bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale Nitrogen Doping in Silicon by Self-Assembled Monolayers
Authors: Guan Bin , Siampour Hamidreza , Fan Zhao , Wang Shun , Kong Xiang Yang , Mesli Abdelmadjid , Zhang Jian , Dan Yaping 
Published: July 2015

AbstractThis Report presents a nitrogen-doping method by chemically forming self-assembled monolayers on silicon. Van der Pauw technique, secondary-ion mass spectroscopy and low temperature Hall effect measurements are employed to characterize the nitrogen dopants. The experimental data show that the diffusion coefficient of nitrogen dopants is 3.66 × 10−15 cm2 s−1, 2 orders magnitude lower than that of phosphorus dopants in silicon. It is found that less than 1% of nitrogen dopants exhibit electrical activity. The analysis of Hall effect data at low temperatures indicates that the donor energy level for nitrogen dopants is located at 189 meV below the conduction band, consistent with the literature value.
Simultaneously targeting inflammatory response and parasite sequestration in brain to treat Experimental Cerebral Malaria
Authors: Dende Chaitanya , Meena Jairam , Nagarajan Perumal , Panda Amulya K. , Rangarajan Pundi N. , Padmanaban Govindarajan 
Published: July 2015

AbstractMalaria afflicts around 200 million people annually, with a mortality number close to 600,000. The mortality rate in Human Cerebral Malaria (HCM) is unacceptably high (15–20%), despite the availability of artemisinin-based therapy. An effective adjunct therapy is urgently needed. Experimental Cerebral Malaria (ECM) in mice manifests many of the neurological features of HCM. Migration of T cells and parasite-infected RBCs (pRBCs) into the brain are both necessary to precipitate the disease. We have been able to simultaneously target both these parameters of ECM. Curcumin alone was able to reverse all the parameters investigated in this study that govern inflammatory responses, CD8+T cell and pRBC sequestration into the brain and blood brain barrier (BBB) breakdown. But the animals eventually died of anemia due to parasite build-up in blood. However, arteether-curcumin (AC) combination therapy even after the onset of symptoms provided complete cure. AC treatment is a promising therapeutic option for HCM.
An invisible soil acidification: Critical role of soil carbonate and its impact on heavy metal bioavailability
Authors: Wang Cheng , Li Wei , Yang Zhongfang , Chen Yang , Shao Wenjing , Ji Junfeng 
Published: July 2015

AbstractIt is well known that carbonates inhibit heavy metals transferring from soil to plants, yet the mechanism is poorly understood. Based on the Yangtze River delta area, we investigated bioaccumulation of Ni and Cd in winter wheat as affected by the presence of carbonates in soil. This study aimed to determine the mechanism through which soil carbonates restrict transport and plant uptake of heavy metals in the wheat cropping system. The results indicate that soil carbonates critically influenced heavy metal transfer from soil to plants and presented a tipping point. Wheat grains harvested from carbonates-depleted (due to severe leaching) soils showed Ni and Cd concentrations 2–3 times higher than those of the wheat grains from carbonates-containing soils. Correspondingly, the incidence of Ni or Cd contamination in the wheat grain samples increased by about three times. With the carbonate concentration >1% in soil, uptake and bioaccumulation of Ni and Cd by winter wheat was independent with the soil pH and carbonate content. The findings suggest that soil carbonates play a critical role in heavy metal transfer from soil to plants, implying that monitoring soil carbonate may be necessary in addition to soil pH for the evaluating soil quality and food safety.
How Properties of Solid Surfaces Modulate the Nucleation of Gas Hydrate
Authors: Bai Dongsheng , Chen Guangjin , Zhang Xianren , Sum Amadeu K. , Wang Wenchuan 
Published: July 2015

