bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the essential links in online commercial networks
Authors: Zeng Wei , Fang Meiling , Shao Junming , Shang Mingsheng 
Published: September 2016

AbstractRecommender systems are designed to effectively support individuals' decision-making process on various web sites. It can be naturally represented by a user-object bipartite network, where a link indicates that a user has collected an object. Recently, research on the information backbone has attracted researchers' interests, which is a sub-network with fewer nodes and links but carrying most of the relevant information. With the backbone, a system can generate satisfactory recommenda- tions while saving much computing resource. In this paper, we propose an enhanced topology-aware method to extract the information backbone in the bipartite network mainly based on the information of neighboring users and objects. Our backbone extraction method enables the recommender systems achieve more than 90% of the accuracy of the top-L recommendation, however, consuming only 20% links. The experimental results show that our method outperforms the alternative backbone extraction methods. Moreover, the structure of the information backbone is studied in detail. Finally, we highlight that the information backbone is one of the most important properties of the bipartite network, with which one can significantly improve the efficiency of the recommender system.
Correlation between structural heterogeneity and plastic deformation for phase separating FeCu metallic glasses
Authors: Peng Chuan-Xiao , Song Kai-Kai , Wang Li , Şopu Daniel , Pauly Simon , Eckert Jürgen 
Published: September 2016

AbstractUnlike crystalline metals, the plastic deformation of metallic glasses (MGs) involves a competition between disordering and structural relaxation ordering, which is not well understood, yet. Molecular dynamics (MD) simulations were performed to investigate the evolutions of strain localizations, short-range order (SRO) as well as the free volume in the glass during compressive deformation of Fe50Cu50 MGs with different degrees of phase separation. Our findings indicate that the free volume in the phase separating MGs decreases while the shear strain localizations increase with increasing degree of phase separation. Cu-centered clusters show higher potential energies and Voronoi volumes, and bear larger local shear strains. On the other hand, Fe-centered pentagon-rich clusters in Cu-rich regions seem to play an important role to resist the shear transformation. The dilatation or annihilation of Voronoi volumes is due to the competition between ordering via structural relaxation and shear stress-induced deformation. The present study could provide a better understanding of the relationship between the structural inhomogeneity and the deformation of MGs.
Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China
Authors: Yin Qing-qin , Liu Hai-can , Jiao Wei-wei , Li Qin-jing , Han Rui , Tian Jian-ling , Liu Zhi-guang , Zhao Xiu-qin , Li Ying-jia , Wan Kang-lin , Shen A-dong , Mokrousov Igor 
Published: September 2016

AbstractMycobacterium tuberculosis Beijing genotype originated in China and has undergone a dramatic population growth and global spread in the last century. Here, a collection of M. tuberculosis Beijing family isolates from different provinces across all China was genotyped by high-resolution (24-MIRU-VNTR) and low-resolution, high-rank (modern and ancient sublineages) markers. The molecular profiles and global and local phylogenies were compared to the strain phenotype and patient data. The phylogeographic patterns observed in the studied collection demonstrate that large-scale (but not middle/small-scale) distance remains one of the decisive factors of the genetic divergence of M. tuberculosis populations. Analysis of diversity and network topology of the local collections appears to corroborate a recent intriguing hypothesis about Beijing genotype originating in South China. Placing our results within the Eurasian context suggested that important Russian B0/W148 and Asian/Russian A0/94-32 epidemic clones of the Beijing genotype could trace their origins to the northeastern and northwestern regions of China, respectively. The higher clustering of the modern isolates in children and lack of increased MDR rate in any sublineage suggest that not association with drug resistance but other (e.g., speculatively, virulence-related) properties underlie an enhanced dissemination of the evolutionarily recent, modern sublineage of the Beijing genotype in China.
Tuberculosis of the Clivus
Authors: Joshi Vijay , Valsangkar Shirish , Valsangkar Ashwin , Dekhne Anish , Nivargi Satish , Agrawal Amit 
Published: September 2016

