bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of theoretical and statistically derived indices for predicting cognitive decline
Authors: Wilhalme Holly , Goukasian Naira , De Leon Fransia , He Angie , Hwang Kristy S. , Woo Ellen , Elashoff David , Zhou Yan , Ringman John M. , Apostolova Liana G. 
Published: November 2016

AbstractIntroductionBoth theoretical and statistically derived approaches have been used in research settings for predicting cognitive decline.MethodsFifty‐eight cognitively normal (NC) and 71 mild cognitive impairment (MCI) subjects completed a comprehensive cognitive battery for up to 5 years of follow‐up. Composite indices of cognitive function were derived using a classic theoretical approach and exploratory factor analysis (EFA). Cognitive variables comprising each factor were averaged to form the EFA composite indices. Logistic regression was used to investigate whether these cognitive composites can reliably predict cognitive outcomes.ResultsNeither method predicted decline in NC. The theoretical memory, executive, attention, and language composites and the EFA‐derived “attention/executive” and “verbal memory” composites were significant predictors of decline in MCI. The best models achieved an area under the curve of 0.94 in MCI.ConclusionsThe theoretical and the statistically derived cognitive composite approaches are useful in predicting decline in MCI but not in NC.
Fatty acid composition of the postmortem corpus callosum of patients with schizophrenia, bipolar disorder, or major depressive disorder
Authors: Hamazaki K. , Maekawa M. , Toyota T. , Dean B. , Hamazaki T. , Yoshikawa T. 
Published: November 2016

AbstractBackgroundStudies investigating the relationship between n-3 polyunsaturated fatty acid (PUFA) levels and psychiatric disorders have thus far focused mainly on analyzing gray matter, rather than white matter, in the postmortem brain. In this study, we investigated whether PUFA levels showed abnormalities in the corpus callosum, the largest area of white matter, in the postmortem brain tissue of patients with schizophrenia, bipolar disorder, or major depressive disorder.MethodsFatty acids in the phospholipids of the postmortem corpus callosum were evaluated by thin-layer chromatography and gas chromatography. Specimens were evaluated for patients with schizophrenia (n = 15), bipolar disorder (n = 15), or major depressive disorder (n = 15) and compared with unaffected controls (n = 15).ResultsIn contrast to some previous studies, no significant differences were found in the levels of PUFAs or other fatty acids in the corpus callosum between patients and controls. A subanalysis by sex gave the same results. No significant differences were found in any PUFAs between suicide completers and non-suicide cases regardless of psychiatric disorder diagnosis.ConclusionsPatients with psychiatric disorders did not exhibit n-3 PUFAs deficits in the postmortem corpus callosum relative to the unaffected controls, and the corpus callosum might not be involved in abnormalities of PUFA metabolism. This area of research is still at an early stage and requires further investigation.
Implementation of subjective cognitive decline criteria in research studies
Authors: Molinuevo José L. , Rabin Laura A. , Amariglio Rebecca , Buckley Rachel , Dubois Bruno , Ellis Kathryn A. , Ewers Michael , Hampel Harald , Klöppel Stefan , Rami Lorena , Reisberg Barry , Saykin Andrew J. , Sikkes Sietske , Smart Colette M. , Snitz Beth E. , Sperling Reisa , van der Flier Wiesje M. , Wagner Michael , Jessen Frank ,   Subjective Cognitive Decline Initiative (SCD-I) Working Group
Published: November 2016

AbstractIntroductionSubjective cognitive decline (SCD) manifesting before clinical impairment could serve as a target population for early intervention trials in Alzheimer's disease (AD). A working group, the Subjective Cognitive Decline Initiative (SCD‐I), published SCD research criteria in the context of preclinical AD. To successfully apply them, a number of issues regarding assessment and implementation of SCD needed to be addressed.MethodsMembers of the SCD‐I met to identify and agree on topics relevant to SCD criteria operationalization in research settings. Initial ideas and recommendations were discussed with other SCD‐I working group members and modified accordingly.ResultsTopics included SCD inclusion and exclusion criteria, together with the informant's role in defining SCD presence and the impact of demographic factors.DiscussionRecommendations for the operationalization of SCD in differing research settings, with the aim of harmonization of SCD measurement across studies are proposed, to enhance comparability and generalizability across studies.
Proteomic analysis and translational perspective of hepatocellular carcinoma: Identification of diagnostic protein biomarkers by an onco‐proteogenomics approach
Authors: Chiou Shyh‐Horng , Lee King‐Teh 
Published: November 2016

