bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpretation of Genetic Testing for Lynch Syndrome in Patients With Putative Familial Colorectal Cancer
Authors: Rybak Christina , Hall Michael J.
Published: April 2017

Colorectal cancer (CRC) risk assessment involves the evaluation of an individual's personal and family history for characteristics of an inherited susceptibility to develop CRC. Lynch syndrome (LS), or hereditary nonpolyposis colorectal cancer, is the most common cause of hereditary CRC, underlying 2% to 3% of patients with newly diagnosed (incident) CRC. Risk assessment for LS is complex, and the interpretation of the many available tests can be challenging even for the genetics specialist. A move toward universal (reflex) LS screening for mismatch repair in all patients with incident CRC supports the importance of improving the awareness and understanding of LS testing, teaching rational testing approaches, and honing interpretive skills among cancer care providers. This article reviews important clinical features of LS genetic evaluation using 3 pedigree-based case examples from the Fox Chase Cancer Center Gastrointestinal Risk Assessment Clinic.
NCCN Task Force Report: Optimizing Treatment of Advanced Renal Cell Carcinoma With Molecular Targeted Therapy
Authors: Hudes Gary R. , Carducci Michael A. , Choueiri Toni K. , Esper Peg , Jonasch Eric , Kumar Rashmi , Margolin Kim A. , Michaelson M. Dror , Motzer Robert J. , Pili Roberto , Roethke Susan , Srinivas Sandy
Published: April 2017

The outcome of patients with metastatic renal cell carcinoma has been substantially improved with administration of the currently available molecularly targeted therapies. However, proper selection of therapy and management of toxicities remain challenging. NCCN convened a multidisciplinary task force panel to address the clinical issues associated with these therapies in attempt to help practicing oncologists optimize patient outcomes. This report summarizes the background data presented at the task force meeting and the ensuing discussion.
Where Your Data Is Going and Where It's Been
Authors: Quigley Jane M.
Published: April 2017

Collecting data is time-consuming and expensive. Electronic transactions, including electronic medical records and the unification of many billing procedures, have transformed the rate at which data are able to be extracted. Although obstacles remain, the rate at which data are de-identified, collected, and aggregated will help improve safety and standards of care for oncology patients. Everyone participating in the care of oncology patients must understand how important data are as the quality initiatives and performance metrics are numerous and growing; these initiatives cannot be successful without timely, accurate, and quantifiable data that address the continuum of oncology care.
New Options for the Management of Castration-Resistant Prostate Cancer: A Case Perspective
Authors: Goetz Dawn
Published: April 2017

Prostate cancer is the leading cause of cancer and second leading cause of death among men. Management of localized disease is fairly straight-forward, but treatment for locally advanced or metastatic disease is much less so. Androgen-deprivation therapy serves as the foundation of treatment for patients with locally advanced or metastatic disease. Although most patients with prostate cancer show a response to medical or surgical castration, many eventually experience a hormone-refractory, incurable state. Until recently, therapeutic options for CRPC have been limited and focused on systemic chemotherapeutic options. Unfortunately, however, this provides a minimal increase in overall survival, at the cost of significant additional toxicities. Therefore, much research has gone into developing other suitable therapies with potentially less toxicity. This article uses a case study approach to discuss new options for the treatment of castration-resistant prostate cancer.
Safe and Successful Implementation of CPOE for Chemotherapy at a Children's Cancer Center
Authors: Hoffman James M. , Baker Donald K. , Howard Scott C. , Laver Joseph H. , Shenep Jerry L.
Published: April 2017

Computerized prescriber order entry (CPOE) for medications has been implemented in only approximately 1 in 6 United States hospitals, with CPOE for chemotherapy lagging behind that for nonchemotherapy medications. The high risks associated with chemotherapy combined with other aspects of cancer care present unique challenges for the safe and appropriate use of CPOE. This article describes the process for safe and successful implementation of CPOE for chemotherapy at a children's cancer center. A core principle throughout the development and implementation of this system was that it must be as safe (and eventually safer) as existing paper systems and processes. The history of requiring standardized, regimen-specific, preprinted paper order forms served as the foundation for safe implementation of CPOE for chemotherapy. Extensive use of electronic order sets with advanced functionality; formal process redesign and system analysis; automated clinical decision support; and a phased implementation approach were essential strategies for safe implementation of CPOE. With careful planning and adequate resources, CPOE for chemotherapy can be safely implemented.
NCCN Biosimilars White Paper: Regulatory, Scientific, and Patient Safety Perspectives
Authors: Zelenetz Andrew D. , Ahmed Islah , Braud Edward Louis , Cross James D. , Davenport-Ennis Nancy , Dickinson Barry D. , Goldberg Steven E. , Gottlieb Scott , Johnson Philip E. , Lyman Gary H. , Markus Richard , Matulonis Ursula A. , Reinke Denise , Li Edward C. , DeMartino Jessica , Larsen Jonathan K. , Hoffman James M.
Published: April 2017

