bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying randomness in real networks
Authors: Orsini Chiara , Dankulov Marija M. , Colomer-de-Simón Pol , Jamakovic Almerima , Mahadevan Priya , Vahdat Amin , Bassler Kevin E. , Toroczkai Zoltán , Boguñá Marián , Caldarelli Guido , Fortunato Santo , Krioukov Dmitri 
Published: October 2015

AbstractRepresented as graphs, real networks are intricate combinations of order and disorder. Fixing some of the structural properties of network models to their values observed in real networks, many other properties appear as statistical consequences of these fixed observables, plus randomness in other respects. Here we employ the dk-series, a complete set of basic characteristics of the network structure, to study the statistical dependencies between different network properties. We consider six real networks—the Internet, US airport network, human protein interactions, technosocial web of trust, English word network, and an fMRI map of the human brain—and find that many important local and global structural properties of these networks are closely reproduced by dk-random graphs whose degree distributions, degree correlations and clustering are as in the corresponding real network. We discuss important conceptual, methodological, and practical implications of this evaluation of network randomness, and release software to generate dk-random graphs.
αB-crystallin expression in breast cancer is associated with brain metastasis
Authors: Voduc K David , Nielsen Torsten O , Perou Charles M , Harrell J Chuck , Fan Cheng , Kennecke Hagen , Minn Andy J , Cryns Vincent L , Cheang Maggie C U 
Published: October 2015

Abstract
Background/objectives:
The molecular chaperone αB-crystallin is expressed in estrogen receptor, progesterone receptor and human epidermal growth factor receptor-2 ‘triple-negative’ breast carcinomas and promotes brain and lung metastasis. We examined αB-crystallin expression in primary breast carcinomas with metastatic data to evaluate its association with prognosis and site-specific metastases.

Methods:
αB-crystallin gene (CRYAB) expression was examined using publically available global-gene expression data (n=855 breast tumors) with first site of distant metastasis information (‘855Met’). αB-crystallin protein expression was determined by immunohistochemistry using the clinically annotated British Columbia Cancer Agency (BCCA) tissue microarray (n=3,987 breast tumors). Kaplan–Meier and multivariable Cox regression analyses were used to evaluate the prognostic value of αB-crystallin. Multivariable logistic regression analysis was used to evaluate risks of αB-crystallin and other markers for site of metastasis.

Results:
In the 855Met data set, αB-crystallin gene (CRYAB) expression was an independent predictor of brain as the first distant site of relapse (hazards ratio, HR=1.2, (95% confidence interval, CI 1.0–1.4), P=0.021). In the BCCA series, αB-crystallin protein expression was an independent prognostic marker of poor breast cancer-specific survival (HR=1.3, (95% CI 1.1–1.6), P=0.014). Among patients with metastases, αB-crystallin was the strongest independent predictor of brain metastasis (odds ratio, OR=2.99 (95% CI 1.83–4.89), P<0.0001) and the only independent predictor of brain as the first site of distant metastasis (OR=3.15 (95% CI 1.43–6.95), P=0.005). αB-crystallin was also associated with worse survival (3.0 versus 4.7 months, P=0.007).

Conclusions:
αB-crystallin is a promising biomarker to identify breast cancer patients at high risk for early relapse in the brain, independent of estrogen receptor and human epidermal growth factor receptor-2 status.
Dental calculus evidence of Taï Forest Chimpanzee plant consumption and life history transitions
Authors: Power Robert C. , Salazar-García Domingo C. , Wittig Roman M. , Freiberg Martin , Henry Amanda G. 
Published: October 2015

