or East Africa also was found to be strongly associated with early‐onset HCC.CONCLUSIONSBirth country was found to be independently associated with age at the time of HCC diagnosis in the United States. Birth in Africa (except for North Africa) and Oceania was strongly associated with very early‐onset HCC. These findings have implications for the design of comprehensive HCC surveillance programs in the United States. Cancer 2016. © 2016 American Cancer Society. Cancer 2017;81–89. © 2016 American Cancer Society.
Perceived barriers to treatment predict adherence to aromatase inhibitors among breast cancer survivors
Authors: Brier Moriah J. , Chambless Dianne L. , Gross Robert , Chen Jinbo , Mao Jun J. 
Published: August 2016

BACKGROUNDAlthough poor adherence to hormonal therapies such as aromatase inhibitors (AIs) is widely documented, to the authors' knowledge less is known regarding whether health beliefs predict treatment nonadherence. The objective of the current study was to evaluate the relationship between health beliefs (perceived susceptibility to breast cancer, perceived benefits of AI treatment, and perceived barriers to AI treatment) and adherence to AIs.METHODSPostmenopausal women with early‐stage, estrogen receptor‐positive breast cancer who were currently receiving treatment with an AI completed the 3‐factor Health Beliefs and Medication Adherence in Breast Cancer scale and questionnaires concerning their demographics and symptoms. Adherence data (treatment gaps and premature discontinuation) were abstracted from participants' medical charts. Logistic regression analyses were conducted to evaluate the relationship between health beliefs and adherence.RESULTSAmong 437 participants, 93 (21.3%) were nonadherent. Those who perceived greater barriers to their AI treatment were more likely to demonstrate AI nonadherence behaviors by the end of their treatment period compared with those who reported fewer barriers to AI therapy (adjusted odds ratio, 1.71; 95% confidence interval, 1.03‐2.86 [P = .04]). In contrast, perceived susceptibility to cancer recurrence and perceived benefits of AIs did not appear to predict AI adherence. Minority individuals were found to have lower perceived susceptibility to breast cancer recurrence and higher perceived barriers to AI treatment (P<.05 for both).ConclusionsGreater perceived barriers appeared to predict nonadherence to AIs. Interventions addressing women's negative beliefs regarding the challenges of AI treatment are needed to help optimize adherence in survivors of breast cancer. Cancer 2017;169–176. © 2016 American Cancer Society.
Application of γ‐Valerolactone as an Alternative Biomass‐Based Medium for Aminocarbonylation Reactions
Authors: Marosvölgyi‐Haskó Diána , Lengyel Blanka , Tukacs József M. , Kollár László , Mika László T. 
Published: August 2016

Abstractγ‐Valerolactone (GVL) was proposed as a renewable, nontoxic reaction medium with negligible vapor pressure for homogeneous Pd‐catalyzed aminocarbonylation reactions. Iodobenzene as a model substrate and its 4‐substituted derivatives were converted to the corresponding 2‐ketocarboxamides with high conversions and chemoselectivities in γ‐valerolactone. The effect of carbon monoxide pressure and reaction temperature on the conversion and selectivities were studied in the range 1–50 bar and 25–100 °C, respectively. The highest conversion and selectivity was achieved at 25 bar and 50 °C for iodobenzene in GVL for 24 h.
Benefits of Cognitive Treatments Administered to Patients Affected by Mild Cognitive Impairment/Mild Neurocognitive Disorder
Authors: Cavallo Marco , Signorino Arianna , Perucchini Maria Luisa 
Published: August 2016

ABSTRACT

Preclinical Research

Mild Cognitive Impairment (MCI) now termed Mild Neurocognitive Disorder (MCD) in DSM‐5, is widely used to define the disorder in individuals who have subjective cognitive deficits, objective memory impairments, or other cognitive deficits, without impairments in daily activities. Cognitive enhancers such as the acetylcholinesterase inhibitors, commonly used with some benefit in overt dementia, have recently started to be used in MCI/MCD. Treatment of disorders associated with cognitive dysfunction represents an expanding area of neurological rehabilitation and continues to be of paramount importance from political, social and ethical perspectives. In the present overview we briefly review recent studies regarding the efficacy of cognitive treatment in MCI/MCD and its potential benefits for MCI/MCD patients. A literature search was performed using studies published in English over the 5‐year period 2012–2016, designed as Randomized Controlled Trials and/or methodologically sound and robust studies that were searchable via MedLine. While findings from the studies reviewed indicate that cognitive intervention has potential in the treatment of MCI/MCD there are significant methodological limitations in current studies that need to be overcome. Drug Dev Res 77 : 444–452, 2016. © 2016 Wiley Periodicals, Inc.
Environmental flows in the context of unconventional natural gas development in the Marcellus Shale
Authors: Buchanan Brian P. , Auerbach Daniel A. , McManamay Ryan A. , Taylor Jason M. , Flecker Alexander S. , Archibald Josephine A. , Fuka Daniel R. , Walter M. Todd 
Published: August 2016