AbstractMolecular dynamics simulations were performed for CO2 dissolved in water near silica surfaces to investigate how the hydrophilicity and crystallinity of solid surfaces modulate the local structure of adjacent molecules and the nucleation of CO2 hydrates. Our simulations reveal that the hydrophilicity of solid surfaces can change the local structure of water molecules and gas distribution near liquid-solid interfaces and thus alter the mechanism and dynamics of gas hydrate nucleation. Interestingly, we find that hydrate nucleation tends to occur more easily on relatively less hydrophilic surfaces. Different from surface hydrophilicity, surface crystallinity shows a weak effect on the local structure of adjacent water molecules and on gas hydrate nucleation. At the initial stage of gas hydrate growth, however, the structuring of molecules induced by crystalline surfaces are more ordered than that induced by amorphous solid surfaces.
Molecular determinants of ATP-sensitive potassium channel MgATPase activity: diabetes risk variants and diazoxide sensitivity
Authors: Fatehi Mohammad , Carter Chris R.J. , Youssef Nermeen , Hunter Beth E. , Holt Andrew , Light Peter E. 
Published: July 2015

ATP-sensitive K+ (KATP) channels play an important role in insulin secretion. KATP channels possess intrinsic MgATPase activity that is important in regulating channel activity in response to metabolic changes, although the precise structural determinants are not clearly understood. Furthermore, the sulfonylurea receptor 1 (SUR1) S1369A diabetes risk variant increases MgATPase activity, but the molecular mechanisms remain to be determined. Therefore, we hypothesized that residue–residue interactions between 1369 and 1372, predicted from in silico modelling, influence MgATPase activity, as well as sensitivity to the clinically used drug diazoxide that is known to increase MgATPase activity. We employed a point mutagenic approach with patch-clamp and direct biochemical assays to determine interaction between residues 1369 and 1372. Mutations in residues 1369 and 1372 predicted to decrease the residue interaction elicited a significant increase in MgATPase activity, whereas mutations predicted to possess similar residue interactions to wild-type (WT) channels elicited no alterations in MgATPase activity. In contrast, mutations that were predicted to increase residue interactions resulted in significant decreases in MgATPase activity. We also determined that a single S1369K substitution in SUR1 caused MgATPase activity and diazoxide pharmacological profiles to resemble those of channels containing the SUR2A subunit isoform. Our results provide evidence, at the single residue level, for a molecular mechanism that may underlie the association of the S1369A variant with type 2 diabetes. We also show a single amino acid difference can account for the markedly different diazoxide sensitivities between channels containing either the SUR1 or SUR2A subunit isoforms.
Smartphone‐based WiFi access point localisation and propagation parameter estimation using crowdsourcing
Authors: Zhuang Y. , Li Y. , Lan H. , Syed Z. , El‐Sheimy N. 
Published: July 2015

The locations of WiFi access points (APs) are important for WiFi positioning, especially when a propagation model is used. The parameters for the propagation model, such as the pathloss exponent and noise variance, usually are not available when localising APs in a new environment. A crowdsourcing‐based prototype system is introduced that automatically generates WiFi databases using the uploaded data during normal usage of smartphones. In this system, the adjustment algorithm is originally used for the estimation of AP localisation and propagation parameters. Preliminary experiments show that the average AP localisation error of the prototype system is about 4.0 m in a typical indoor environment with considerably reduced time and labour costs compared with traditional methods.
Efficient method to optimize antibodies using avian leukosis virus display and eukaryotic cells
Authors: Yu Changming , Pike Gennett M. , Rinkoski Tommy A. , Correia Cristina , Kaufmann Scott H. , Federspiel Mark J. 
Published: July 2015

Significance
There is a need for a robust and efficient eukaryotic polypeptide display platform for the discovery and affinity maturation of antibodies and other scaffolds, offering a powerful addition to the existing display technologies that use microorganisms. This study is significant in that it demonstrates just such a technology, avian leukosis virus (ALV) polypeptide display, supplying an innovative and substantive departure from the status quo of antibody display that uses platforms based on microorganisms. The use of eukaryotic cells provides the assurance of maximizing the proper folding, posttranslational modifications, and display of the single-chain Fv antibodies and the virus fusion proteins in virions and on the cell surface. ALV display offers virus and cell display platforms in a eukaryotic expression system.
Novel serologic biomarkers provide accurate estimates of recent
Plasmodium falciparum
exposure for individuals and communities
Authors: Helb Danica A. , Tetteh Kevin K. A. , Felgner Philip L. , Skinner Jeff , Hubbard Alan , Arinaitwe Emmanuel , Mayanja-Kizza Harriet , Ssewanyana Isaac , Kamya Moses R. , Beeson James G. , Tappero Jordan , Smith David L. , Crompton Peter D. , Rosenthal Philip J. , Dorsey Grant , Drakeley Christopher J. , Greenhouse Bryan 
Published: July 2015