AbstractDental calculus (calcified dental plaque) is a source of multiple types of data on life history. Recent research has targeted the plant microremains preserved in this mineralised deposit as a source of dietary and health information for recent and past populations. However, it is unclear to what extent we can interpret behaviour from microremains. Few studies to date have directly compared the microremain record from dental calculus to dietary records and none with long-term observation dietary records, thus limiting how we can interpret diet, food acquisition and behaviour. Here we present a high-resolution analysis of calculus microremains from wild chimpanzees (Pan troglodytes verus) of Taï National Park, Côte d’Ivoire. We test microremain assemblages against more than two decades of field behavioural observations to establish the ability of calculus to capture the composition of diet. Our results show that some microremain classes accumulate as long-lived dietary markers. Phytolith abundance in calculus can reflect the proportions of plants in the diet, yet this pattern is not true for starches. We also report microremains can record information about other dietary behaviours, such as the age of weaning and learned food processing techniques like nut-cracking.
The cell competition-based high-throughput screening identifies small compounds that promote the elimination of RasV12-transformed cells from epithelia
Authors: Yamauchi Hajime , Matsumaru Takanori , Morita Tomoko , Ishikawa Susumu , Maenaka Katsumi , Takigawa Ichigaku , Semba Kentaro , Kon Shunsuke , Fujita Yasuyuki 
Published: October 2015

AbstractRecent studies have revealed that cell competition can occur between normal and transformed epithelial cells; normal epithelial cells recognize the presence of the neighboring transformed cells and actively eliminate them from epithelial tissues. Here, we have established a brand-new high-throughput screening platform that targets cell competition. By using this platform, we have identified Rebeccamycin as a hit compound that specifically promotes elimination of RasV12-transformed cells from the epithelium, though after longer treatment it shows substantial cytotoxic effect against normal epithelial cells. Among several Rebeccamycin-derivative compounds, we have found that VC1-8 has least cytotoxicity against normal cells but shows the comparable effect on the elimination of transformed cells. This cell competition-promoting activity of VC1-8 is observed both in vitro and ex vivo. These data demonstrate that the cell competition-based screening is a promising tool for the establishment of a novel type of cancer preventive medicine.
Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus
Authors: Zhang Xiao-Feng , Guo Jiangbo , Zhang Xiuchun , Meulia Tea , Paul Pierce , Madden Laurence V. , Li Dawei , Qu Feng 
Published: October 2015

AbstractInfection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants.
'Visual’ parsing can be taught quickly without visual experience during critical periods
Authors: Reich Lior , Amedi Amir 
Published: October 2015

AbstractCases of invasive sight-restoration in congenital blind adults demonstrated that acquiring visual abilities is extremely challenging, presumably because visual-experience during critical-periods is crucial for learning visual-unique concepts (e.g. size constancy). Visual rehabilitation can also be achieved using sensory-substitution-devices (SSDs) which convey visual information non-invasively through sounds. We tested whether one critical concept – visual parsing, which is highly-impaired in sight-restored patients – can be learned using SSD. To this end, congenitally blind adults participated in a unique, relatively short (~70 hours), SSD-‘vision’ training. Following this, participants successfully parsed 2D and 3D visual objects. Control individuals naïve to SSDs demonstrated that while some aspects of parsing with SSD are intuitive, the blind’s success could not be attributed to auditory processing alone. Furthermore, we had a unique opportunity to compare the SSD-users’ abilities to those reported for sight-restored patients who performed similar tasks visually and who had months of eyesight. Intriguingly, the SSD-users outperformed the patients on most criteria tested. These suggest that with adequate training and technologies, key high-order visual features can be quickly acquired in adulthood and lack of visual-experience during critical-periods can be somewhat compensated for. Practically, these highlight the potential of SSDs as standalone-aids or combined with invasive restoration approaches.
Visualizing chemical states and defects induced magnetism of graphene oxide by spatially-resolved-X-ray microscopy and spectroscopy
Authors: Wang Y. F. , Singh Shashi B. , Limaye Mukta V. , Shao Y. C. , Hsieh S. H. , Chen L. Y. , Hsueh H. C. , Wang H. T. , Chiou J. W. , Yeh Y. C. , Chen C. W. , Chen C. H. , Ray Sekhar C. , Wang J. , Pong W. F. , Takagi Y. , Ohigashi T. , Yokoyama T. , Kosugi N. 
Published: October 2015