AbstractQuantitative flow–ecology relationships are needed to evaluate how water withdrawals for unconventional natural gas development may impact aquatic ecosystems. Addressing this need, we studied current patterns of hydrologic alteration in the Marcellus Shale region and related the estimated flow alteration to fish community measures. We then used these empirical flow–ecology relationships to evaluate alternative surface water withdrawals and environmental flow rules. Reduced high‐flow magnitude, dampened rates of change, and increased low‐flow magnitudes were apparent regionally, but changes in many of the flow metrics likely to be sensitive to withdrawals also showed substantial regional variation. Fish community measures were significantly related to flow alteration, including declines in species richness with diminished annual runoff, winter low‐flow, and summer median‐flow. In addition, the relative abundance of intolerant taxa decreased with reduced winter high‐flow and increased flow constancy, while fluvial specialist species decreased with reduced winter and annual flows. Stream size strongly mediated both the impact of withdrawal scenarios and the protection afforded by environmental flow standards. Under the most intense withdrawal scenario, 75% of reference headwaters and creeks (drainage areas <99 km2) experienced at least 78% reduction in summer flow, whereas little change was predicted for larger rivers. Moreover, the least intense withdrawal scenario still reduced summer flows by at least 21% for 50% of headwaters and creeks. The observed 90th quantile flow–ecology relationships indicate that such alteration could reduce species richness by 23% or more. Seasonally varying environmental flow standards and high fixed minimum flows protected the most streams from hydrologic alteration, but common minimum flow standards left numerous locations vulnerable to substantial flow alteration. This study clarifies how additional water demands in the region may adversely affect freshwater biological integrity. The results make clear that policies to limit or prevent water withdrawals from smaller streams can reduce the risk of ecosystem impairment.
Plant diversity enhances moth diversity in an intensive forest management experiment
Authors: Root Heather T. , Verschuyl Jake , Stokely Thomas , Hammond Paul , Scherr Melissa A. , Betts Matthew G. 
Published: August 2016

AbstractIntensive forest management (IFM) promises to help satisfy increasing global demand for wood but may come at the cost of local reductions to forest biodiversity.IFMoften reduces early seral plant diversity as a result of efforts to eliminate plant competition with crop trees. If diversity is a function of bottom‐up drivers, theory predicts that specialists at lower trophic levels (e.g., insect herbivores) should be particularly sensitive to reductions in plant diversity. We conducted a stand‐level experiment to test bottom‐up controls on moth community structure, as mediated by degrees of forest management intensity. Using a dataset of 12,003 moths representing 316 moth species, moth richness decreased only slightly, if at all, as herbicide intensity increased (P = 0.062); the moderate treatment, which is most commonly applied in the northwesternUSA, was estimated to have 4.72 (±2.14SE,P = 0.039) fewer species than the control. Structural equation modeling revealed strong support for an effect of herbicide on plant abundance, which influenced plant species richness and subsequently moth species richness. Moth species richness was associated with plant species richness and followed a power law function (z = 0.42,P = 0.006), which is surprisingly consistent with a recent large‐scale experiment in agricultural systems, and provides support for bottom‐up drivers of moth community structure. Moth abundance was not influenced by the direct effects of silvicultural herbicide treatments. Site‐level effects and variation in pre‐harvest vegetation communities resulted in residual broadleaf and herbaceous vegetation in even the most intensive treatment. Even at low densities, these residual deciduous and herbaceous plants supported higher than expected moth abundance and richness. We conclude that forest management practices that retain early seral vegetation diversity are the most likely to conserve moth communities.
Lake zooplankton δ13C values are strongly correlated with the δ13C values of distinct phytoplankton taxa
Authors: Taipale Sami J. , Vuorio Kristiina , Brett Michael T. , Peltomaa Elina , Hiltunen Minna , Kankaala Paula 
Published: August 2016