Significance
Widely available accurate estimates of malaria exposure are essential for targeting and evaluation of public health interventions. Antibody responses to the malaria parasite can provide information on past exposure, but to date, most such measurements have been based on responses to a small number of parasite proteins chosen by convenience rather than utility and have not provided quantitative information on an individual’s exposure. Our results generated by screening hundreds of responses in children with known exposure histories indicate that responses to a few appropriately selected antigens can provide such information. This new approach can be transformed into high-throughput, low-cost, field-based assays useful for surveillance of malaria and has the potential to be translated into similar tools for other infectious diseases.
Inactive conformation enhances binding function in physiological conditions
Authors: Yakovenko Olga , Tchesnokova Veronika , Sokurenko Evgeni V. , Thomas Wendy E. 
Published: July 2015

Significance
The binding pocket of a receptor often switches between two conformations, with the tight “active” conformation binding ligand with higher affinity than the loose “inactive” one. We demonstrate here that in physiologically relevant nonequilibrium conditions, stabilizing the active conformation actually reduces binding. We furthermore show that ligand binds most rapidly to the inactive conformation, but detaches most slowly from the active conformation, so that each conformation provides an advantage to binding. Mechanical force regulates many adhesive receptors in a way that creates a nonequilibrium cycle that would take advantage of the best property of each conformation, creating a higher effective affinity than either state alone. This provides new insights into the importance of both the inactive state and nonequilibrium conditions.
Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon
Authors: Ijssennagger Noortje , Belzer Clara , Hooiveld Guido J. , Dekker Jan , van Mil Saskia W. C. , Müller Michael , Kleerebezem Michiel , van der Meer Roelof 
Published: July 2015

Significance
Consumption of red meat is associated with increased colorectal cancer risk. We show that the gut microbiota is pivotal in this increased risk. Mice receiving a diet with heme, a proxy for red meat, show a damaged gut epithelium and a compensatory hyperproliferation that can lead to colon cancer. Mice receiving heme together with antibiotics do not show this damage and hyperproliferation. Our data indicate that microbial hydrogen sulfide opens the protective mucus barrier and exposes the epithelium to cytotoxic heme. Antibiotics block microbial sulfide production and thereby maintain the mucus barrier that prevents heme-induced hyperproliferation. Our study indicates that fecal trisulfide is a novel biomarker of mucus barrier integrity, which could be of relevance in human colon disease diagnostics.
Accumulation of non-outer segment proteins in the outer segment underlies photoreceptor degeneration in Bardet–Biedl syndrome
Authors: Datta Poppy , Allamargot Chantal , Hudson Joseph S. , Andersen Emily K. , Bhattarai Sajag , Drack Arlene V. , Sheffield Val C. , Seo Seongjin 
Published: July 2015

Significance
The photoreceptor outer segment (OS) is a cellular compartment that senses light in the eye. Structural and functional defects in the OS are common causes of inherited blindness. Bardet–Biedl syndrome (BBS) is a human genetic disease associated with defective protein trafficking and blindness. However, it is not well understood why or how photoreceptors die in BBS. In this article, we show that the primary cause of photoreceptor degeneration in BBS is likely aberrant accumulation of non-OS proteins in the OS, which is accompanied by OS disorganization and deficiencies of certain proteins in the cell body, resulting from their sequestration in the OS. Our study provides important clues to the pathogenic mechanisms of BBS and the molecular functions of BBS proteins in vivo.
AAV9 delivering a modified human Mullerian inhibiting substance as a gene therapy in patient-derived xenografts of ovarian cancer
Authors: Pépin David , Sosulski Amanda , Zhang Lihua , Wang Dan , Vathipadiekal Vinod , Hendren Katherine , Coletti Caroline M. , Yu Aaron , Castro Cesar M. , Birrer Michael J. , Gao Guangping , Donahoe Patricia K. 
Published: July 2015

