bluuebunny/crossref_metadata_2025_split huggingface dataset:
The direct-to-indirect band gap crossover in two-dimensional van der Waals Indium Selenide crystals
Authors: Mudd G. W. , Molas M. R. , Chen X. , Zólyomi V. , Nogajewski K. , Kudrynskyi Z. R. , Kovalyuk Z. D. , Yusa G. , Makarovsky O. , Eaves L. , Potemski M. , Fal’ko V. I. , Patanè A. 
Published: December 2016

AbstractThe electronic band structure of van der Waals (vdW) layered crystals has properties that depend on the composition, thickness and stacking of the component layers. Here we use density functional theory and high field magneto-optics to investigate the metal chalcogenide InSe, a recent addition to the family of vdW layered crystals, which transforms from a direct to an indirect band gap semiconductor as the number of layers is reduced. We investigate this direct-to-indirect bandgap crossover, demonstrate a highly tuneable optical response from the near infrared to the visible spectrum with decreasing layer thickness down to 2 layers, and report quantum dot-like optical emissions distributed over a wide range of energy. Our analysis also indicates that electron and exciton effective masses are weakly dependent on the layer thickness and are significantly smaller than in other vdW crystals. These properties are unprecedented within the large family of vdW crystals and demonstrate the potential of InSe for electronic and photonic technologies.
High resolution spectroscopy reveals fibrillation inhibition pathways of insulin
Authors: Deckert-Gaudig Tanja , Deckert Volker 
Published: December 2016

AbstractFibril formation implies the conversion of a protein’s native secondary structure and is associated with several neurodegenerative diseases. A better understanding of fibrillation inhibition and fibril dissection requires nanoscale molecular characterization of amyloid structures involved. Tip-enhanced Raman scattering (TERS) has already been used to chemically analyze amyloid fibrils on a sub-protein unit basis. Here, TERS in combination with atomic force microscopy (AFM), and conventional Raman spectroscopy characterizes insulin assemblies generated during inhibition and dissection experiments in the presence of benzonitrile, dimethylsulfoxide, quercetin, and β-carotene. The AFM topography indicates formation of filamentous or bead-like insulin self-assemblies. Information on the secondary structure of bulk samples and of single aggregates is obtained from standard Raman and TERS measurements. In particular the high spatial resolution of TERS reveals the surface conformations associated with the specific agents. The insulin aggregates formed under different inhibition and dissection conditions can show a similar morphology but differ in their β-sheet structure content. This suggests different aggregation pathways where the prevention of the β-sheet stacking of the peptide chains plays a major role. The presented approach is not limited to amyloid-related reasearch but can be readily applied to systems requiring extremely surface-sensitive characterization without the need of labels.
A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement
Authors: Valuchova Sona , Fulnecek Jaroslav , Petrov Alexander P. , Tripsianes Konstantinos , Riha Karel 
Published: December 2016

AbstractMany fundamental biological processes depend on intricate networks of interactions between proteins and nucleic acids and a quantitative description of these interactions is important for understanding cellular mechanisms governing DNA replication, transcription, or translation. Here we present a versatile method for rapid and quantitative assessment of protein/nucleic acid (NA) interactions. This method is based on protein induced fluorescence enhancement (PIFE), a phenomenon whereby protein binding increases the fluorescence of Cy3-like dyes. PIFE has mainly been used in single molecule studies to detect protein association with DNA or RNA. Here we applied PIFE for steady state quantification of protein/NA interactions by using microwell plate fluorescence readers (mwPIFE). We demonstrate the general applicability of mwPIFE for examining various aspects of protein/DNA interactions with examples from the restriction enzyme BamHI, and the DNA repair complexes Ku and XPF/ERCC1. These include determination of sequence and structure binding specificities, dissociation constants, detection of weak interactions, and the ability of a protein to translocate along DNA. mwPIFE represents an easy and high throughput method that does not require protein labeling and can be applied to a wide range of applications involving protein/NA interactions.
Disentangling genetic and environmental risk factors for individual diseases from multiplex comorbidity networks
Authors: Klimek Peter , Aichberger Silke , Thurner Stefan 
Published: December 2016