AbstractAnalyses of carbon stable isotopes are often used to estimate the contributions of allochthonous and autochthonous dietary resources to aquatic consumers. Most pelagic food web studies assume that all phytoplankton taxa have a similar δ13C value. We studied pelagic food web compartments (dissolved inorganic carbon [DIC], phytoplankton, bacteria, seston, cladoceran zooplankton) in 12 small (< 0.1 km2) lakes in southern Finland. These lakes were classified as oligotrophic, mesotrophic, eutrophic, and dystrophic based on their concentrations of total phosphorus and dissolved organic carbon. Additionally, we studied phytoplankton photosynthetic carbon fractionation (εp) in laboratory conditions. The photosynthetic fractionation in 28 phytoplankton cultures from nine different phytoplankton classes varied significantly at the class level, and fractionation correlated significantly with the DIC concentration of the growth media. In small boreal lakes, the δ13C values of different phytoplankton taxa, as directly measured or estimated from the δ13C values of biomarker fatty acids, varied greatly (−18‰ to −44.5‰). Phytoplankton δ13C values varied significantly by lake type and were most depleted in dystrophic lakes even though the δ13C values of the DIC was similar to mesotrophic lakes. Further within‐taxa variation was found between lakes and between different depths within a lake. Vertical samples from dystrophic lakes also showed lower εp in the phytoplankton from meta‐ and hypolimnion, possibly as a result of reduced light intensity. Altogether, in nine of the 10 sampled lakes, the δ13C values of cladoceran zooplankton were between the minimum and the maximum phytoplankton δ13C value of each lake, and thus, phytoplankton alone could explain zooplankton δ13C values. We conclude that stable isotope mixing models should take into account carbon variation among different phytoplankton taxa.
A poly(dimethylsiloxane) microfluidic sheet reversibly adhered on a glass plate for creation of emulsion droplets for droplet digital PCR
Authors: Nakashoji Yuta , Tanaka Hironari , Tsukagoshi Kazuhiko , Hashimoto Masahiko 
Published: August 2016

A PDMS microfluidic chip with T‐junction channel geometry, two inlet reservoirs, and one outlet reservoir was reversibly adhered on a glass plate through the viscoelastic properties of PDMS. This formed a detachable microfluidic device for creation of water‐in‐oil emulsion droplets that were used as discrete reaction compartments for the droplet digital PCR. The PDMS/glass device could continuously produce monodisperse droplets without leakage of fluids using a vacuum‐driven autonomous micropumping method. This droplet preparation technique only required evacuation of air dissolved in the PDMS before loading of oil and aqueous phases into separate inlet reservoirs. Degassing of the PDMS chip at approximately 300 Pa for 1.5 h in a vacuum desiccator gave 40 000 droplets in 80 min, which corresponded to a generation frequency of up to nine droplets per second. Over multiple runs the droplet creation was very reproducible, and the size reproducibility of generated droplets (polydispersity of up to 4.1%) was comparable to that acquired using other microfluidic droplet preparation techniques. Because the PDMS chip can be peeled off the glass plate, blocked channels can easily be fixed when they arise, and this extends the lifetime of the chip. Single DNA molecules partitioned into the droplets were successfully amplified by PCR. In addition, the droplet digital PCR platform allowed absolute quantification of low copy numbers of target DNA, and was robust against instrumental variance.
Thermodynamics and regeneration studies of CO2 adsorption on activated carbon
Authors: Cen Qigang , Fang Mengxiang , Wang Tao , Majchrzak‐Kucęba Izabela , Wawrzyńczak Dariusz , Luo Zhongyang 
Published: August 2016

AbstractThe kinetic and thermodynamic studies of CO2 adsorption on activated carbon were carried out in a fixed bed. Six different CO2 concentrations (from 5% up to 18 vol.%) and four temperatures (303 K, 313 K, 323 K, and 333 K) were applied to investigate dynamic adsorption behaviors. It showed that the increase in temperature led to faster adsorption kinetics, but also reduced the adsorption capacity. An isotherms modeling was made by the Langmuir isotherm model. The experimental isotherms data were well fitted. Then, based on the adsorption isotherms, the isosteric heats of CO2 adsorption were determined by Clausius‐Clapeyron equation. The calculated isosteric heat declined slightly with the adsorbed amount on activated carbon, and had an average value of 16.09 kJ/mol, which is much lower than the actual heat of adsorption measured by calorimeter. Moreover, regeneration experiments by vacuum evacuation (<10 kPa) were conducted to assess the regeneration efficiency (RE) of activated carbon. Regeneration efficiency increased with the reduction of vacuum pressure and reached over 90% at the vacuum of 4 kPa. A temperature swing integrated into the vacuum evacuation process resulted in a remarkable increase of RE with an increase in regeneration temperature, which confirmed the favorable effect of temperature on regeneration of activated carbon and providing almost full regeneration. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd
Modification of traditionally impregnated Fe2O3/Al2O3 oxygen carriers by ultrasonic method and their performance in chemical looping combustion
Authors: Chen Xing , Zhang Shuai , Xiao Rui , Li Peng 
Published: August 2016