AbstractThe rarity of the tubercular involvement of the clivus makes the preoperative diagnosis difficult. We report a case of a 40-year-old man who presented with right-sided trigeminal neuralgia without any other neurological symptoms or deficits. Postcontrast images showed a dural-based lesion in the region of the clivus which was isointense on T1 images and hypointense on T2 images and the lesion was enhancing after contrast administration suggestive of a tumor. The patient underwent surgical excision of the lesion and the histopathological examination was suggestive of tuberculosis. The patient completed the course of antitubercular therapy and recovered well. Tuberculosis of the clivus region runs an indolent course and following appropriate treatment these patient do well.
Komplikationen bei fehlerhafter Versorgungsstrategie rheumatisch Erkrankter
Authors: Gaulke R. 
Published: September 2016

ZusammenfassungDer orthopädische Rheumatologe muss als Generalist befähigt sein, Behandlungsstrategien zu entwickeln um den komplexen Erkrankungsmustern seiner Patienten gerecht zu werden. Neben umfassender Kennnisse der konservativen und operativen Therapie muss er gute Kenntnisse der immunsuppressiven Therapie aufweisen, um keine iatrogenen Komplikationen zu induzieren. Die Grundprinzipien der orthopädisch-rheumatologischen Versorgungsstrategie beinhalten als oberstes Ziel den Erhalt oder die Wiederherstellung der Selbstständigkeit sowie die Schmerzbefreiung des Patienten. Nach der Schmerzbefreiung kommt der Gehfähigkeit des Patienten die höchste Priorität zu. Die Funktion der Hand, an der auch fortgeschrittene Fehlstellungen häufig lange kompensiert werden, spielt gleichfall eine große Rolle bei der Selbstversorgung. Da die Effekte einer zentralen Korrektur auf die peripheren Gelenke deutliche ausgeprägter ist als umgekehrt, sollte grundsätzlich von zentral nach peripher korrigiert werden. Die Missachtung dieser Prinzipien führt zu vermeidbaren Komplikationen, welche an Fallbeispielen dargestellt werden.
Sequence–structure relations of biopolymers
Authors: Barrett Christopher , Huang Fenix W , Reidys Christian M 
Published: September 2016

Abstract

Motivation
DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded ‘patterns’ in DNA and RNA sequences.

Results
We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence–structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold into the same structure and derive a criterion to identify native structures. We illustrate that there are multiple sequences in the partition function of a fixed structure, each having nearly the same mutual information, that are nevertheless poorly aligned. This indicates the possibility of the existence of relevant patterns embedded in the sequences that are not discoverable using alignments.

Availability and Implementation
The source code is freely available at http://staff.vbi.vt.edu/fenixh/Sampler.zip

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulation-based estimation of branching models for LTR retrotransposons
Authors: Moulin Serge , Seux Nicolas , Chrétien Stéphane , Guyeux Christophe , Lerat Emmanuelle 
Published: September 2016

Abstract

Motivation
LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level.

Results
Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation model. We applied this method to the study of the spread of the transposable elements ROO, GYPSY and DM412 on a chromosome of Drosophila melanogaster.

Availability and Implementation
Our proposal has been implemented using Python software. Source code is freely available on the web at https://github.com/SergeMOULIN/retrotransposons-spread.

Supplementary information
are available at Bioinformatics online.
The Information Research Department, Unattributable Propaganda, and Northern Ireland, 1971–1973: Promising Salvation but Ending in Failure?
Authors: Cormac Rory 
Published: September 2016

Abstract
This article examines the role of the Information Research Department (IRD) in Northern Ireland during the first half of the 1970s. After discussing British conceptualisations of propaganda, it offers a detailed account of IRD activity, including how a Foreign Office department came to be involved in operations on British soil; how IRD propaganda fitted into the broader British state apparatus in Northern Ireland; the activity in which the IRD was engaged—both in Northern Ireland and beyond; and some of the challenges it faced, which ultimately limited the campaign’s effectiveness. It argues that the IRD’s role was driven by decisions taken at the very top of government and took shape against a context of financial cuts, a deteriorating security situation in Northern Ireland, and a tradition of domestic propaganda in the UK. The IRD sought to advance four key themes: exploiting divisions within the IRA; undermining the IRA’s credibility amongst the population; linking the IRA to international terrorism; and portraying the IRA as communist.
Pisan Perspectives: The Carmen in victoriam and Holy War, c.1000–1150
Authors: Grant Alasdair C. 
Published: September 2016