AbstractThis investigation studies the various magnetic behaviors of graphene oxide (GO) and reduced graphene oxides (rGOs) and elucidates the relationship between the chemical states that involve defects therein and their magnetic behaviors in GO sheets. Magnetic hysteresis loop reveals that the GO is ferromagnetic whereas photo-thermal moderately reduced graphene oxide (M-rGO) and heavily reduced graphene oxide (H-rGO) gradually become paramagnetic behavior at room temperature. Scanning transmission X-ray microscopy and corresponding X-ray absorption near-edge structure spectroscopy were utilized to investigate thoroughly the variation of the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups, as well as the C 2p(σ*)-derived states in flat and wrinkle regions to clarify the relationship between the spatially-resolved chemical states and the magnetism of GO, M-rGO and H-rGO. The results of X-ray magnetic circular dichroism further support the finding that C 2p(σ*)-derived states are the main origin of the magnetism of GO. Based on experimental results and first-principles calculations, the variation in magnetic behavior from GO to M-rGO and to H-rGO is interpreted and the origin of ferromagnetism is identified as the C 2p(σ*)-derived states that involve defects/vacancies rather than the C 2p(π*) states that are bound with oxygen-containing and hydroxyl groups on GO sheets.
Species extinction thresholds in the face of spatially correlated periodic disturbance
Authors: Liao Jinbao , Ying Zhixia , Hiebeler David E. , Wang Yeqiao , Takada Takenori , Nijs Ivan 
Published: October 2015

AbstractThe spatial correlation of disturbance is gaining attention in landscape ecology, but knowledge is still lacking on how species traits determine extinction thresholds under spatially correlated disturbance regimes. Here we develop a pair approximation model to explore species extinction risk in a lattice-structured landscape subject to aggregated periodic disturbance. Increasing disturbance extent and frequency accelerated population extinction irrespective of whether dispersal was local or global. Spatial correlation of disturbance likewise increased species extinction risk, but only for local dispersers. This indicates that models based on randomly simulated disturbances (e.g., mean-field or non-spatial models) may underestimate real extinction rates. Compared to local dispersal, species with global dispersal tolerated more severe disturbance, suggesting that the spatial correlation of disturbance favors long-range dispersal from an evolutionary perspective. Following disturbance, intraspecific competition greatly enhanced the extinction risk of distance-limited dispersers, while it surprisingly did not influence the extinction thresholds of global dispersers, apart from decreasing population density to some degree. As species respond differently to disturbance regimes with different spatiotemporal properties, different regimes may accommodate different species.
A potential mechanism underlying atypical antipsychotics-induced lipid disturbances
Authors: Cai H L , Tan Q Y , Jiang P , Dang R L , Xue Y , Tang M M , Xu P , Deng Y , Li H D , Yao J K 
Published: October 2015