AbstractThe selection of high‐performance oxygen carriers has always been a major focus of attention and considered to be a determining factor in chemical‐looping combustion (CLC). The traditional impregnation method by agitator for material synthesis usually causes a long crystallization time, uncontrollable crystalline size formation, and insufficient penetration and dispersion of the active component into the binder. The physical incorporation of ultrasound technology into the impregnation process is considered an effective method in the material synthesis field. In this study, the modification of a traditionally impregnated Fe2O3/Al2O3 oxygen carrier by ultrasonic method and its performance in the CLC process with methane as fuel were investigated to clarify the ultrasonic effect on the physicochemical properties of the Fe2O3/Al2O3 oxygen carrier. The characterization and optimization of an ultrasonic‐assisted Fe2O3/Al2O3 oxygen carrier by varying the ultrasonic time and ultrasonic power were especially in focus. The results confirmed a significant improvement in the physical properties of the Fe2O3/Al2O3 oxygen carrier and its reactivity performance by ultrasonic modification. Ultrasound effectively promoted the penetration and dispersion of Fe2O3 into the pores and on the surface of Al2O3 powder, resulting in a great reduction in crystalline size. Higher methane conversion was obtained by an ultrasonic‐assisted Fe2O3/Al2O3 oxygen carrier. The optimal ultrasonic parameters determined by orthogonal experimental design (OED) method and characterization analyses were 30 min of ultrasonic time and 500 W of ultrasonic power. Cyclic tests showed that the CO2 yield and CH4 conversion increased slightly from around 28% to 34% and 70% to 76%, respectively. Characterization indicated that the pore structural properties of reduced UI‐20Fe/Al‐30‐300 samples were improved at typical cycles, resulting in more CH4 converted. Overall, ultrasound technology is a promising way to promote the physicochemical properties of oxygen carriers in the CLC process. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd.
Advance hydrological studies utilizing open access internet databases
Authors: Sun Kerang , Sun Kevin W. 
Published: August 2016

AbstractThis paper introduces three web‐based databases relating to hydrological and water resources studies in the United States of America with the intention of promoting public awareness of their existence. These open access databases are the products of efforts taken by federal and state governments to make government‐owned data more accessible to the general public. The megadata sets of climate, surface water, groundwater, and water quality contained in these databases provide hydrologists and environmental scientists with unprecedented opportunities to conduct research across multiple regions and on different scales.
Improved B cell development in humanized NOD‐scid IL2Rγnull mice transgenically expressing human stem cell factor, granulocyte‐macrophage colony‐stimulating factor and interleukin‐3
Authors: Jangalwe Sonal , Shultz Leonard D. , Mathew Anuja , Brehm Michael A. 
Published: August 2016

IntroductionImmunodeficient mice engrafted with human immune systems support studies of human hematopoiesis and the immune response to human‐specific pathogens. A significant limitation of these humanized mouse models is, however, a severely restricted ability of human B cells to undergo class switching and produce antigen‐specific IgG after infection or immunization.MethodsIn this study, we have characterized the development and function of human B cells in NOD‐scid IL2Rγnull (NSG) mice transgenically expressing human stem cell factor (SCF), granulocyte macrophage colony‐stimulating factor (GM‐CSF), and IL‐3 (NSG‐SGM3) following engraftment with human hematopoietic stem cells, autologous fetal liver, and thymic tissues (bone marrow, liver, thymus or BLT model). The NSG‐SGM3 BLT mice engraft rapidly with human immune cells and develop T cells, B cells, and myeloid cells.ResultsA higher proportion of human B cells developing in NSG‐SGM3 BLT mice had a mature/naive phenotype with a corresponding decrease in immature/transitional human B cells as compared to NSG BLT mice. In addition, NSG‐SGM3 BLT mice have higher basal levels of human IgM and IgG as compared with NSG BLT mice. Moreover, dengue virus infection of NSG‐SGM3 BLT mice generated higher levels of antigen‐specific IgM and IgG, a result not observed in NSG BLT mice.ConclusionsOur studies suggest that NSG‐SGM3 BLT mice show improved human B cell development and permit the generation of antigen‐specific antibody responses to viral infection.