Biologics are essential to oncology care. As patents for older biologics begin to expire, the United States is developing an abbreviated regulatory process for the approval of similar biologics (biosimilars), which raises important considerations for the safe and appropriate incorporation of biosimilars into clinical practice for patients with cancer. The potential for biosimilars to reduce the cost of biologics, which are often high-cost components of oncology care, was the impetus behind the Biologics Price Competition and Innovation Act of 2009, a part of the 2010 Affordable Care Act. In March 2011, NCCN assembled a work group consisting of thought leaders from NCCN Member Institutions and other organizations, to provide guidance regarding the challenges health care providers and other key stakeholders face in incorporating biosimilars in health care practice. The work group identified challenges surrounding biosimilars, including health care provider knowledge, substitution practices, pharmacovigilance, naming and product tracking, coverage and reimbursement, use in off-label settings, and data requirements for approval.
Controversies in Radiation for Upper Rectal Cancers
Authors: Chan Emily , Wise Paul E. , Chakravarthy A. Bapsi
Published: April 2017

Over the past few decades substantial improvement has occurred in the diagnosis and treatment of rectal cancers. This disease requires the close cooperation of a multidisciplinary team, including radiologists, gastroenterologists, surgeons, medical oncologists, and radiation oncologists, to provide optimum treatment with minimal morbidity. The widespread use of total mesorectal excision (TME) and improvements in chemotherapy and radiation delivery have resulted in decreases in locoregional recurrence. Large randomized studies have shown a benefit with the use of preoperative chemoradiation for most patients with transmural and/or node-positive disease. Controversy remains, however, regarding whether this treatment paradigm should be applied uniformly to all patients regardless of tumor location. As the risk of local recurrence decreases with high rectal tumors and the benefit in terms of sphincter preservation is not applicable to this subgroup of patients, up-front surgery to allow for more accurate pathologic staging prior to making final treatment decisions is recommended. In patients with pathologically staged T3,N0,M0 tumors of the upper rectum who have undergone TME with 12 or more nodes removed, the addition of chemoradiation has very little benefit.
Our Experience With Photodynamic Diagnosis and Photodynamic Therapy for Lung Cancer
Authors: Kato Harubumi
Published: April 2017

The diagnosis of lung cancer was significantly enhanced by the development of the fiberoptic bronchoscope in 1965. Since then, advances in photosensitizers and light sources have brought photodynamic medicine into the light. This article offers an historic overview of the emergence of photodynamic medicine through the perspective of a pioneer with more than 30 years’ experience. Along with a discussion of photodynamic diagnosis of lung cancers via optical coherence tomography, the curative, palliative, and neoadjuvant roles of photodynamic therapy for early and advanced lung cancers are explored. An emerging strategy of using PDM to treat peripheral early-stage lung tumors is briefly discussed.
Photodynamic Therapy and Antitumor Immunity
Authors: Gollnick Sandra O.
Published: April 2017

Preclinical studies have shown that local photodynamic therapy (PDT) enhances systemic antitumor immunity. In addition, it has long been known that the long-term efficacy of PDT depends on the presence of an intact adaptive immune system. Years of research in the laboratory have attempted to shed light on the mechanisms of the PDT-enhanced antitumor immune response, suggesting that increased expression of proinflammatory cytokines may play a key role. This overview on the immunologic potential of PDT briefly explores these proposed mechanisms and addresses preliminary results with PDT vaccines in combination with surgery as perhaps a new clinical strategy for cancer treatment outside the laboratory.
Where Does Photodynamic Therapy Fit in the Esophageal Cancer Treatment Jigsaw Puzzle?
Authors: Moghissi Keyvan
Published: April 2017

Traditional treatment options for esophageal cancer have centered on the triad of surgery, chemotherapy, and radiotherapy. Although surgery remains the gold standard for operable disease, photodynamic therapy (PDT) is emerging as a valid minimally invasive option for select patients with inoperable disease. Years of experience with PDT for esophageal cancer seem to suggest that it may be particularly useful for treatment of early unresectable lesions, palliation of locally advanced disease, and salvage therapy for stent blockage or local tumor recurrence. Further investigation into the ideal role for PDT, perhaps through a comparative study with other nonsurgical options, may help clarify where it fits in the treatment armamentarium for esophageal cancer.
How Mainstream Medicine Sees Photodynamic Therapy in the United Kingdom
Authors: Bown Stephen G.
Published: April 2017

Although photodynamic therapy (PDT) has been used successfully to treat an assortment of different types of cancer, it has yet to reach the level of mainstream medicine on either side of the Atlantic. Unsubstantiated claims of PDT’s efficacy in the past may be part of the reason for this. However, perhaps the main obstacle to PDT’s endorsement by conventional medicine is the limited number of high-quality randomized controlled trials (RCTs) comparing it with relevant comparators for all meaningful outcomes, including effectiveness, safety, adverse events, quality of life, survival, and cost. Based on a Health Technology Assessment report on the current status of PDT and consultation with professional groups, specialist societies, and clinical study groups in the United Kingdom, this article explores the current clinical guidelines for use of PDT in cancer treatment and the dearth of supportive data from RCTs.
Clinical Antimicrobial Photodynamic Therapy: Phase II Studies in Chronic Wounds
Authors: Brown Stan
Published: April 2017

Microbiologically based diseases continue to pose serious global health problems. Effective alternative treatments that are not susceptible to resistance are sorely needed, and the killing of photosensitized bacteria through photodynamic therapy (PDT) may ultimately emerge as such an option. In preclinical research and early in vivo studies, PDT has demonstrated the ability to kill an assortment of microorganisms. Antimicrobial PDT has the potential to accelerate wound healing and prevent clinical infection, particularly in patients with chronic leg ulcers. Larger trials are needed to confirm its early promise and suggest its ultimate role in caring for chronic wounds.
The Role of Bridge Therapy Prior to Orthotopic Liver Transplantation
Authors: Prasad Meena A. , Kulik Laura M.
Published: April 2017

