bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of motivations and expectations of patients seen in phase 1 oncology clinics
Authors: Dolly Saoirse O. , Kalaitzaki Eleftheria , Puglisi Martina , Stimpson Sarah , Hanwell Janet , Fandos Sonia Serrano , Stapleton Sarah , Ansari Thushara , Peckitt Clare , Kaye Stan , Lopez Juanita , Yap Timothy A. , van der Graaf Winette , de Bono Johann , Banerji Udai 
Published: September 2016

BACKGROUNDTo better inform clinical practice, this study was aimed at capturing patients' motivations for enrolling in phase 1 trials and at quantifying their expectations of the benefits, risks, and commitment associated with clinical trials and the impact of the initial consultation on their expectations.METHODSThis was a single‐center, prospective, quantitative study of newly referred adult patients considering their first phase 1 oncology trial. Participants completed questionnaires before they were seen and an abbreviated follow‐up version after their consultation.RESULTSQuestionnaires were completed by 396 (99%) and 301 (76%) before and after the clinic, respectively. Participants ranked the possibility of tumor shrinkage (84%) as the most important motivation for considering a phase 1 trial; this was followed by no alternative treatments (56%), their physician's recommendation (44%), and the fact that the research might benefit others (38%). When they were asked about the potential personal benefit, 43% predicted tumor shrinkage initially. After the consultation, this increased to 47%. Fourteen percent of patients expected a cure. When asked about risks, 71% of the participants expected moderate side effects. When asked about expectations of time commitments, a majority of patients did not anticipate weekly visits, although this was understood by 93% of patients after the consultation. Overall, patients were keen to consider trials and when asked before and after the consultation 72% and 84% were willing to enroll in studies, respectively.CONCLUSIONSThis study reports that more than 80% of patients enroll in early‐phase clinical oncology trials motivated by the potential of a clinical benefit, with approximately half expecting tumor shrinkage and approximately a tenth anticipating a cure. The typical phase 1 response rate is 4% to 20%, and this discrepancy exemplifies the challenges faced by patients and healthcare professionals during their interactions for phase 1 studies. Cancer 2016;122:3501–3508. © 2016 American Cancer Society
Young investigator challenge: Can the Ion AmpliSeq Cancer Hotspot Panel v2 be used for next‐generation sequencing of thyroid FNA samples?
Authors: Bellevicine Claudio , Sgariglia Roberta , Malapelle Umberto , Vigliar Elena , Nacchio Mariantonia , Ciancia Giuseppe , Eszlinger Markus , Paschke Ralf , Troncone Giancarlo 
Published: September 2016

BACKGROUNDFine‐needle aspiration (FNA) cytology is accurate and cost‐effective in the evaluation of thyroid nodules. Molecular techniques may contribute to risk stratification in indeterminate cases. Although next‐generation sequencing (NGS) is a promising technique for the molecular testing of thyroid FNA specimens, thyroid‐specific cancer gene panels are not commercially available. Conversely, the Ion AmpliSeq Cancer Hotspot Panel v2 (CHPv2), which includes the genes most frequently mutated in thyroid neoplasms, is commercially available and may represent an alternative to thyroid‐specific panels. To the authors’ knowledge to date, CHPv2 has performed well only on “ideal” cytological samples featuring abundant, high‐quality DNA and satisfactory postsequencing metrics. The objective of the current study was to extend NGS to less‐than‐ideal samples, which represent a large percentage of routine clinical specimens.METHODSA total of 37 thyroid smears were retrospectively analyzed using CHPv2, regardless of any preanalytical and postsequencing metric thresholds. Specifically, the authors evaluated the performance of CHPv2 on the BRAF, NRAS, HRAS, KRAS, and RET genes. Results were verified by pyrosequencing.RESULTSOf the 37 thyroid FNA specimens, 34 (91.8%) were successfully processed. BRAF, NRAS, and RET somatic variants were detected in 22 of these 34 specimens (64.7%). NGS was found to have a high sensitivity (89.4%), specificity (85.7%), and accuracy (88.4%).CONCLUSIONSCHPv2 is a valid option for the molecular evaluation of thyroid FNA specimens by NGS. It is interesting to note that this approach is accurate and effective even when applied to routine cytology samples that usually do not have optimal preanalytical and postsequencing requirements. Cancer Cytopathol 2016;124:776‐84. © 2016 American Cancer Society.
Hierarchically Templated Synthesis of Hollow Nanoporous Gold Rods and TiO2‐Coated Gold Rods
Authors: Gao Lei , Liang Chen‐Nan , Li Hui‐Hui , Lu Zhe‐Xue 
Published: September 2016