AbstractPrevious findings suggested that a four-protein complex, including sterol-regulatory element-binding protein (SREBP), SREBP-cleavage-activating protein (SCAP), insulin-induced gene (INSIG) and progesterone receptor membrane component 1 (PGRMC1), within the endoplasmic reticulum appears to be an important regulator responsible for atypical antipsychotic drug (AAPD)-induced lipid disturbances. In the present study, effects of typical antipsychotic drug and AAPDs as well as treatment outcome of steroid antagonist mifepristone (MIF) on the PGRMC1/INSIG/SCAP/SREBP pathway were investigated in rat liver using real-time quantitative polymerase chain reaction (qPCR) and western blot analysis. In addition, serum triacylglycerol, total cholesterol, free fatty acids and various hormones including progesterone, corticosterone and insulin were measured simultaneously. Following treatment with clozapine or risperidone, both lipogenesis and cholesterogenesis were enhanced via inhibition of PGRMC1/INSIG-2 and activation of SCAP/SREBP expressions. Such metabolic disturbances, however, were not demonstrated in rats treated with aripiprazole (ARI) or haloperidol (HAL). Moreover, the add-on treatment of MIF was effective in reversing the AAPD-induced lipid disturbances by upregulating the expression of PGRMC1/INSIG-2 and subsequent downregulation of SCAP/SREBP. Taken together, our findings suggest that disturbances in lipid metabolism can occur at an early stage of AAPD treatment before the presence of weight gain. Such metabolic defects can be modified by an add-on treatment of steroid antagonist MIF enhancing the PGRMC1 pathway. Thus, it is likely that PGRMC1/INSIG-2 signaling may be a therapeutic target for AAPD-induced weight gain.
Noncombatant Immunity and War-Profiteering
Authors: Bazargan Saba 
Published: October 2015

Abstract
The principle of noncombatant immunity prohibits warring parties from intentionally targeting noncombatants. I explicate the moral version of this view and its criticisms by reductive individualists; they argue that certain civilians on the unjust side are morally liable to be lethally targeted to forestall substantial contributions to that war. I then argue that reductivists are mistaken in thinking that causally contributing to an unjust war is a necessary condition for moral liability. Certain noncontributing civilians—notably, war-profiteers—can be morally liable to be lethally targeted. Thus, the principle of noncombatant immunity is mistaken as a moral (though not necessarily as a legal) doctrine, not just because some civilians contribute substantially, but because some unjustly enriched civilians culpably fail to discharge their restitutionary duties to those whose victimization made the unjust enrichment possible. Consequently, the moral criterion for lethal liability in war is even broader than reductive individualists have argued.
Small Intestinal Angioectasias Are Not Randomly Distributed in the Small Bowel and Most May Be Reached by Push Enteroscopy
Authors: Plotkin Eileen , Imaeda Avlin 
Published: October 2015

Goals:
The goal was to describe the location of angioectasias within small bowel on capsule endoscopy and the utility of push enteroscopy versus deep enteroscopy in treatment of overt bleeding from these.

Background:
Overt bleeding from small bowel angioectasias is a clinical challenge. Thalidomide and octreotide can be difficult to prescribe and may not be effective. Endoscopy remains a mainstay of treatment for overt bleeding from angioectasias but data regarding the long-term efficacy of endoscopic therapy are limited. We sought to define the location of small bowel angioectasias using capsule endoscopy and review our outcomes for push and double-balloon enteroscopy.

Methods:
We retrospectively reviewed all 428 capsule endoscopy studies from the Veterans Administration Hospital in West Haven, CT from 2005 to 2012. Location of angioectasias was evaluated using lead mapping and small bowel transit time.

Results:
We identified 69 patients with small bowel angioectasia. At least 66.8% of lesions were in duodenum or ligament of Treitz, with 78.3% within the first 25% of small bowel transit. Twenty-four patients underwent endoscopic treatment of overt bleeding from small bowel angioectasias. Thirty-three percent rebled requiring multiple procedures. Eight patients had 10 anterograde double-balloon examinations. Only 2 patients had both cessation of bleeding with double balloon and lesions outside the reach of push enteroscopy.

Conclusions:
Push enteroscopy for bleeding angioectasias is effective in many patients. Deep enteroscopy may not benefit most patients as most angioectasias are proximal. Patients with deeper lesions tended to have multiple lesions and rebleeding despite deep enteroscopy.
Iron and Vitamin D Deficiency in Healthy Young Children in Western Europe Despite Current Nutritional Recommendations
Authors: Akkermans Marjolijn D. , van der Horst‐Graat Judith M. , Eussen Simone R.B.M. , van Goudoever Johannes B. , Brus Frank 
Published: October 2015