Orthotopic liver transplantation (OLT) offers the best chance for cure in the setting of unresectable hepatocellular carcinoma (HCC). A consensus statement recommends locoregional therapy (LRT) be considered in patients with HCC who are expected to wait more than 6 months for OLT to diminish dropout from the waiting list because of tumor progression. This article reviews LRT as a bridge to OLT in patients with HCC.
Genomic Analysis of Breast Cancer Heralds a Changing Treatment Paradigm
Authors: Ellis Matthew
Published: April 2017

Deep genomic analysis in breast cancer and the identification of driver mutations will result in treatments based on molecular subtypes and pathways. Mutations not yet familiar to most oncologists will become part of the clinical oncology vernacular. Such discoveries will advance the concept of “biology first, not drug first,” because molecular biology will drive drug development and clinical trial design involving small, molecularly defined subsets of patients, according to a presentation at the NCCN 19th Annual Conference.
New Developments in the Treatment of Castration-Resistant Prostate Cancer
Authors: Higano Celestia S.
Published: April 2017

During the past 4 years, a host of new agents have been approved for the treatment of patients with advanced prostate cancer. As a result, selecting the right agent for the right patient at the right time is a clinical challenge. At the NCCN 19th Annual Conference, Dr. Celestia Higano explored the rationale behind such therapeutic decisions and the supporting clinical trial data. She reviewed the different classes of therapeutic agents, from immunotherapy and hormonal therapies to chemotherapy and radioisotopes, and offered suggestions for the clinical scenarios in which they may be used most successfully.
Agents Make “Preferred List” in Metastatic Melanoma
Authors: Thompson John A.
Published: April 2017

The 2014 version of the NCCN Guidelines for Melanoma lists 6 pre-ferred regimens, most with a category 1 recommendation, and 8 “other active regimens.” Effective new agents include ipilimumab, a monoclonal anti-CTLA4 antibody, and agents targeted against mutated BRAF and MEK. Researchers are now focused on the optimal way to combine or sequence these agents, while exploring other new classes.
Optimal Treatment of Unresectable Nonmelanoma Skin Cancers
Authors: Olencki Thomas
Published: April 2017

Unlike in other types of cancer, in metastatic nonmelanoma, there are few dedicated oncologists to care for patients with unresectable skin cancers and little reliable clinical evidence to craft a therapeutic strategy. In his presentation at the NCCN 19th Annual Conference, Dr. Thomas Olencki offered a glimpse of some of the therapeutic regimens tried in the past for these rare skin cancers and briefly reviewed some of the more promising agents for advanced squamous cell, basal cell, and Merkel cell carcinomas, although the current evidence base is limited.
Targeted Agents: Management of Dermatologic Toxicities
Authors: Burtness Barbara
Published: April 2017

Epidermal growth factor receptor (EGFR) inhibitors are widely used in the treatment of many cancers, and the cutaneous toxicity profile associated with these agents has become prominent. In fact, dermatologic side effects have also been reported with other targeted agents, including both BRAF and mTOR inhibitors. During her presentation at the NCCN 19th Annual Conference, Dr. Barbara Burtness reviewed the array of skin complications caused by many targeted therapies, focusing on the more common culprits, the role of prophylactic versus reactive management strategies, the need to be attentive to potential infections, the importance of mastering local measures to improve quality of life and cosmetic issues, the therapeutic mainstays (oral and topical antibiotics and topical steroids), and the preference of improving these cutaneous complications over suspending anticancer treatment.
Guidelines for NHL: Updates to the Management of Diffuse Large B-Cell Lymphoma and New Guidelines for Primary Cutaneous CD30+ T-Cell Lymphoproliferative Disorders and T-Cell Large Granular Lymphocytic Leukemia
Authors: Zelenetz Andrew D.
Published: April 2017

During his presentation at the NCCN 19th Annual Conference, Dr. Andrew D. Zelenetz reviewed the updates to the 2014 NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Non-Hodgkin’s Lymphomas. Dr. Zelenetz first discussed the updates for diffuse large B-cell lymphoma (DLBCL), focusing primarily on the emergence of MYC-positive DLBCL; the limited role of imaging in early-stage disease; new treatment options; the challenge of tumor heterogeneity; and the impact of cell of origin in the selection of future therapies. Then, on behalf of Dr. Steven Horwitz, Dr. Zelenetz presented the new guidelines for primary cutaneous CD30+ T-cell lymphoproliferative disorders and T-cell large granular lymphocytic leukemia.
NCCN Guidelines for Survivorship Expanded to Address Two Common Conditions
Authors: Kvale Elizabeth , Urba Susan G.
Published: April 2017

The NCCN Clinical Practice Guidelines in Oncology for Survivorship include a new section on cancer-associated cognitive impairment and an expanded section on adult cancer pain that more completely addresses chemotherapy-induced peripheral neuropathy. These additions to the guidelines are the result of increasing awareness that long-term cancer survivors struggle with many late effects. Both the assessment and the management of cognitive impairment still lack a strong evidence-based foundation. The management of peripheral neuropathy, including the use of anti-depressants and opioids, often in combination, is backed by data primarily derived from clinical trials performed for various types of peripheral neuropathy.
Vertical midscale ionospheric disturbances caused by surface seismic waves based on Irkutsk chirp ionosonde data in 2011–2016
Authors: Berngardt O. I. , Perevalova N. P. , Podlesnyi A. V. , Kurkin V. I. , Zherebtsov G. A.
Published: April 2017