Abstract
The Carmen in victoriam Pisanorum, a verse account of a successful Pisan and Genoese attack of 1087 on the Zīrid King Tamīm ibn al-Muʿizz ibn Bādīs of al-Mahdiyya and Zawīla, should be dated to 1087–95, making it a source of huge importance both for the maritime cities’ wars against the ‘Saracens’, and for the pre-First Crusade development of ideas of holy war. This study argues that the expedition was to a large degree motivated by local, economically charged adventurism in Pisa, but that it found itself under the leadership and intellectual domination of a close-knit, pro-Gregorian party. This party, based around Matilda of Canossa, Pope Victor III, Bishop Benedict of Modena and, most probably, the Pisan author of the Carmen himself, ensured that the attack was publicised as a great success for the Gregorian papacy, at this time in competition with Antipope Clement III. The attack also set a seal upon Pisa’s return from a pro-imperial to a pro-papal position. In publicising the victory, the poet expounded a highly developed discourse of holy war that, while representing his own party’s particular interests, is indicative of wider trends in the Mediterranean that developed over the course of the second half of the eleventh century, rather than appearing suddenly after 1095.
Seasonal shifts in the vertical distribution of fish in a shallow coastal area
Authors: Mustamäki Noora , Jokinen Henri , Scheinin Matias , Bonsdorff Erik , Mattila Johanna 
Published: September 2016

Abstract
Depth structures aquatic habitats, creating substantial differences in the species composition of underwater communities even at small intervals. Those communities also undergo considerable cyclic variation annually. In this study, we surveyed variation in the vertical distribution of fish in a shallow (20 m) coastal basin in the northern Baltic Sea during the ice-free period from May to October. The waters were strongly mixed throughout the season and only transient signs of stratification were observed. As production shifted towards higher trophic levels over summer, with sequential biomass peaks in zooplankton and juvenile fish, the vertical distribution of the entire fish assemblage became increasingly even. The results suggest that spatial resource partitioning can be strongly correlated with seasonal productivity cycles even in physically uniform environments with high connectivity. Further, the results stress the importance of sampling design (seasonal and vertical coverage) of fish studies in shallow coastal areas.
Proton beam therapy for liver metastases from gastric cancer
Authors: Fukumitsu Nobuyoshi , Okumura Toshiyuki , Takizawa Daichi , Numajiri Haruko , Ohnishi Kayoko , Mizumoto Masashi , Aihara Teruhito , Ishikawa Hitoshi , Tsuboi Koji , Sakurai Hideyuki 
Published: September 2016

Abstract
Liver metastases from gastric cancer (LMGC) is a non-curable, fatal disease with a 5-year survival rate of &lt;10%. Although various local treatments have been applied, their clinical utility has not been established. The purpose of this study was to investigate the safety and effectiveness of proton beam therapy (PBT) for the treatment of patients with LMGC. A total of nine patients (seven men, two women; aged 56–78 years) with LMGC who received PBT between 2002 and 2012 were retrospectively reviewed. Patients who had tumors confined to the liver were investigated, and patients who had extrahepatic tumors were excluded. Six of the patients had solitary tumors, and three patients had multiple tumors. The total irradiation dose was 64–77 Gy relative biological effectiveness (RBE), and three patients received concurrent chemotherapy. The overall and progression-free survival (OS and PFS) rates, local control (LC) rate, and adverse effects were investigated. All patients completed treatment without interruption, and late adverse effects of higher than Grade 3 were not observed. The OS rates at 1, 3 and 5 years were 100%, 78% and 56%, respectively (median, 5.5 years); the PFS rates were 67%, 40% and 40% (median, 2.6 years); and the LC rates were 89%, 71% and 71%. PBT was demonstrated to be a safe treatment, and the OS and PFS rates were not inferior to those for other types of local treatment. Therefore, PBT should be considered as an effective local treatment option for patients with LMGC.
Worrying About Crime: Experience, Moral Panics and Public Opinion in London, 1660–1800*
Authors: Shoemaker Robert B 
Published: September 2016