Significance
To improve ovarian cancer patient survival, effective treatments addressing chemoresistant recurrences are particularly needed. Mullerian inhibiting substance (MIS) has been shown to inhibit the growth of a stem-like population of ovarian cancer cells. To test this protein therapeutic, malignant ascites from patients with highly resistant recurrent ovarian cancer were used to create patient-derived ovarian cancer xenografts. Mice bearing tumors were treated with adeno-associated virus serotype 9 gene therapy delivering MIS, which inhibited three of five models without signs of toxicity. Finally, we found that 88% of serous tumors express MIS type II receptor by immunohistochemistry. These preclinical data suggest that gene therapy with MIS provides a potentially well-tolerated and effective treatment strategy for chemoresistant serous ovarian cancer.
Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations
Authors: Wang Zhijie , Shen Zhirong , Li Zhenxiang , Duan Jianchun , Fu Shuai , Liu Zhentao , Bai Hua , Zhang Zemin , Zhao Jun , Wang Xiaodong , Wang Jie 
Published: July 2015

Significance
Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI) have demonstrated clinical benefits for patients suffering from non–small cell lung cancer of adenocarcinoma with activating mutation of EGFR. Same mutations observed in lung squamous cell carcinoma do not offer similar benefits. The underlining resistance mechanism revealed in this study turns out to be the concurrent activation of bone morphogenetic proteins (BMPs) signaling pathway in lung squamous cell carcinoma. The combination of EGFR-TKI with inhibitors of BMP receptors signaling pathway overcame the resistance. Such a finding provided a viable clinical strategy to treat those patients.
Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacteriumAnabaenasp. PCC 7120
Authors: Omairi-Nasser Amin , Mariscal Vicente , Austin Jotham R. , Haselkorn Robert 
Published: July 2015

SignificanceCellular communication along the filaments of heterocyst-forming, nitrogen-fixing cyanobacteria has been discussed for at least 50 y but how this might be accomplished is not fully understood. We recently showed that the septum between heterocysts and vegetative cells is pierced by channels 12 nm in diameter and 20 nm long. Here, we show that three proteins, FraC, FraD, and FraG, participate in the formation of the channels although none of them appears to be a structural component of the channels. Moreover, using gold particle-labeled antibody, FraG was found around the cyanophycin plug as well as associated with the cytoplasmic membrane in the neighborhood of the peptidoglycan that forms the septum.
Revisiting Sverdrup's critical depth hypothesis
Authors: Sathyendranath Shubha , Ji Rubao , Browman Howard I. 
Published: July 2015

Abstract
Published more than 60 years ago in this Journal, the article in which Sverdrup proposed the concept of critical depth to explain the initiation of the spring bloom in the North Atlantic has accrued an exceptionally large number of citations and continues to be cited more than 50 times per year. The framework provided by Sverdrup has now been applied, adapted, and tested across many aquatic systems worldwide. Datasets have been collected; models have been built on the framework: these studies have generated new insights into phytoplankton dynamics and interesting debates on the relative importance of the various factors responsible for phytoplankton blooms. This article theme set presents some of the most recent efforts to discuss and test Sverdrup's critical depth hypothesis using a diverse set of approaches, ranging from controlled experiments to field observations as well as numerical and analytical models. The set of papers celebrates an elegant and powerful hypothesis that has had long-lasting influence. It is to be expected that it will also stimulate future research, adding even more to our understanding of one of the most fundamental processes in biological oceanography.
Brainstem and Cranial Nerves
Authors: Flemming Kelly D. , Brazis Paul W. 
Published: July 2015

Abstract
The midbrain (or mesencephalon) is the uppermost segment of the brainstem. This chapter reviews the important structures in the midbrain, including cranial nerves III and IV. The midbrain extends from the level of the trochlear nucleus to an imaginary line drawn between the mammillary bodies and the posterior commissure. Important structures at this level include the cerebral peduncles, superior and inferior colliculi, the red nucleus, the substantia nigra, decussation of the middle cerebellar peduncle, and cranial nerves III and IV.
Cortex Topography and Organization
Authors: Caselli Richard J. , Jones David T. 
Published: July 2015