Based on the Irkutsk fast monostatic chirp ionosonde data, we made a statistical analysis of ionospheric effects for 28 earthquakes which appeared in 2011–2016 years. These effects are related with surface (Rayleigh) seismic waves far from epicenter. The analysis has shown that nine of these earthquakes were accompanied by vertical midscale ionospheric irregularities (multicusp). To estimate the ionospheric efficiency of the seismic waves, we proposed new index KW. The index estimates the maximal amplitude of the acoustic shock wave generated by given spatial distribution of seismic vibrations and related with maximal spectral power of seismic oscillations. Based on the analysis of experimental data, we have shown that earthquake‐related multicusp (5–25 s irregularities) is observed mostly at daytime [07:00–17:00] LST for KW≥4.7. The observations of acoustic waves by GPS technique in the epicenter vicinity (120–600 s irregularities) do not show such a daytime dependence. Based on 24 May 2013 Okhotsk Sea earthquake example, we demonstrated that deep‐focus earthquakes can produce strong multicusp far from the epicenter, although do not produce significant GPS ionospheric response in the epicenter vicinity.
Formation of multiple energy dispersion of H+, He+, and O+ ions in the inner magnetosphere in response to interplanetary shock
Authors: Tsuji H. , Ebihara Y. , Tanaka T.
Published: April 2017

An interplanetary (IP) shock has a large impact on magnetospheric ions. Satellite observations have shown that soon after arrival of the IP shock, overall intensity of the ions rapidly increases and multiple energy dispersion appears in an energy‐time spectrogram of the ions. In order to understand the response of the magnetospheric ions to IP shock, we have performed test particle simulation under the electric and magnetic fields provided by the global magnetohydrodynamic simulation. We reconstructed the differential flux of H+, He+, and O+ ions at (7, 0, 0) Re in GSM coordinates by means of the semi‐Lagrangian (phase space mapping) method. Simulation results show that the ions respond to the IP shock in two different ways. First, overall intensity of the flux gradually increases at all pitch angles. As the compressional wave propagates tailward, the magnetic field increases, which accelerates the ions due to the gyrobetatron. Second, multiple energy‐time dispersion appears in the reconstructed spectrograms of the ion flux. The energy‐time dispersion is caused by the ion moving toward mirror point together with tailward propagating compressional wave at off‐equator. The ions are primarily accelerated by the drift betatron under the strong electric field looking dawnward. The dispersion is absent in the spectrogram of equatorially mirroring ions. The dispersion appears at higher energy for heavier ions. These features are consistent with the satellite observations. Because the acceleration depends on bounce phase, the bounce‐averaged approximation is probably invalid for the ions during the interval of geomagnetic sudden commencement.
Flow and turbulence structure in a hypertidal estuary with the world's biggest tidal bore
Authors: Tu Junbiao , Fan Daidu
Published: April 2017

Turbulent and flow structure associated with breaking tidal bores are deliberately investigated on the basis of field measurements. High‐resolution velocity and hydrographic data are collected in the middle Qiantang Estuary by a vertical array of acoustic Doppler velocimeters and optical backscatter sensors, collaborated with a bottom‐mounted acoustic Doppler current profiler. Besides obvious variations in diurnal and spring‐neap tidal cycles, the estuarine dynamics is featured by extreme asymmetry in flood and ebb tides. The flood tide is abnormally accelerated to generate tidal bores at the first 10 min or more, with breaking or undular configurations at the front. The occurrence of peak flow velocity, turbulent kinetic energy (TKE), and TKE dissipation rate (ε) is definitely associated with breaking bores, with their values several times to 2 orders of magnitude larger than the corresponding secondary peak values during the maximum ebb flows. Flow and turbulence dynamics are significantly affected by the tidal‐bore Froude number. A sandwich ε structure is clear exhibited with the maximum value at the surface, secondary maximum near the bed, and the minimum at the intermediate. Dual TKE sources are indicated by an approximate local balance between shear production and dissipation near the bottom, and a top‐down TKE dissipation using the modified Froude scaling in the vertical water column. The highly elevated dissipation by breaking bores is comparable to that by intense breaking waves in the surf zone, and the former potentially penetrates the entire water column to produce extreme sediment‐resuspension events in combination with intense bottom shear stress.
Nonbreaking wave‐induced mixing in upper ocean during tropical cyclones using coupled hurricane‐ocean‐wave modeling
Authors: Aijaz S. , Ghantous M. , Babanin A. V. , Ginis I. , Thomas B. , Wake G.
Published: April 2017