Abstract
This article considers the nature and significance of public opinion about crime in the eighteenth century. Existing research suggests that a combination of increasing crime and the growth of printed literature about crime led to public anxieties which contributed to important changes in judicial and penal policy. The prominent role accorded to the media in these arguments has led some historians to adopt the concept of the moral panic to encapsulate this phenomenon. But this article argues that the impact of such panics on policy was limited, and we need to examine the issue of ‘panic’, and public opinion more generally, from the point of view of the participants, the public who were supposedly rendered anxious by the widespread negative reporting of crime in print. Based on extensive research into diaries and correspondence, the article presents new evidence about Londoners’ actual experiences of crime, what they read about it, and their responses to such reports, during periods of both the presence and absence of supposed moral panics. It suggests that actual experiences of crime were relatively rare, and that Londoners relied primarily on printed sources for their information about crime. Since those representations were actually very diverse, and were often read sceptically, public opinion was resistant to the efforts of ‘moral entrepreneurs’ to induce anxiety. Attitudes were shaped by a complex combination of printed representations, oral discussions, and personal experiences, all reflected through the prism of individual personalities. Consequently, neither individual experiences of crime, nor print culture, created sufficiently strong support for policy changes. Instead, Londoners focused on their ability to shape judicial outcomes through the exercise of discretion when dealing with individual criminals. There are reasons to believe that this individualised approach to crime changed in the nineteenth century, with the adoption of the idea of a ‘criminal class’
Behcet's syndrome in nonendemic regions
Authors: Leccese Pietro , Yazici Yusuf , Olivieri Ignazio 
Published: September 2016

Purpose of review
Behcet's syndrome is more common in certain geographic regions, however, can be seen outside of these areas and need to be included in the differential diagnosis of many patients, as it has overlapping features with many rheumatologic conditions.

Recent findings
Especially in regions with immigrant populations, there seem to be similarities to originating countries in Behcet's prevalence, but the syndrome is not limited to those from certain backgrounds and can be seen in others also. There is emerging evidence that even though the prevalence of Behcet's may be similar to that of endemic areas, in nonendemic regions the condition may be less severe, suggesting potential environment agents in determining the severity of the disease. In addition, women seem to be overrepresented in nonendemic areas and may explain part of the reason for less severe symptoms, as Behcet's tends to be more severe in men.

Summary
The somewhat different presentation of Behcet's syndrome in nonendemic areas needs to be considered when thinking about Behcet's in the differential diagnosis of patients. Research into potentially less severe form of the disease in nonendemic areas may provide new clues to the pathogenesis of this condition.
Microcirculatory Response In Vivo on Local Intraarterial Infusion of Autogenic Adipose-derived Stem Cells or Stromal Vascular Fraction
Authors: Wang Wei Z. 
Published: September 2016

Background:
Both adipose-derived stem cells (ASCs) and stromal vascular fraction (SVF) have been demonstrated to have regenerative properties with therapeutic potential for numerous diseases through local or topical applications. However, it is unclear whether ASC or SVF can be delivered systemically through an intra-arterial infusion. The purpose of this study was to examine the microcirculatory response in vivo on local intraarterial infusion of autogenic ASCs or SVF in a vascular pedicle isolated rat cremaster microcirculation model.

Materials and Methods:
Fat tissue was surgically harvested from the flanks of male Sprague–Dawley rats (n = 12) and processed for SVF isolation. Some SVF samples were cultured for 24 hours for ASC purification. The autogenic SVF (1 × 105) cells (n = 6) or purified ASC (1 × 105) cells (n = 6) cells were infused into the microcirculation of cremaster muscle at a speed of 0.05 mL/min through the cannulation of femoral artery. As this is a vascular pedicle isolated preparation, the infused SVF or ASC cells went nowhere but the cremaster muscle. The video image of the microcirculation was monitored in real time during infusion.