AbstractGold nanomaterials have shown promising applications in catalysis and sensing. Among the current directions in the research and development of gold catalysts, the exploration of new forms is one of the major priorities. Using bacteria as the supporting template and polystyrene spheres as the pore‐generation template, a hierarchical‐template synthesis strategy was developed in the present study to synthesize hollow nanoporous gold rods. The pore size can be easily adjusted by using polystyrene spheres (PSS) with different diameters as the template (the pore size is about 160 nm and 70 nm when using 200 nm and 110 nm PSS, respectively, as the template). Moreover, with the simple sol–gel method, different amounts of TiO2 can be coated on these nanoporous gold rods. The results showed the thermal stability and catalytic activity of the nanoporous gold rods were improved dramatically with moderate TiO2 coating. Using reduction of 4‐nitrophenol to 4‐aminophenol with sodium borohydride as the model reaction, excellent catalytic properties (reaction rate constant k=0.246 min−1) of the prepared TiO2‐coated gold rods catalysts were confirmed.
A Complex Catalytic Reaction Caught in the Act: Intermediates and Products Sampling Online by Liquid μ‐Beam Mass Spectrometry and Theoretical Modeling
Authors: Stolz Ferdinand , Appun Johannes , Naumov Sergej , Schneider Christoph , Abel Bernd 
Published: September 2016

AbstractLiquid‐beam IR–laser desorption mass spectrometry has been used to monitor the reactants, intermediates, and products of a complex organic signature reaction in real time on multiple timescales directly from the liquid phase. The reaction was chosen because it has advantages in medicinal chemistry applications, and the three‐component, modular construction provides a means to generate molecular diversity rapidly. Under Lewis acid catalysis, a vinylogous Mannich reaction was monitored as it generated a δ‐amino‐α‐silyloxy‐α,β‐unsaturated ester, which upon hydrolysis to the corresponding α‐keto ester spontaneously reacted in a [3+2] cycloannulation to the final pyrrolo[2,1‐b]benzoxazole. The kinetic data were compared with predictions of quantum chemical calculations to elucidate and verify or exclude reaction pathways and mechanisms for a possible rational optimization of the reaction. The simplicity and rapid response of this approach make it a very powerful technique for online characterization of chemical reactions on timescales spanning several orders of magnitude. This enables full control over chemical reactions, thereby maximizing the product yield. This combined experimental and theoretical approach opens up a new route for the study of novel chemistry in liquid‐phase reactions.
Insights into the Ligand Shell, Coordination Mode, and Reactivity of Carboxylic Acid Capped Metal Oxide Nanocrystals
Authors: De Roo Jonathan , Baquero Edwin A. , Coppel Yannick , De Keukeleere Katrien , Van Driessche Isabel , Nayral Céline , Hens Zeger , Delpech Fabien 
Published: September 2016

AbstractA detailed knowledge of surface chemistry is necessary to bridge the gap between nanocrystal synthesis and applications. Although it has been proposed that carboxylic acids bind to metal oxides in a dissociative NC(X)2 binding motif, this surface chemistry was inferred from indirect evidence on HfO2 nanocrystals (NCs). Here, a more detailed picture of the coordination mode of carboxylate ligands on HfO2 and ZrO2 NC surfaces is shown by direct observation through solid‐state NMR techniques. Surface‐adsorbed protons are clearly distinguished and two coordination modes of the carboxylic acid are noted: chelating and bridging. It is also found that secondary ligands penetrate the ligand shell and have the same orientation with respect to the surface as the primary ligands, indicating that the ionic or hydrogen‐bonding interactions with the surface are more important than the van der Waals interactions with neighboring ligands. During ligand exchange with amines, the chelating carboxylate is removed preferentially. Finally, it is shown that the HfO2 and ZrO2 NCs catalyze imine formation from acetone and oleylamine. Together with the previously reported catalytic activity of HfO2, these results put colloidal metal oxide nanocrystals squarely in the focus of catalysis research.
Metastatic breast carcinoma in pleural fluid: Correlation of receptor and HER2 status with the primary carcinoma—a pilot study
Authors: Francis Issam M. , Alath Preeta , George Sara S. , Jaragh Mohammed , Al Jassar Ayesha , Kapila Kusum 
Published: September 2016