The effects of turbulence generated by nonbreaking waves have been investigated by testing and evaluating a new nonbreaking wave parameterization in a coupled hurricane‐ocean‐wave model. The MPI version of the Princeton Ocean Model (POM) with hurricane forcing is coupled with the WAVEWATCH‐III (WW3) surface wave model. Hurricane Ivan is chosen as the test case due to its extreme intensity and availability of field data during its passage. The model results are validated against field observations of wave heights and sea surface temperatures (SSTs) from the National Data Buoy Centre (NDBC) during Hurricane Ivan and against limited in situ current and bottom temperature data. A series of numerical experiments is set up to examine the influence of the nonbreaking wave parameterization on the mixing of upper ocean. The SST response from the modeling experiments indicates that the nonbreaking wave‐induced mixing leads to significant cooling of the SST and deepening of the mixed layer. It was found that the nondimensional constant b1 in the nonbreaking wave parameterization has different impacts on the weak and the strong sides of the storm track. A constant value of b1 leads to improved predictions on the strong side of the storm while a steepness‐dependent b1 provides a better agreement with in situ observations on the weak side. A separate simulation of the intense tropical cyclone Olwyn in north‐west Australia revealed the same trend for b1 on the strong side of the tropical cyclone.
Turbulent kinetic energy of the ocean winds over the Kuroshio Extension from QuikSCAT winds (1999–2009)
Authors: Yu Kai , Dong Changming , King Gregory P.
Published: April 2017

We investigate mesoscale turbulence (10–1000 km) in the ocean winds over the Kuroshio Extension (
N–
N,
E–
E) using the QuikSCAT data set (November 1999 to October 2009). We calculate the second (Djj) and third‐order structure functions (Djjj) and the spatial variance (Vj) as a function of scale r (
denotes, respectively, the longitudinal (divergent) and transverse (vortical) component). The most interesting results of the analysis follow. Although both
and
measure the turbulent kinetic energy (TKE), we find that
is the more robust measure. The spatial variance density (dVj/dr) has a broad peak near 450 km (close to the midlatitude Rossby radius of deformation). On interannual time scales, TKE correlates well with the El Niño 3.4 index. According to turbulence theory, the kinetic energy cascades downscale (upscale) if
(also skewness
) is negative (positive). Our results for the Kuroshio Extension are consistent with a downscale cascade (indicating convergence dominates). Furthermore, classical turbulence theory predicts that
and independent of r; however, we find SL varies strongly with r, from −4 at small scales to −0.3 at large scales. This nonclassical behavior implies strong‐scale interaction, which we attribute to the rapid, and sometimes explosive, growth of storms in the region through baroclinic instability. Finally, we find that ST (a measure of cyclonic/anticyclonic asymmetry) is positive (cyclonic) and also varies strongly with r, from 4 at small scales to 0.5 at large scales. New turbulence models are needed to explain these results, and that will benefit Weather Prediction and climate modeling.
A probabilistic approach to remote compositional analysis of planetary surfaces
Authors: Lapotre M. G. A. , Ehlmann B. L. , Minson S. E.
Published: April 2017

Reflected light from planetary surfaces provides information, including mineral/ice compositions and grain sizes, by study of albedo and absorption features as a function of wavelength. However, deconvolving the compositional signal in spectra is complicated by the nonuniqueness of the inverse problem. Trade‐offs between mineral abundances and grain sizes in setting reflectance, instrument noise, and systematic errors in the forward model are potential sources of uncertainty, which are often unquantified. Here we adopt a Bayesian implementation of the Hapke model to determine sets of acceptable‐fit mineral assemblages, as opposed to single best fit solutions. We quantify errors and uncertainties in mineral abundances and grain sizes that arise from instrument noise, compositional end members, optical constants, and systematic forward model errors for two suites of ternary mixtures (olivine‐enstatite‐anorthite and olivine‐nontronite‐basaltic glass) in a series of six experiments in the visible‐shortwave infrared (VSWIR) wavelength range. We show that grain sizes are generally poorly constrained from VSWIR spectroscopy. Abundance and grain size trade‐offs lead to typical abundance errors of ≤1 wt % (occasionally up to ~5 wt %), while ~3% noise in the data increases errors by up to ~2 wt %. Systematic errors further increase inaccuracies by a factor of 4. Finally, phases with low spectral contrast or inaccurate optical constants can further increase errors. Overall, typical errors in abundance are <10%, but sometimes significantly increase for specific mixtures, prone to abundance/grain‐size trade‐offs that lead to high unmixing uncertainties. These results highlight the need for probabilistic approaches to remote determination of planetary surface composition.
Hydrological controls on glacially exported microbial assemblages
Authors: Dubnick Ashley , Kazemi Sina , Sharp Martin , Wadham Jemma , Hawkings Jon , Beaton Alexander , Lanoil Brian
Published: April 2017

The Greenland Ice Sheet (GrIS) exports approximately 400 km3 of freshwater annually to downstream freshwater and marine ecosystems. These meltwaters originate in a wide range of well‐defined habitats that can be associated with very different physical environments within the ice sheet, ranging from oxygenated surface environments that are exposed to light and supplied with nutrients from atmospheric/aeolian sources to subglacial environments that are permanently dark, isolated from the atmosphere, and potentially anoxic. Hydrological conditions in the latter likely favor prolonged rock‐water contact. The seasonally evolving hydrological system that drains meltwaters from the GrIS connects these distinct microbial habitats and exports the microbes contained within them to downstream ecosystems. The microbial assemblages exported in glacier meltwater may have an impact on downstream ecosystem function and development. We explored how the seasonal development of a glacial drainage system influences the character of microbial assemblages exported from the GrIS by monitoring the seasonal changes in hydrology, water chemistry, and microbial assemblage composition of meltwaters draining from a glacier in southwest Greenland. We found that the microbial assemblages exported in meltwaters varied in response to glacier hydrological flow path characteristics. Whether or not meltwaters passed through the subglacial environment was the first‐order control on the composition of the microbial assemblages exported from the glacier, while water source (i.e., supraglacial or extraglacial) and subglacial residence times were second‐order controls. Glacier hydrology therefore plays a fundamental role in determining the microbial exports from glaciated watersheds.
Spatial heterogeneity of within‐stream methane concentrations
Authors: Crawford John T. , Loken Luke C. , West William E. , Crary Benjamin , Spawn Seth A. , Gubbins Nicholas , Jones Stuart E. , Striegl Robert G. , Stanley Emily H.
Published: April 2017