Results:
Arteriole diameter was measured as A1 (100–160 µm), A2 (40–80 µm), and A3/A4 (10–30 µm). Capillary perfusion was quantified in 18 capillary fields of each muscle. There was a significant increase in the diameter of terminal arterioles (P = 0.049) and the capillary density (P = 0.02) after ASC intraarterial infusion. However, a significant cell aggregation, embolisms, and arterial obstruction were observed in the microcirculation in every case during SVF infusion.

Conclusions:
Intraarterial infusion is an appropriate route for the delivery of autogenic ASCs, but not of SVF. SVF-induced microembolisms were the reason for narrowing or blocking the lumen of terminal arterioles, resulting in no flow in the corresponding capillaries.
RETINAL VASCULAR TORTUOSITY AND EXUDATIVE RETINOPATHY IN A FAMILY WITH DYSKERATOSIS CONGENITA MASQUERADING AS FAMILIAL EXUDATIVE VITREORETINOPATHY
Authors: Thanos Aristomenis , Todorich Bozho , Hypes Stephen M. , Yonekawa Yoshihiro , Thomas Benjamin , Randhawa Sandeep , Drenser Kimberly A. , Trese Michael T. 
Published: September 2016

Purpose:
To report a novel presentation of dyskeratosis congenita masquerading as familial exudative vitreoretinopathy.

Methods:
Observational case series involving single family and literature review.

Results:
A brother and sister were diagnosed with familial exudative vitreoretinopathy at ages 4 and 2, respectively. Both patients were managed with laser photocoagulation. Eight years after the initial presentation, both siblings developed pancytopenia secondary to bone marrow failure. Laboratory work-up revealed severely shortened telomere length in both patients, and genetic testing revealed a missense mutation in the gene that encodes the reverse transcriptase component of telomerase, confirming the diagnosis of dyskeratosis congenita. The father of both children was a carrier of the same mutation, who exhibited marked retinal vascular tortuosity of the second-order vessels.

Conclusion:
Dyskeratosis congenita is a severe multisystem disorder, which should be considered in cases of pediatric exudative retinopathies with concurrent signs and/or symptoms of bone marrow failure.
A CASE OF CONE DYSTROPHY ASSOCIATED WITH CHOROIDAL NEOVASCULARIZATION
Authors: Gulkilik Gokhan , Erdur Sevil Karaman , Eliacik Mustafa , Odabasi Mahmut , Ozsutcu Mustafa , Demirci Goktug , Kocabora Mehmet Selim 
Published: September 2016

Purpose:
To report a case of choroidal neovascularization (CNV) in a patient with cone dystrophy (CD).

Methods:
Case report.

Results:
A 20-year-old woman presented with diminished vision in her right eye. Fundus examination showed perifoveal retinal pigment epithelial changes and retinal hemorrhage consistent with subretinal CNV in the right eye, and mild retinal pigment epithelial changes with a dull foveal reflex in the left eye. Optical coherence tomography analysis and fundus fluorescein angiography also confirmed the subfoveal CNV in the right eye. Electroretinography showed decreased amplitudes in photopic and 30-Hz flicker tests in both eyes, which confirmed cone dystrophy. A single intravitreal ranibizumab injection resolved the edema and stabilized the CNV during the follow-up of 6 months.

Conclusion:
Cone dystrophy is an inherited ocular disorder characterized by loss of cone photoreceptors. Association of CNV has been reported in patients with fundus flavimaculatus, best dystrophy, gyrate atrophy, choroideremia, retinitis pigmentosa, adult-onset foveomacular vitelliform dystrophy, Sorsby macular dystrophy, Bietti crystalline dystrophy, and myotonic dystrophy-related macular dystrophy. We report a case of a patient with CD in whom CNV developed in one eye and responded to a single ranibizumab injection.