AbstractMost disorders are caused by a combination of multiple genetic and/or environmental factors. If two diseases are caused by the same molecular mechanism, they tend to co-occur in patients. Here we provide a quantitative method to disentangle how much genetic or environmental risk factors contribute to the pathogenesis of 358 individual diseases, respectively. We pool data on genetic, pathway-based, and toxicogenomic disease-causing mechanisms with disease co-occurrence data obtained from almost two million patients. From this data we construct a multiplex network where nodes represent disorders that are connected by links that either represent phenotypic comorbidity of the patients or the involvement of a certain molecular mechanism. From the similarity of phenotypic and mechanism-based networks for each disorder we derive measure that allows us to quantify the relative importance of various molecular mechanisms for a given disease. We find that most diseases are dominated by genetic risk factors, while environmental influences prevail for disorders such as depressions, cancers, or dermatitis. Almost never we find that more than one type of mechanisms is involved in the pathogenesis of diseases.
HbA1c as a Screening tool for Ketosis in Patients with Type 2 Diabetes Mellitus
Authors: Zhu Bing , Bu Le , Zhang Manna , Gusdon Aaron M. , Zheng Liang , Rampersad Sharvan , Li Jue , Qu Shen 
Published: December 2016

AbstractKetosis in patients with type 2 diabetes mellitus (T2DM) is overlooked due to atypical symptoms. The objective of this study is to evaluate the value of hemoglobin A1c (HbA1c) as a screening tool for ketosis in T2DM patients. This retrospective study consisted of 253 T2DM patients with ketosis at Shanghai 10th People’s Hospital during a period from January 1, 2011 to June 30, 2015. A control group consisted of 221 T2DM patients without ketosis randomly selected from inpatients during the same period. Receiver operating characteristic curve (ROC) analysis was used to examine the sensitivity and specificity of HbA1c as an indicator for ketosis. Higher HbA1c levels were correlated with ketosis. In patients with newly diagnosed T2DM, the area under the curve (AUC) was 0.832, with 95% confidence interval (CI) 0.754–0.911. The optimal threshold was 10.1% (87 mmol/mol). In patients with previously diagnosed T2DM, the AUC was 0.811 (95% CI: 0.767–0.856), with an optimal threshold of 8.6% (70 mmol/mol). HbA1c is a potential screening tool for ketosis in patients with T2DM. Ketosis is much more likely with HbA1c values at ≥10.1% in patients with newly diagnosed T2DM and HbA1c values at ≥8.6% in patients with previously diagnosed T2DM.
Antiretroviral Treatment with Efavirenz Disrupts the Blood-Brain Barrier Integrity and Increases Stroke Severity
Authors: Bertrand Luc , Dygert Levi , Toborek Michal 
Published: December 2016

AbstractThe introduction of antiretroviral drugs (ARVd) changed the prognosis of HIV infection from a deadly disease to a chronic disease. However, even with undetectable viral loads, patients still develop a wide range of pathologies, including cerebrovascular complications and stroke. It is hypothesized that toxic side effects of ARVd may contribute to these effects. To address this notion, we evaluated the impact of several non-nucleoside reverse transcriptase inhibitors (NNRTI; Efavirenz, Etravirine, Rilpivirine and Nevirapine) on the integrity of the blood-brain barrier, and their impact on severity of stroke. Among studied drugs, Efavirenz, but not other NNRTIs, altered claudin-5 expression, increased endothelial permeability, and disrupted the blood-brain barrier integrity. Importantly, Efavirenz exposure increased the severity of stroke in a model of middle cerebral artery occlusion in mice. Taken together, these results indicate that selected ARVd can exacerbate HIV-associated cerebrovascular pathology. Therefore, careful consideration should be taken when choosing an anti-retroviral therapy regimen.
Instant snapshot of the internal structure of Unzen lava dome, Japan with airborne muography
Authors: Tanaka Hiroyuki K. M. 
Published: December 2016