Streams, rivers, and other freshwater features may be significant sources of CH4 to the atmosphere. However, high spatial and temporal variabilities hinder our ability to understand the underlying processes of CH4 production and delivery to streams and also challenge the use of scaling approaches across large areas. We studied a stream having high geomorphic variability to assess the underlying scale of CH4 spatial variability and to examine whether the physical structure of a stream can explain the variation in surface CH4. A combination of high‐resolution CH4 mapping, a survey of groundwater CH4 concentrations, quantitative analysis of methanogen DNA, and sediment CH4 production potentials illustrates the spatial and geomorphic controls on CH4 emissions to the atmosphere. We observed significant spatial clustering with high CH4 concentrations in organic‐rich stream reaches and lake transitions. These sites were also enriched in the methane‐producing mcrA gene and had highest CH4 production rates in the laboratory. In contrast, mineral‐rich reaches had significantly lower concentrations and had lesser abundances of mcrA. Strong relationships between CH4 and the physical structure of this aquatic system, along with high spatial variability, suggest that future investigations will benefit from viewing streams as landscapes, as opposed to ecosystems simply embedded in larger terrestrial mosaics. In light of such high spatial variability, we recommend that future workers evaluate stream networks first by using similar spatial tools in order to build effective sampling programs.
Modes of temperature and pressure variability in midlatitude troposphere and lower stratosphere in relation to cosmic ray variations
Authors: Morozova A. L. , Blanco J. J. , Ribeiro P.
Published: April 2017

The study is based on the analysis of atmospheric and space weather parameters in the midlatitude region (Iberian Peninsula) during, approximately, the epoch of the 24th solar cycle maximum. The principal component analysis was applied to sets of air temperature and geopotential height measurement at different pressure levels from a near‐ground level (930 hPa) to the stratosphere (up to 10 hPa). The analysis of extracted modes shows couplings between atmospheric and medium‐term variations (from weeks to months) of space weather parameters. The first mode of the atmospheric variability is related to the atmospheric dynamic processes that are common for the extratropical Northern Hemisphere. Extracted temperature and pressure variations are located in the upper troposphere‐lower stratosphere region and positively correlate with ozone content variations. Among space weather parameters, this atmospheric mode shows statistically significant negative correlation with the ground‐measured cosmic ray flux measured by the Castilla‐La Mancha neutron monitor (Spain) and weaker or no correlation with geomagnetic parameters.
Physical effects of thermal pollution in lakes
Authors: Råman Vinnå Love , Wüest Alfred , Bouffard Damien
Published: April 2017

Anthropogenic heat emissions into inland waters influence water temperature and affect stratification, heat and nutrient fluxes, deep water renewal, and biota. Given the increased thermal stress on these systems by growing cooling demands of riparian/coastal infrastructures in combination with climate warming, the question arises on how to best monitor and manage these systems. In this study, we investigate local and system‐wide physical effects on the medium‐sized perialpine Lake Biel (Switzerland), influenced by point‐source cooling water emission from an upstream nuclear power plant (heat emission ∼700 MW, ∼18 W m−2 lake wide). We use one‐dimensional (SIMSTRAT) and three‐dimensional (Delft3D‐Flow) hydrodynamic numerical simulations and provide model resolution guidelines for future studies of thermal pollution. The effects on Lake Biel by the emitted excess heat are summarized as: (i) clear seasonal trend in temperature increase, locally up to 3.4°C and system‐wide volume mean ∼0.3°C, which corresponds to one decade of regional surface water climate warming; (ii) the majority of supplied thermal pollution (∼60%) leaves this short residence time (∼58 days) system via the main outlet, whereas the remaining heat exits to the atmosphere; (iii) increased length of stratified period due to the stabilizing effects of additional heat; (iv) system‐wide effects such as warmer temperature, prolonged stratified period, and river‐caused epilimnion flushing are resolved by both models whereas local raised temperature and river short circuiting was only identifiable with the three‐dimensional model approach. This model‐based method provides an ideal tool to assess man‐made impacts on lakes and their downstream outflows.
Persistent or repeated surface habitability on Mars during the late Hesperian ‐ Amazonian
Authors: Kite Edwin S. , Sneed Jonathan , Mayer David P. , Wilson Sharon A.
Published: April 2017