AbstractHepatocellular carcinoma (HCC) has been ranked as the third leading cause of cancer‐related mortality worldwide. Typically, patients are already in advanced stages of liver cirrhosis at the time of HCC diagnosis. Because HCC is often detected at a late stage and is highly aggressive, noninvasive biomarkers are urgently needed for early diagnosis. Recent advances in gene‐expression profiling technologies have enabled molecular classification of HCC into defined subclasses that provide a firm basis for further study of potential mechanisms and biomarkers underlying the development of HCC. This study applied an integrated onco‐proteogenomics approach to identify and characterize HCC biomarkers. Specifically, this study integrated proteomic, genomic, and transcriptomic methods to obtain protein expression profiles of urine and tissue samples from HCC patients and from normal controls. Two mediators of inflammation were positively identified: S100A9 and granulin protein markers, which belong to the cytoplasmic alarmin family of the host innate immune system. These HCC‐associated cancer‐specific biomarkers may have contributing roles not only in the dysregulated processes associated with various inflammatory and autoimmune conditions, but also in tumorigenesis and cancer metastasis.
Organic geochemistry, petrology and palynofacies of Middle Devonian lacustrine flagstones in the Orcadian Basin, Scotland: depositional environment, thermal history and petroleum generation potential
Authors: GHAZWANI ASSAD , LITTKE RALF , SACHSE VICTORIA , FINK REINHARD , MAHLSTEDT NICOLAJ , HARTKOPF-FRÖDER CHRISTOPH 
Published: November 2016

AbstractDuring Middle Devonian time a thick succession of organic-rich, mainly lacustrine flagstones developed within the Orcadian Basin. These petroleum source rocks crop out in northern Scotland. Nineteen samples were studied using organic petrology, palynology and organic geochemistry in order to characterize kerogen type, depositional environment, thermal maturity and petroleum generation potential. Corg, carbonate and sulphur content as well as hydrogen index (HI) values are quite variable (e.g. HI from 79 to 744 mg HC/g Corg). Based on biomarker data, organic material mainly originates from aquatic organic matter deposited under lacustrine conditions with oxygen-depleted, but not permanently anoxic, bottom waters. Petrography reveals small quantities of vitrinite particles, indicating minor input of terrestrial material. This is supported by biomarker data and the palynofacies, which is characterized by a high amount of oil-prone amorphous organic matter (AOM) and generally few miospores. Maturity of the succession studied in Caithness and Orkney is between immature and oil mature. One-dimensional basin modelling shows that a significant remaining hydrocarbon generation potential exists within the Middle Devonian succession. In contrast to the low hydrocarbon generation in the onshore area, offshore oil generation was significant, especially after deposition of thick Upper Jurassic – Upper Cretaceous sediments. At the end of Cretaceous time, hydrocarbon generation ceased due to uplift. The contribution to known oil fields from the Devonian flagstones is a realistic scenario, including a contribution to the Beatrice oil field in the south of the modelled area.
Spiral effect of the law: migrants’ experiences of the state law in Russia – a comparative perspective
Authors: Kubal Agnieszka 
Published: November 2016