AbstractAn emerging elementary particle imaging technique called muography has increasingly been used to resolve the internal structures of volcanoes with a spatial resolution of less than 100 m. However, land-based muography requires several days at least to acquire satisfactory image contrast and thus, it has not been a practical tool to diagnose the erupting volcano in a real time manner. To address this issue, airborne muography was implemented for the first time, targeting Heisei-Shinzan lava dome of Unzen volcano, Japan. Obtained in 2.5 hours, the resultant image clearly showed the density contrast inside the dome, which is essential information to predict the magnitude of the dome collapse. Since airborne muography is not restricted by topographic conditions for apparatus placements, we anticipate that the technique is applicable to creating images of this type of lava dome evolution from various angles in real time.
Precipitation and carbon-water coupling jointly control the interannual variability of global land gross primary production
Authors: Zhang Yao , Xiao Xiangming , Guanter Luis , Zhou Sha , Ciais Philippe , Joiner Joanna , Sitch Stephen , Wu Xiaocui , Nabel Julia , Dong Jinwei , Kato Etsushi , Jain Atul K. , Wiltshire Andy , Stocker Benjamin D. 
Published: December 2016

AbstractCarbon uptake by terrestrial ecosystems is increasing along with the rising of atmospheric CO2 concentration. Embedded in this trend, recent studies suggested that the interannual variability (IAV) of global carbon fluxes may be dominated by semi-arid ecosystems, but the underlying mechanisms of this high variability in these specific regions are not well known. Here we derive an ensemble of gross primary production (GPP) estimates using the average of three data-driven models and eleven process-based models. These models are weighted by their spatial representativeness of the satellite-based solar-induced chlorophyll fluorescence (SIF). We then use this weighted GPP ensemble to investigate the GPP variability for different aridity regimes. We show that semi-arid regions contribute to 57% of the detrended IAV of global GPP. Moreover, in regions with higher GPP variability, GPP fluctuations are mostly controlled by precipitation and strongly coupled with evapotranspiration (ET). This higher GPP IAV in semi-arid regions is co-limited by supply (precipitation)-induced ET variability and GPP-ET coupling strength. Our results demonstrate the importance of semi-arid regions to the global terrestrial carbon cycle and posit that there will be larger GPP and ET variations in the future with changes in precipitation patterns and dryland expansion.
Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis
Authors: Pan Yuchen , Sackmann Eric K. , Wypisniak Karolina , Hornsby Michael , Datwani Sammy S. , Herr Amy E. 
Published: December 2016

AbstractHigh-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
Acetyl-11-Keto-β-Boswellic Acid Attenuates Prooxidant and Profibrotic Mechanisms Involving Transforming Growth Factor-β1, and Improves Vascular Remodeling in Spontaneously Hypertensive Rats
Authors: Shang Peijin , Liu Wenxing , Liu Tianlong , Zhang Yikai , Mu Fei , Zhu Zhihui , Liang Lingfei , Zhai Xiaohu , Ding Yi , Li Yuwen , Wen Aidong 
Published: December 2016