ABSTRACTBackground and aim:Iron deficiency (ID) and vitamin D deficiency (VDD) are the 2 most common micronutrient deficiencies in young children worldwide and may lead to impaired neurodevelopment and rickets, respectively. Risk factors for ID and VDD differ between populations. The objective of this study was to determine the prevalence of and risk factors for ID and VDD in 12‐ to 36‐month‐old children in Western Europe.Methods:This study took place in Germany, the Netherlands, and the United Kingdom from 2012 to 2014. A venous blood sample was taken to establish iron and vitamin D status. ID was defined as serum ferritin <12 μg/L in the absence of infection (high sensitivity C‐reactive protein <10 mg/L). VDD was defined as serum 25‐hydroxyvitamin D <50 nmol/L (20 ng/mL). Furthermore, parents were asked to fill out a questionnaire regarding their child's demographic‐ and socioeconomic characteristics, food intake, sun exposure, and medical history.Results:In 325 children (white race 95%, boys 56%, mean age 20.7 months) the overall prevalence of ID and VDD was 11.8% and 22.8%, respectively. The use of primarily cow's milk as major type of milk was associated with ID (odds ratio [OR] 3.20, 95% confidence interval [CI] 1.12–8.53) and VDD (OR 7.17, 95% CI 3.10–16.57). The use of vitamin D supplements (OR 0.20, 95% CI 0.07–0.56) was associated with a lower prevalence of VDD.Conclusion:Despite current nutritional recommendations, ID and VDD are common in healthy young white children. Health programs focusing on adequate iron and vitamin D intake at an early age should be implemented to prevent deficiencies.
Resolution of Hepatic Artery Thrombosis in 2 Pediatric Liver Transplant Patients
Authors: Banc‐Husu Anna M. , Anupindi Sudha A. , Lin Henry C. 
Published: October 2015

ABSTRACTHepatic artery thrombosis (HAT) is a serious complication after liver transplantation. This is the first report of spontaneous resolution of HAT in pediatric liver transplant patients on low molecular weight heparin therapy. A total of 2 patients, a 26‐month‐old boy who presented with acute liver failure and required emergent liver transplantation and a 15‐year‐old boy with ulcerative colitis and autoimmune hepatitis‐primary sclerosing cholangitis overlap underwent liver transplantation for progressive cirrhosis; both developed HAT during the postoperative period. They were both treated with low molecular weight heparin. Follow‐up imaging for both patients showed resolution of HAT without evidence of collateral flow.
Hierarchical Compression ofC. elegansLocomotion Reveals Phenotypic Differences in the Organisation of Behaviour
Authors: Gomez-Marin Alex , Stephens Greg J. , Brown André E.X. 
Published: October 2015

AbstractRegularities in animal behaviour offer insight into the underlying organisational and functional principles of nervous systems and automated tracking provides the opportunity to extract features of behaviour directly from large-scale video data. Yet how to effectively analyse such behavioural data remains an open question. Here we explore whether a minimum description length principle can be exploited to identify meaningful behaviours and phenotypes. We apply a dictionary compression algorithm to behavioural sequences from the nematode wormCaenorhabditis elegansfreely crawling on an agar plate both with and without food and during chemotaxis. We find that the motifs identified by the compression algorithm are rare but relevant for comparisons between worms in different environments, suggesting that hierarchical compression can be a useful step in behaviour analysis. We also use compressibility as a new quantitative phenotype and find that the behaviour of wild-isolated strains ofC. elegansis more compressible than that of the laboratory strain N2 as well as the majority of mutant strains examined. Importantly, in distinction to more conventional phenotypes such as overall motor activity or aggregation behaviour, the increased compressibility of wild isolates is not explained by the loss of function of the genenpr-1, which suggests that erratic locomotion is a laboratory-derived trait with a novel genetic basis. Because hierarchical compression can be applied to any sequence, we anticipate that compressibility can offer insight into the organisation of behaviour in other animals including humans.