AbstractThrough an ethnographic study of the immigration law system in Russia, and interviews with legal professionals and Central Asian migrants themselves, this paper asks: What are the lived experiences of the highly complex, though ambiguous immigration law regime of Russia? According to what ‘rules of the game’ does it operate? Are they specific to Russia only? This paper develops the concept of ‘the spiral effect of the law’ to capture the image of law, as formed through people's experiences of the legal system. Drawing on the comparative tool of analogy, this paper suggests that ‘the spiral effect of the law’ is perhaps not that different from the observable effects of immigration law in other major migration-receiving jurisdictions, namely the US, framed as ‘legal violence’ by Cecilia Menjívar and Leisy Abrego (2012).
Structural and mechanistic insights into regulation of the retromer coat by TBC1d5
Authors: Jia Da , Zhang Jin-San , Li Fang , Wang Jing , Deng Zhihui , White Mark A. , Osborne Douglas G. , Phillips-Krawczak Christine , Gomez Timothy S. , Li Haiying , Singla Amika , Burstein Ezra , Billadeau Daniel D. , Rosen Michael K. 
Published: November 2016

AbstractRetromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Here we demonstrate that TBC1d5, a GTPase-activating protein (GAP) for Rab7, is a high-affinity ligand of the retromer cargo selective complex VPS26/VPS29/VPS35. The crystal structure of the TBC1d5 GAP domain bound to VPS29 and complementary biochemical and cellular data show that a loop from TBC1d5 binds to a conserved hydrophobic pocket on VPS29 opposite the VPS29–VPS35 interface. Additional data suggest that a distinct loop of the GAP domain may contact VPS35. Loss of TBC1d5 causes defective retromer-dependent trafficking of receptors. Our findings illustrate how retromer recruits a GAP, which is likely to be involved in the timing of Rab7 inactivation leading to membrane uncoating, with important consequences for receptor trafficking.
Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II
Authors: Amin Muhamed , Badawi Ashraf , Obayya S. S. 
Published: November 2016

AbstractStructural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 1016 to 1017 W/cm2, but changes increase dramatically if the beam intensity is increased to 1018 W/cm2. In addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.
Examining the themes of STD-related Internet searches to increase specificity of disease forecasting using Internet search terms
Authors: Johnson Amy K. , Mikati Tarek , Mehta Supriya D. 
Published: November 2016

AbstractUS surveillance of sexually transmitted diseases (STDs) is often delayed and incomplete which creates missed opportunities to identify and respond to trends in disease. Internet search engine data has the potential to be an efficient, economical and representative enhancement to the established surveillance system. Google Trends allows the download of de-identified search engine data, which has been used to demonstrate the positive and statistically significant association between STD-related search terms and STD rates. In this study, search engine user content was identified by surveying specific exposure groups of individuals (STD clinic patients and university students) aged 18–35. Participants were asked to list the terms they use to search for STD-related information. Google Correlate was used to validate search term content. On average STD clinic participant queries were longer compared to student queries. STD clinic participants were more likely to report using search terms that were related to symptomatology such as describing symptoms of STDs, while students were more likely to report searching for general information. These differences in search terms by subpopulation have implications for STD surveillance in populations at most risk for disease acquisition.
Synchronization and Bellerophon states in conformist and contrarian oscillators
Authors: Qiu Tian , Boccaletti Stefano , Bonamassa Ivan , Zou Yong , Zhou Jie , Liu Zonghua , Guan Shuguang 
Published: November 2016

AbstractThe study of synchronization in generalized Kuramoto models has witnessed an intense boost in the last decade. Several collective states were discovered, such as partially synchronized, chimera, π or traveling wave states. We here consider two populations of globally coupled conformist and contrarian oscillators (with different, randomly distributed frequencies), and explore the effects of a frequency–dependent distribution of the couplings on the collective behaviour of the system. By means of linear stability analysis and mean–field theory, a series of exact solutions is extracted describing the critical points for synchronization, as well as all the emerging stationary coherent states. In particular, a novel non-stationary state, here named as Bellerophon state, is identified which is essentially different from all other coherent states previously reported in the Literature. A robust verification of the rigorous predictions is supported by extensive numerical simulations.
Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White-winged Flufftail (Sarothrura ayresi)
Authors: Dalton Desire L. , Vermaak Elaine , Smit-Robinson Hanneline A. , Kotze Antoinette 
Published: November 2016