BackgroundDocumenting the four molecular subtypes of breast carcinoma is significant as they determine response to therapy, disease free interval and survival. Our aim was to document the subtypes defined by immunohistochemistry (IHC) expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2): namely ER + PR+ HER2+; ER + PR + HER2−; ER−PR−HER2+; and ER−PR−HER2− in metastatic breast carcinoma in pleural fluid and compare them with their expression in the primary breast tumor.MethodsOver a period of 18 months, 13 cases of invasive breast carcinoma with metastases to the pleural cavity were studied for subtypes. ER, PR, and HER2 were determined by IHC in the primary breast tumor and the cell blocks of the pleural fluid with metastatic carcinoma.ResultsAge ranged from 33 to 75 years. The primary tumor was ER + PR + HER2+; ER + PR + HER2−; ER−PR−HER2+ and ER−PR−HER2− in 2,9,0 and two cases, respectively while the metastatic tumor in pleural fluid was ER + PR + HER2+; ER + PR + HER2−; ER−PR− HER2+ and ER−PR−HER2− in 6, 3, 3, and 1, respectively. In five cases there was complete correlation between the primary and metastatic tumor. In 7 cases with HER2‐ primary tumor the metastases was HER2+. One from ER + PR+ HER2− primary tumor showed triple negative expression in the metastasis.ConclusionsDetermining the molecular subtype in metastatic breast carcinoma is of importance as it affects the management. In our series 63% of metastatic tumors to the pleural fluid became HER2 positive and would thus require appropriate therapy. Diagn. Cytopathol. 2016;44:980–986. © 2016 Wiley Periodicals, Inc.
Fishing‐induced changes in adult length are mediated by skipped‐spawning
Authors: Wang Hui‐Yu , Chen Ying‐Shiuan , Hsu Chien‐Chung , Shen Sheng‐Feng 
Published: September 2016

AbstractElucidating fishing effects on fish population dynamics is a critical step toward sustainable fisheries management. Despite previous studies that have suggested age or size truncation in exploited fish populations, other aspects of fishing effects on population demography, e.g., via altering life histories and density, have received less attention. Here, we investigated the fishing effects altering adult demography via shifting reproductive trade‐offs in the iconic, overexploited, Pacific bluefin tuna Thunnus orientalis. We found that, contrary to our expectation, mean lengths of catch increased over time in longline fisheries. On the other hand, mean catch lengths for purse seine fisheries did not show such increasing trends. We hypothesized that the size‐dependent energetic cost of the spawning migration and elevated fishing mortality on the spawning grounds potentially drive size‐dependent skipped spawning for adult tuna, mediating the observed changes in the catch lengths. Using eco‐genetic individual‐based modeling, we demonstrated that fishing‐induced evolution of skipped spawning and size truncation interacted to shape the observed temporal changes in mean catch lengths for tuna. Skipped spawning of the small adults led to increased mean catch lengths for the longline fisheries, while truncation of small adults by the purse seines could offset such a pattern. Our results highlight the eco‐evolutionary dynamics of fishing effects on population demography and caution against using demographic traits as a basis for fisheries management of the Pacific bluefin tuna as well as other migratory species.
Predator contributions to belowground responses to warming
Authors: Maran A. M. , Pelini S. L. 
Published: September 2016