AbstractVascular remodeling is an important complication of hypertension with oxidative stress-related profibrotic pathways involved. The transforming growth factor β1 (TGF-β1) has been shown to be a potential target of vasoprotection, and has multiple roles in vascular remodeling. Acetyl-11-Keto-β-Boswellic Acid (AKBA) is one of the active principles of Boswellic acids, and shows antioxidant activity in many diseases. The study is to determine effects of AKBA on systemic oxidative stress of hypertension and vascular remodeling. In the experiments, spontaneously hypertensive rats (SHR) were used. And in vitro, fibroblast was pretreated with AKBA before Ang II stimuli. In the results, treatment of AKBA markedly reduced oxidative stress, and decreased vascular remodeling by restoring vascular wall parameters and improving vascular reactivity. AKBA dramatically reduced TGF-β1 and Smad3 expression, as shown in immunofluorescence and immunohistochemistry. In cultured fibroblast, AKBA decreased intracellular ROS levels. Cell viability and proliferation, as well as migration were inhibited by AKBA. Additionally, treatment of AKBA significantly decreased TGF-β1 secretion in culture supernatant. Expression of TGF-β1, Smad3, P-Smad3 and Smad7 were also decreased by AKBA in fibroblast. In conclusion, AKBA is able to attenuate oxidative stress and profibrotic mechanisms, and improve vascular remodeling in hypertension through TGF-β1/Smad3 pathway.
A bio-enabled maximally mild layer-by-layer Kapton surface modification approach for the fabrication of all-inkjet-printed flexible electronic devices
Authors: Fang Yunnan , Hester Jimmy G. D. , Su Wenjing , Chow Justin H. , Sitaraman Suresh K. , Tentzeris Manos M. 
Published: December 2016

AbstractA bio-enabled, environmentally-friendly, and maximally mild layer-by-layer approach has been developed to surface modify inherently hydrophobic Kapton HN substrates to allow for great printability of both water- and organic solvent-based inks thus facilitating the full-inkjet-printing of flexible electronic devices. Different from the traditional Kapton surface modification approaches which are structure-compromising and use harsh conditions to target, and oxidize and/or remove part of, the surface polyimide of Kapton, the present Kapton surface modification approach targeted the surface electric charges borne by its additive particles, and was not only the first to utilize environmentally-friendly clinical biomolecules to build up a thin film of protamine-heparin complex on Kapton, but also the first to be conducted under minimally destructive and maximally mild conditions. Besides, for electrically charged ink particles, the present surface modification method can enhance the uniformity of the inkjet-printed films by reducing the “coffee ring effect”. As a proof-of-concept demonstration, reduced graphene oxide-based gas sensors, which were flexible, ultra-lightweight, and miniature-sized, were fully-inkjet-printed on surface modified Kapton HN films and tested for their sensitivity to dimethyl methylphosphonate (a nerve agent simulant). Such fabricated sensors survived a Scotch-tape peel test and were found insensitive to repeated bending to a small 0.5 cm radius.
Impaired Function of Peripherally Induced Regulatory T Cells in Hosts at High Risk of Graft Rejection
Authors: Inomata Takenori , Hua Jing , Di Zazzo Antonio , Dana Reza 
Published: December 2016

AbstractRegulatory T cells (Tregs) are crucial for allograft survival. Tregs can be divided into thymus-derived natural Tregs (tTregs) and peripherally-derived induced Tregs (pTregs). Here, we determine whether the suppressive function of Treg subsets is hampered in hosts who are at high risk for rejecting their graft. To induce graft beds that promote high risk of transplant rejection, intrastromal corneal sutures were placed two weeks prior to the transplant procedure in mice. We demonstrate that in high-risk recipients the frequencies and function of pTregs (but not tTregs) are suppressed. Reduced function of pTregs correlated with decreased expression of CTLA-4, interleukin-10, and transforming growth factor-β. Adoptive transfer of pTregs from mice at low risk of subsequent graft rejection is able to rescue graft survival in recipients that are at high risk of rejecting their grafts. Our data suggest that impaired function of pTregs, but not tTregs, mediates the loss of immune tolerance and promotes allograft rejection.
The clinical characteristics of corticosteroid-resistant refractory Mycoplasma Pneumoniae pneumonia in children
Authors: Yan Yongdong , Wei Yuzhen , Jiang Wujun , Hao Chuangli 
Published: December 2016