AbstractThe White-winged Flufftail (Sarothrura ayresi) population is listed as globally Critically Endangered. White-winged Flufftails are only known to occur, with any regularity, in the high-altitude wetlands of South Africa and Ethiopia. Threats to the species include the limited number of suitable breeding sites in Ethiopia and severe habitat degradation and loss both in Ethiopia and South Africa. Toll-like receptors (TLRs) are increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune regions of the White-winged Flufftail similar to that observed in other bird species that have undergone population bottlenecks. Low TLR diversity in White-winged Flufftail indicates that this species is more likely to be threatened by changes to the environment that would potentially expose the species to new diseases. Thus, conservation efforts should be directed towards maintaining pristine habitat for White-winged Flufftail in its current distribution range. To date, no studies on immunogenetic variation in White-winged Flufftail have been conducted and to our knowledge, this is the first study of TLR genetic diversity in a critically endangered species.
Cross-linking reveals laminin coiled-coil architecture
Authors: Armony Gad , Jacob Etai , Moran Toot , Levin Yishai , Mehlman Tevie , Levy Yaakov , Fass Deborah 
Published: November 2016

Significance
Large, fibrous, and flexible extracellular matrix proteins are integral to development and maintenance of tissues in the body. Laminin is an extracellular matrix component that provides a physical substrate for cell adhesion and induces signaling pathways that maintain cell health and functionality. Despite the physiological importance of laminin, major gaps remain in our understanding of how its three subunits come together to form the characteristic cross-shaped laminin structure. Laminin was treated with chemicals that link amino acids close in space, providing a map of the subunit arrangement and correcting previous suppositions made on the basis of amino acid sequence inspection alone.
Highly selective inhibition of myosin motors provides the basis of potential therapeutic application
Authors: Sirigu Serena , Hartman James J. , Planelles-Herrero Vicente José , Ropars Virginie , Clancy Sheila , Wang Xi , Chuang Grace , Qian Xiangping , Lu Pu-Ping , Barrett Edward , Rudolph Karin , Royer Christopher , Morgan Bradley P. , Stura Enrico A. , Malik Fady I. , Houdusse Anne M. 
Published: November 2016

Significance
Defects in myosin function are linked to a number of widespread and debilitating diseases, including asthma, chronic obstructive pulmonary disease, and hypertrophic cardiomyopathy. We report here the discovery of an allosteric site that modulates myosin motor function with high specificity that opens the path toward new therapeutic solutions. Identification of specific antimyosin drugs that significantly alter a motor’s function is an imperative first step toward the development of targeted and effective treatments for such diseases. Highly specific drugs against different members of the superfamily would also provide exquisite tools to investigate in cells their functional role. Additionally, detailed, high-resolution studies of the interaction of drugs with their myosin targets provide insights into the molecular mechanism of motor function.
More Landscape, Less Language: Digital Gaming, Moral Panic, and the Linguistic Landscapes of Southern Peru
Authors: Smith Benjamin 
Published: November 2016

AbstractIn this article, I offer an account of the “linguistic landscapes” associated with the commodification and purchase of internet services in southern Peru. Through an account of public signage deployed by internet lounges in this area as well as the ideologies that make sense of it, the analysis reveals one of the ways in which moral panic over digital gaming gets semiotically mediated. To do this, the article develops a theoretical machinery that makes sense of the ways in which public signs—relative to their infrastructural contexts—come to project channels for their uptake. When these relationships are considered relative to the ideologies that target them, what gets revealed are the moral contours of Southern Peruvian public life. The analysis ultimately shows how the concept “linguistic landscape” can be useful for the semiotic study of infrastructure as well as the forms of the public life that it helps to mediate.
A Field Guide for the Review Process: Writing and Responding to Peer Reviews
Authors: Bagchi Rajesh , Block Lauren , Hamilton Rebecca W , Ozanne Julie L 
Published: November 2016