AbstractIdentifying the factors that control soil CO2 emissions will improve our ability to predict the magnitude of climate change–soil ecosystem feedbacks. Despite the integral role of invertebrates in belowground systems, they are excluded from climate change models. Soil invertebrates have consumptive and nonconsumptive effects on microbes, whose respiration accounts for nearly half of soil CO2 emissions. By altering the behavior and abundance of invertebrates that interact with microbes, invertebrate predators may have indirect effects on soil respiration. We examined the effects of a generalist arthropod predator on belowground respiration under different warming scenarios. Based on research suggesting invertebrates may mediate soil CO2 emission responses to warming, we predicted that predator presence would result in increased emissions by negatively affecting these invertebrates. We altered the presence of wolf spiders (Pardosa spp.) in mesocosms containing a forest floor community. To simulate warming, we placed mesocosms of each treatment in ten open‐top warming chambers ranging from 1.5° to 5.5°C above ambient at Harvard Forest, Massachusetts, USA. As expected, CO2 emissions increased under warming and we found an interactive effect of predator presence and warming, although the effect was not consistent through time. The interaction between predator presence and warming was the inverse of our predictions: Mesocosms with predators had lower respiration at higher levels of warming than those without predators. Carbon dioxide emissions were not significantly associated with microbial biomass. We did not find evidence of consumptive effects of predators on the invertebrate community, suggesting that predator presence mediates response of microbial respiration to warming through nonconsumptive means. In our system, we found a significant interaction between warming and predator presence that warrants further research into mechanism and generality of this pattern to other systems.
One health—Transdisciplinary opportunities for SETAC leadership in integrating and improving the health of people, animals, and the environment
Authors: Aguirre A. Alonso , Beasley Val R. , Augspurger Tom , Benson William H. , Whaley Janet , Basu Niladri 
Published: September 2016

Abstract

One Health is a collaborative, transdisciplinary effort working locally, nationally, and globally to improve health for people, animals, plants, and the environment. The term is relatively new (from ∼2003), and it is increasingly common to see One Health included by name in interinstitutional research partnerships, conferences, communications, and organizational frameworks, particularly those championed by the human health and veterinary medical communities. Environmental quality is arguably the least developed component within the One Health framework, but can be guided by expertise within the Society of Environmental Toxicology and Chemistry (SETAC). Despite SETAC's long history of tripartite (academic, government, business) interdisciplinary environmental science activities, the term “One Health” is seldom used in SETAC communications (i.e., many of SETAC's activities are guided by One Health, but it is called by other names in SETAC's journals, newsletters, and presentations). Accordingly, the objective of this Focus article is to introduce the One Health concept to the SETAC membership. The article discusses the origins, evolution, and utility of the One Health approach as an organizational framework and provides key examples of ways in which SETAC expertise can benefit the One Health community. The authors assert that One Health needs SETAC and, to be most effective, SETAC needs One Health. Given that One Health to date has focused too little on the environment, on ecosystems, and on contaminants, SETAC's constructive involvement in One Health presents an opportunity to accelerate actions that will ultimately better protect human and ecosystem health. Environ Toxicol Chem 2016;35:2383–2391. © 2016 SETAC
Novel network coding approaches for diffusion‐based molecular nanonetworks
Authors: Akdeniz Bayram Cevdet , Tepekule Burcu , Pusane Ali Emre , Tuğcu Tuna 
Published: September 2016

AbstractThis paper proposes 2 novel network coding approaches for diffusion‐based nanonetworks. In these 2 methods, messages from nanomachines are jointly decoded at the receiver, and in one of the methods multiple molecule types are simultaneously employed to provide simultaneous communications over both nanomachine‐to‐relay and relay‐to‐nanomachine channels. As a result of the simultaneous use of the channel, each communication channel is allowed to use longer symbol intervals. This, in turn, results in a drastically reduced intersymbol interference component in all channels and enables communicating over longer ranges with higher data rates. The performance of the proposed communication system is investigated both analytically and via computer simulations.
A nonrandomized, prospective, clinical study on the impact of circulating tumor cells on outcomes of urothelial carcinoma of the bladder patients treated with radical cystectomy with or without adjuvant chemotherapy
Authors: Soave Armin , Riethdorf Sabine , Dahlem Roland , von Amsberg Gunhild , Minner Sarah , Weisbach Lars , Engel Oliver , Fisch Margit , Pantel Klaus , Rink Michael 
Published: September 2016