AbstractTo analyze the clinical characteristics of corticosteroid-resistant refractory Mycoplasma pneumoniae pneumonia (RMPP) and explore the related factors that predict corticosteroid-resistant RMPP. Retrospective analysis of 183 children with RMPP in our hospital admitted between January 1, 2012, and December 31, 2014 was performed. Of the 183 RMPP cases, 36 (19.7%) were corticosteroid-resistant RMPP cases. Corticosteroid-resistant RMPP cases had a longer duration of fever and hospitalization compared with corticosteroid-sensitive RMPP cases (P < 0.05). The radiographic findings of 123 (83.7%) cases of corticosteroid-sensitive RMPP apparently resolved after one week of corticosteroid treatment compared with 4 (11.1%) corticosteroid-resistant RMPP cases that had apparently resolution (P < 0.01). Twenty-four (75%) corticosteroid-resistant RMPP patients who received bronchoscopy had mucus plug formation while none of the corticosteroid-sensitive RMPP patients had mucus plug formation (P < 0.05). Multiple logistic regression analysis showed that duration of fever ≥11 days, percentage of lymphocytes ≤32%, CRP ≥48.73 mg/L and LDH ≥ 545.7 U/L were significant predictors of corticosteroid-resistant RMPP. Patients with corticosteroid-resistant RMPP had more severe presentations and more serious radiological findings. Clinicians might use the parameters of duration of fever, CRP, LDH and proportion of lymphocytes to identify children at higher risk of corticosteroid-resistant RMPP.
Facile synthesis of magnetic Co nanofoam by low‐temperature thermal decomposition of Co glycerolate
Authors: Bartůněk Vilém , Huber Štěpán , Luxa Jan , Sofer Zdeněk , Kuchař Martin , Dobrovolný Kryštof , Jankovský Ondřej 
Published: December 2016

Fine metal cobalt (Co) nanofoam was prepared via simple thermal decomposition of amorphous non‐stoichiometric Co glycerolate under 50 vol% H2/50 vol% N2 atmosphere at 450°C. The nanofoam was characterised by X‐ray diffraction, scanning electron microscope/energy dispersive spectroscopy and its magnetic properties were investigated by SQUID magnetometer. This magnetic nanofoam consisted of slightly sintered Co nanocrystals; their average size was 30 nm.
Conscience in the Public Square: The Pivoting Positions of the USCCB and ACLU around the Religious Freedom Restoration Act
Authors: Gatta Luke A. 
Published: December 2016

The debate on the meaning of the Religious Freedom Restoration Act (RFRA) is rapidly developing. Taking three snapshots in the bill's history (in 1993 at its origin, in 2014 during Burwell v. Hobby Lobby, and in 2015 after Obergefell v. Hodges), this essay evaluates the stances taken on the RFRA by the American Civil Liberties Union (ACLU) and the US Conference of Catholic Bishops (USCCB). Although the ACLU initially supported the bill, it now campaigns against it. In contrast the USCCB, once hesitant to endorse the RFRA, fervently defends it today. Evaluating these pivoting positions, this essay suggests that at the heart of the debate on RFRA lies a difference in understanding the right to follow one's conscience in the public square. Lay Summary: This essay evaluates how the ACLU and the USCCB differ in their understanding of conscience. Next, the essay demonstrates that this difference leads to opposing viewpoints on the Religious Freedom Restoration Act today. Although both initially supported the Religious Freedom Restoration Act at its signing in 1993, the ACLU has now disavowed the bill after it had been used to permit following religious-based conscience in the public square.
SED-ML web tools: generate, modify and export standard-compliant simulation studies
Authors: Bergmann Frank T , Nickerson David , Waltemath Dagmar , Scharm Martin 
Published: December 2016

Abstract

Summary
The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions.

Availability and Implementation
http://sysbioapps.dyndns.org/SED-ML_Web_Tools/.
Primerize-2D: automated primer design for RNA multidimensional chemical mapping
Authors: Tian Siqi , Das Rhiju 
Published: December 2016

Abstract

Summary
Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications.

Availability and Implementation
http://primerize2d.stanford.edu

Supplementary information
Supplementary data are available at Bioinformatics online.