Large alluvial fan deposits on Mars record relatively recent habitable surface conditions (≲3.5 Ga, Late Hesperian ‐ Amazonian). We find net sedimentation rate <(4–8) μm/yr in the alluvial fan deposits, using the frequency of craters that are interbedded with alluvial fan deposits as a fluvial‐process chronometer. Considering only the observed interbedded craters sets a lower bound of >20 Myr on the total time interval spanned by alluvial fan aggradation, >103‐fold longer than previous lower limits. A more realistic approach that corrects for craters fully entombed in the fan deposits raises the lower bound to >(100–300) Myr. Several factors not included in our calculations would further increase the lower bound. The lower bound rules out fan formation by a brief climate anomaly. Therefore, during the Late Hesperian ‐ Amazonian on Mars, persistent or repeated processes permitted habitable surface conditions.
UV‐Triggered Polymerization, Deposition, and Patterning of Plant Phenolic Compounds
Authors: Behboodi‐Sadabad Farid , Zhang Huijie , Trouillet Vanessa , Welle Alexander , Plumeré Nicolas , Levkin Pavel A.
Published: April 2017

Plant‐derived phenolic compounds, rich in catechol and pyrogallol moieties, can form multifunctional coatings on various substrates following polymerization under mildly alkaline conditions. Despite many appealing features of such coatings, the difficulty to control polymerization of phenolic compounds spatially and temporally limits their number of potential applications. In this study, it is demonstrated that UV irradiation can trigger oxidative polymerization and deposition of plant‐derived phenolic compounds, which opens the possibility to create 2D gradients and patterns of polyphenol coatings and control this polymerization temporally. UV–vis spectroscopy, electrospray ionization mass spectrometry, and cyclic voltammetry analyses are used to investigate the UV‐induced polymerization of several plant‐derived phenolic compounds including pyrogallol, tannic acid, caffeic acid, and gallic acid. Formation of polyphenol coatings on polar and nonpolar substrates after UV irradiation has been studied using water contact angle measurements, atomic force microscopy, time of flight secondary ion mass spectrometry, and X‐ray photoelectron spectroscopy (XPS). The possibility to use UV‐light to accelerate polymerization of phenolic compounds and perform micropatterning can extend the scope of potential applications of the large class of structurally diverse plant‐derived phenolic compounds.
Growth‐Induced Strain in Chemical Vapor Deposited Monolayer MoS2: Experimental and Theoretical Investigation
Authors: Kataria Satender , Wagner Stefan , Cusati Teresa , Fortunelli Alessandro , Iannaccone Giuseppe , Pandey Himadri , Fiori Gianluca , Lemme Max C.
Published: April 2017

Monolayer molybdenum disulfide (MoS2) is a promising 2D material for nanoelectronic and optoelectronic applications. The large‐area growth of MoS2 has been demonstrated using chemical vapor deposition (CVD) in a wide range of deposition temperatures from 600 to 1000 °C. However, a direct comparison of growth parameters and resulting material properties has not been made so far. Here, a systematic experimental and theoretical investigation of optical properties of monolayer MoS2 grown at different temperatures is presented. Micro‐Raman and photoluminescence (PL) studies reveal observable inhomogeneities in optical properties of the as‐grown single crystalline grains of MoS2. Close examination of the Raman and PL features clearly indicate that growth‐induced strain is the main source of distinct optical properties. Density functional theory calculations are carried out to describe the interaction of growing MoS2 layers with the growth substrate as the origin of strain. This work explains the variation of bandgap energies of CVD‐grown monolayer MoS2, extracted using PL spectroscopy, as a function of deposition temperature. The methodology has general applicability to model and predict the influence of growth conditions on strain in 2D materials.
Chemoselective and Enantioselective Hydrogenation of 2,4‐Diaryl‐3H‐benzo[b]azepines Catalyzed by Dendritic Phosphinooxazoline Iridium Complexes
Authors: Miao Tingting , Ma Baode , Ding Ziyuan , Liu Youran , He Yan‐Mei , Fan Qing‐Hua
Published: April 2017

An asymmetric hydrogenation of 2,4‐diaryl‐3H‐benzo[b]azepines, catalyzed by dendritic phosphinooxazoline (PHOX) iridium complexes, has been developed. Only the imine group was reduced, while the C=C bond remained untouched, affording a range of chiral 2,3‐dihydro‐1H‐benzo[b]azepine derivatives with good to excellent enantioselectivity (up to 91 % ee). A slightly positive dendritic effect on catalytic reactivity (up to 10 000 TON) was observed.
The relative effects of reproductive condition, stress, and seasonality on patterns of parasitism in wild female black howler monkeys (Alouatta pigra)
Authors: Martínez‐Mota Rodolfo , Garber Paul A. , Palme Rupert , Gillespie Thomas R.
Published: April 2017

Parasitic infections in wildlife are shaped by host‐related traits including individual reproductive condition. It has been argued that female primates are more susceptible to infectious diseases during pregnancy due to short‐term changes in immune function that result in reduced ability to combat infections. Likewise, lactation, which is the most energetically expensive state, may affect immunity and infection risk due to tradeoffs between milk production and maintenance of immune function. Here, we examine the degree to which parasite prevalence and parasite richness are affected by female reproductive condition and stress levels in wild female black howler monkeys (Alouatta pigra). Over the course of one year, we collected fresh fecal samples from 15 adult females belonging to seven black howler groups living in Escárcega, Mexico. Fecal samples were used for parasitological analysis and for measuring fecal glucocorticoid metabolites (i.e., stress biomarker). We found that the prevalence of intestinal parasites and parasite richness did not differ among non‐pregnant, pregnant, and lactating females. Fecal glucocorticoid metabolite levels increased significantly during pregnancy and during the first month of lactation, and positively predicted the probability ofControrchis biliophilusinfection. Parasite prevalence and richness decreased during the months of increased rainfall. We conclude that reproductive physiology has limited consequences on intestinal parasitic infection risk in female black howler monkeys and that seasonal environmental fluctuations have greater effects.
Binding CO2 by a Cr8 Metallacrown
Authors: Vitórica‐Yrezábal Iñigo J. , Sava Daniel Florin , Timco Grigore A. , Brown Martyn S. , Savage Mathew , Godfrey Harry G. W. , Moreau Florian , Schröder Martin , Siperstein Flor , Brammer Lee , Yang Sihai , Attfield Martin P. , McDouall Joseph J. W. , Winpenny Richard E. P.
Published: April 2017