Abstract
The peer review process––both writing reviews for academic journals and responding to reviews of one’s own work––is fundamental to building scientific knowledge. In this article, we explain why you should invest time reviewing, how to write a constructive review, and how to respond effectively to reviews of your own work.
Burden of Healthcare-Associated Viral Respiratory Infections in Children’s Hospitals
Authors: Quach Caroline , Shah Rita , Rubin Lorry G 
Published: November 2016

AbstractObjectiveAlthough healthcare-associated (HA) viral respiratory infections (VRIs) are common in pediatrics, no benchmark for comparison exists. We aimed to determine, compare, and assess determinants of unit-specific HA-VRI incidence rates in 2 children’s hospitals.MethodsThis study was a retrospective comparison of prospective cohorts. The Montreal Children’s Hospital and the Cohen Children’s Medical Center of New York perform prospective surveillance for HA-VRI using standardized definitions that require the presence of symptoms compatible with VRI and virus detection. Cases detected between April 1, 2010, and March 31, 2013, were identified using surveillance databases. Annual incidence rates were calculated, and a generalized estimating equation model was used to assess determinants of HA-VRI rates.ResultsThe overall HA-VRI rate during the 3-year study period was significantly higher at Montreal Children’s Hospital than that at Cohen Children’s Medical Center of New York (1.91 vs 0.80 per 1000 patient-days, respectively;P &lt; .0001). Overall, the HA-VRI incidence rate was lowest in the neonatal intensive care unit. Rates in the pediatric intensive care, oncology, and medical/surgical units were similar. The most common etiology of HA-VRI at both institutions was rhinovirus (49% of cases), followed by parainfluenza virus and respiratory syncytial virus. Hospitals with less than 50% single rooms had HA-VRI rates 1.33 (95% confidence interval, 1.29–1.37) times higher than hospitals with more than 50% single rooms for a given unit type.ConclusionsHA-VRI rates were substantial but different among 2 children’s hospitals. Future studies should examine the effect of HA-VRI and evaluate best practices for preventing such infections.
Evaluation of pseudoprogression in patients with glioblastoma
Authors: Kucharczyk Michael Jonathan , Parpia Sameer , Whitton Anthony , Greenspoon Jeffrey Noah 
Published: November 2016

Abstract

Background.
Management of glioblastoma is complicated by pseudoprogression, a radiological phenomenon mimicking progression. This retrospective cohort study investigated the incidence, prognostic implications, and most clinically appropriate definition of pseudoprogression.

Methods.
Consecutive glioblastoma patients treated at the Juravinski Hospital and Cancer Centre, Hamilton, Ontario between 2004 and 2012 with temozolomide chemoradiotherapy and with contrast-enhanced MRI at standard imaging intervals were included. At each imaging interval, patient responses as per the RECIST (Response Evaluation Criteria in Solid Tumors), MacDonald, and RANO (Response Assessment in Neuro-Oncology) criteria were reported. Based on each set of criteria, subjects were classified as having disease response, stable disease, pseudoprogression, or true progression. The primary outcome was overall survival.

Results.
The incidence of pseudoprogression among 130 glioblastoma patients treated with chemoradiotherapy was 15%, 19%, and 23% as defined by RANO, MacDonald, and RECIST criteria, respectively. Using the RANO definition, median survival for patients with pseudoprogression was 13.0 months compared with 12.5 months for patients with stable disease (hazard ratio [HR]=0.70; 95% confidence interval [CI], 0.35–1.42). Similarly, using the MacDonald definition, median survival for the pseudoprogression group was 11.8 months compared with 12.0 months for the stable disease group (HR=0.86; 95% CI, 0.47–1.58). Furthermore, disease response compared with stable disease was also similar using the RANO (HR=0.52; 95% CI, 0.20–1.35) and MacDonald (HR=0.51: 95% CI, 0.20–1.31) definitions.

Conclusions.
Of all conventional glioblastoma response criteria, the RANO criteria gave the lowest incidence of pseudoprogression. Regardless of criteria, patients with pseudoprogression did not have statistically significant difference in survival compared with patients with stable disease.