To investigate outcomes of urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC) according to the presence of circulating tumor cells (CTC) and the administration of adjuvant chemotherapy (AC). We prospectively enrolled 226 UCB patients treated with RC without neoadjuvant chemotherapy at our institution between 2007 and 2013. Blood samples were obtained from all patients preoperatively and analyzed for CTC using the CellSearch® system. Platinum‐based AC was administered in 50 patients (27.0%). Cox regression models evaluated the association of CTC with disease recurrence, cancer‐specific and overall mortality according to AC administration. 185 patients were available for analyses. CTC were present in 41 patients (22.2%). Patients with presence of CTC received AC more frequently, compared to patients without CTC (p = 0.027). At a median follow‐up of 31 months, the presence of CTC was associated with disease recurrence, cancer‐specific and overall mortality (p‐values < 0.001) in patients without AC administration. In patients who received AC, there was no difference in either endpoint between patients with or without presence of CTC. In multivariable analysis of patients without AC administration, the presence of CTC was an independent predictor for disease recurrence (HR: 4.9; p < 0.001), cancer‐specific (HR: 4.2; p = 0.003) and overall mortality (HR: 4.2; p = 0.001). The CTC status may be implemented in decision‐making regarding AC administration in UCB patients following RC. CTC measurement should be implemented in future UCB studies on systemic chemotherapy to validate our findings.
Evaluation of the sacral nerve plexus in pelvic endometriosis by three‐dimensional MR neurography
Authors: Zhang Xiaoling , Li Meizhi , Guan Jian , Wang Huanjun , Li Shurong , Guo Yan , Liu Mingjuan 
Published: September 2016

PurposeTo investigate the feasibility of three‐dimensional MR neurography (3D MRN) for the sacral plexus using sampling perfection with application‐optimized contrasts using different flip angle evolution (SPACE) sequences, and to demonstrate structural abnormalities in the pelvic nerve of women with pelvic endometriosis.Materials and MethodsTwenty patients with pelvic endometriosis and 20 healthy controls were examined by contrast‐enhanced 3D short time inversion recovery T2‐weighted imaging (CE 3D STIR T2WI) SPACE sequences on 3 Tesla MRI. Image quality and diagnostic confidence of the sequences in identifying abnormalities of the sacral plexus were analyzed and compared with conventional three‐plane images of 2D turbo‐spin echo T2‐weighted images (2D TSE T2WI). The changes in the sacral plexus caused by endometrial lesions were evaluated.ResultsThe sacral plexus was clearly revealed in both healthy controls and patients with endometriosis on 3D STIR SPACE images. A good agreement was reached in the evaluation of both imaging quality (Kappa value [κ] = 0.73–1.00) and diagnostic confidence (κ = 0.66–0.81) when compared between the two independent readers. Abnormalities caused by endometriosis were identified in 17 patients, unilaterally in 10 patients, and bilaterally in 7 patients. Nerve fiber abnormalities of lumbar 5 (L5) were detected in 11 patients, of sacral 1 (S1) in 14 patients and of sacral 2 (S2) in 9 patients.ConclusionCE 3D STIR SPACE sequences demonstrate its significant capacity to investigate and map the sacral plexus, and reveal the compression and adhesion of the sacral plexus nerve as a result of ectopic lesions.Level of Evidence: 3J. Magn. Reson. Imaging 2017;45:1225–1231
Auditory brainstem implant program development
Authors: Schwartz Marc S. , Wilkinson Eric P. 
Published: September 2016

ObjectiveAuditory brainstem implants (ABIs), which have previously been used to restore auditory perception to deaf patients with neurofibromatosis type 2 (NF2), are now being utilized in other situations, including treatment of congenitally deaf children with cochlear malformations or cochlear nerve deficiencies. Concurrent with this expansion of indications, the number of centers placing and expressing interest in placing ABIs has proliferated. Because ABI placement involves posterior fossa craniotomy in order to access the site of implantation on the cochlear nucleus complex of the brainstem and is not without significant risk, we aim to highlight issues important in developing and maintaining successful ABI programs that would be in the best interests of patients.Data SourcesEspecially with pediatric patients, the ultimate benefits of implantation will be known only after years of growth and development. These benefits have yet to be fully elucidated and continue to be an area of controversy. The limited number of publications in this area were reviewed.Review MethodsReview of the current literature was performed.ResultsDisease processes, risk/benefit analyses, degrees of evidence, and U.S. Food and Drug Administration approvals differ among various categories of patients in whom auditory brainstem implantation could be considered for use.ConclusionWe suggest sets of criteria necessary for the development of successful and sustaining ABI programs, including programs for NF2 patients, postlingually deafened adult nonneurofibromatosis type 2 patients, and congenitally deaf pediatric patients. Laryngoscope, 127:1909–1915, 2017