Abstract
The cerebral cortex functions in a wide variety of simple and complex activities. It is made up of layers of neuronal cell bodies, hence the term gray matter. These layers of cell bodies are then organized into gyri (convolutions). The cortex can be divided into functional components in several different ways. Various schemes exist and may be based on function, cytoarchitecture, topography, or Brodmann areas.
Longitudinal Survey of Microbiota in Hospitalized Preterm Very‐Low‐Birth‐Weight Infants
Authors: Patel Aloka L. , Mutlu Ece A. , Sun Yan , Koenig Lars , Green Stefan , Jakubowicz Andrew , Mryan Janet , Engen Phillip , Fogg Louis , Chen Andrea L. , Pombar Xavier , Meier Paula P. , Keshavarzian Ali 
Published: July 2015

ABSTRACTObjectives:The aim of the present study was to examine the changes in bacteria in hospitalized preterm infants during the first month of life.Methods:Rectal swabs were collected daily from 12 preterm infants. DNA was extracted from swabs from day of birth and weekly thereafter. Bacterial taxa were identified with next generation sequencing using universal bacterial primers targeted at the 16S ribosomal DNA on a 454 Roche titanium platform. Sequences were clustered into operational taxonomic units, and taxonomy was assigned against the Greengenes databank using Quantitative Insights Into Microbial Ecology version 1.4. Quantitative polymerase chain reaction was used to determine the abundance of Bifidobacterium spp. Functional assessment of the microbiome was performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).Results:Average birth weight and gestational age were 1055 g and 28 weeks, respectively. There were 6 to 35 different bacterial families identified in the day‐of‐birth samples, unrelated to the mode of delivery. Richness decreased through hospitalization (week 1, 16.9 ± 7.7 vs weeks 3–5, 10.7 ± 3.4, P < 0.001). The Shannon diversity index demonstrated the lowest diversity at birth, an increase at week 2, followed by a rapid decline at weeks 3 to 5, suggesting the development of a more uniform microbiota composition after 2 weeks of stay at a neonatal intensive care unit. Enterobacteriaceae, Staphylococcaceae, and Enterococcaceae constituted the majority of the bacterial families. Bifidobacterium spp were infrequently detected at extremely low levels. PICRUSt analysis revealed the enhancement of peroxisome, PPAR, and adipocytokine signaling; plant–pathogen interaction; and aminobenzoate degradation pathways in week 1 samples.Conclusions:Our results suggest that although preterm infants have individualized microbiota that are detectable at birth, the differences decrease during the neonatal intensive care unit hospitalization with increasing prominence of pathogenic microbiota.
Superiority of local antimoniate over systemic liposomal amphotericin B therapy in a Leishmania infantum cutaneous leishmaniasis
Authors: Murat Jean-Benjamin , Maubon Danièle , Ravel Christophe , Templier Isabelle , Epaulard Olivier 
Published: July 2015

Introduction:
The therapeutic choice for treating cutaneous leishmaniasis (CL) can be difficult, notably in countries where autochthonous cases are rare. In France, CL is mostly due to imported cases. Leishmania infantum, which is the endemic species in the French south-eastern region, is usually responsible for visceral leishmaniasis but rarely causes the autochthonous cutaneous form of the disease. Intralesional injection of antimonials seems to be the most recommended therapy in the latter case, but particular situations can justify the use of systemic amphotericin B (AmB).

Case presentation:
We report and illustrate a French case of locally acquired CL due to L. infantum that was surprisingly unresponsive to systemic AmB, with clinical worsening and parasitic invasion of the lesion. Thereafter, the patient was successfully treated by intralesional pentavalent antimonial.

Conclusion:
This case supports the choice of intralesional therapy as the first therapeutic option in L. infantum CL, an infrequent situation in France.
destiny– diffusion maps for large-scale single-cell data in R
Authors: Angerer Philipp , Haghverdi Laleh , Büttner Maren , Theis Fabian J. , Marr Carsten , Buettner Florian 
Published: July 2015

ABSTRACTSummaryDiffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single cell expression data. Here we presentdestiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily applydestinyto a recent time-resolved mass cytometry dataset of cellular reprogramming.Availability and implementationdestinyis an open-source R/Bioconductor packagehttp://bioconductor.org/packages/destiny also available athttps://www.helmholtz-muenchen.de/icb/destiny. A detailed vignette describing functions and workflows is provided with the package.Contactcarsten.marr@helmholtz-muenchen.de,f.buettner@helmholtz-muenchen.de