The {Cr8} metallacrown [CrF(O2CtBu)2]8, containing a F‐lined internal cavity, shows high selectivity for CO2 over N2. DFT calculations and absorption studies support the multiple binding of F‐groups to the C‐center of CO2 (C⋅⋅⋅F 3.190(9)–3.389(9) Å), as confirmed by single‐crystal X‐ray diffraction.
Uncovering the Atomistic Mechanism for Calcite Step Growth
Authors: De La Pierre Marco , Raiteri Paolo , Stack Andrew G. , Gale Julian D.
Published: April 2017

Determining a complete atomic‐level picture of how minerals grow from aqueous solution remains a challenge as macroscopic rates can be a convolution of many reactions. For the case of calcite (CaCO3) in water, computer simulations have been used to map the complex thermodynamic landscape leading to growth of the two distinct steps, acute and obtuse, on the basal surface. The carbonate ion is found to preferentially adsorb at the upper edge of acute steps while Ca2+ only adsorbs after CO32−. In contrast to the conventional picture, ion pairs prefer to bind at the upper edge of the step with only one ion, at most, coordinated to the step and lower terrace. Migration of the first carbonate ion to a growth site is found to be rate‐limiting for kink nucleation, with this process having a lower activation energy on the obtuse step.
Hydrophobic and tribological behaviors of a poly(p‐phenylene benzobisoxazole) fabric composite reinforced with nano‐TiO2
Authors: Li Deke , Guo Zhiguang
Published: April 2017

1H,1H,2H,2H‐Perfluorooctyl trichlorosilane (PFTS) was used to modify TiO2 nanoparticles, and hydrophobic PFTS–TiO2 nanoparticles were obtained by an ultrasonic reaction method. The PFTS–TiO2 surface morphological and hydrophobic properties were analyzed with scanning electron microscopy (SEM), Fourier transform infrared spectrometry, and contact angle (CA) testing. Then, the poly(p‐phenylene benzobisoxazole) fabric–phenolic composite filled with PFTS–TiO2 as a lubricant additive was fabricated by a dip‐coating process. The tribological properties of the composite were investigated, and the wear surface morphology was observed by SEM. The experimental results show that the water CA of the composite filled with PFTS–TiO2 was 158°, and the composite containing 4 wt % PFTS–TiO2 exhibited excellent antifriction and abrasion resistance. The hydrophobic surface of the composite showed excellent durable performance with a static water CA of 126.7° after abrasion. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45077.
Depolymerization of PET waste to potentially applicable aromatic amides: Their characterization and DFT study
Authors: Teotia Meenu , Tarannum Nazia , Soni Rakesh Kumar
Published: April 2017

Poly(ethylene terephthalate) waste has been depolymerized to a series of potentially applicable aromatic amides through aminolysis with different amines such as methylamine, ethylenediamine, ethanolamine, and butylamine at ambient conditions of temperature and pressure. The amides prepared were characterized by different techniques like Fourier transform infrared (FTIR), UV‐Visible spectroscopy, nuclear magnetic resonance (NMR), elemental analysis, mass spectrometry, powdered X‐ray diffraction (XRD), Raman spectroscopy, and thermal analysis. Further more, an attempt is being made to insight the physical parameters of the aromatic amides using ab initio DFT (Density Functional Theory) study. DFT calculations were performed at Becke's three parameter functional and Lee–Yang–Parr functional (B3LYP) level of calculation with 321‐G basis set. The atomic orbital energy (HOMO and LUMO) and energy gap is also represented. The vibrational frequencies optimized by DFT were in agreement with the experimental FTIR data. An efficient conversion of PET waste to amides was achieved without catalyst through environment friendly clean approach. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45153.
A local context‐aware LDA model for topic modeling in a document network
Authors: Liu Yang , Xu Songhua
Published: April 2017

With the rapid development of the Internet and its applications, growing volumes of documents increasingly become interconnected to form large‐scale document networks. Accordingly, topic modeling in a network of documents has been attracting continuous research attention. Most of the existing network‐based topic models assume that topics in a document are influenced by its directly linked neighbouring documents in a document network and overlook the potential influence from indirectly linked ones. The existing work also has not carefully modeled variations of such influence among neighboring documents. Recognizing these modeling limitations, this paper introduces a novel Local Context‐Aware LDA Model (LC‐LDA), which is capable of observing a local context comprising a rich collection of documents that may directly or indirectly influence the topic distributions of a target document. The proposed model can also differentiate the respective influence of each document in the local context on the target document according to both structural and temporal relationships between the two documents. The proposed model is extensively evaluated through multiple document clustering and classification tasks conducted over several large‐scale document sets. Evaluation results clearly and consistently demonstrate the effectiveness and superiority of the new model with respect to several state‐of‐the‐art peer models.