bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do you know the way to solve equations? Spinning tops and chaotic rabbits
Authors: Goriely Alain 
Published: February 2018

Abstract
In applied mathematics it is of the greatest importance to solve equations. These solutions provide information on key quantities and allow us to give specific answers to scientific problems. ‘Do you know the way to solve equations? Spinning tops and chaotic rabbits’ describes the ways to solve equations and differential equations, outlining the key work of mathematicians Sofia Kovalevskaya, Pierre-Simon Laplace, Paul Painlevé, and Henri Poincaré, whose discovery led to the birth of the theory of chaos and dynamical systems. The difference between an exact and a numerical solution is also explained. Numerical analysis has become the principal tool for querying and solving scientific models.
Mathematics, what is it good for? Quaternions, knots, and more DNA
Authors: Goriely Alain 
Published: February 2018

Abstract
Mathematics has an important place in society, but one that is not always obvious. ‘Mathematics, what is it good for? Quarternions, knots, and more DNA’ considers examples of mathematical theories—quarternions and knot theory—that have found unexpected applicability in sciences and engineering. Quaternions, introduced by William Rowan Hamilton in 1843 during his work on complex numbers, are now routinely used in computer graphics, robotics, missile and satellite guidance, as well as in orbital mechanics and control theory. Knot theory has found unexpected applications in the study of many physical and biological systems, including the study of DNA. Another example is the use of number theory in cryptography.
Where are we going? Networks and the brain
Authors: Goriely Alain 
Published: February 2018

Abstract
Applied mathematics sits at the convergence of collaborative modelling and data research. Its role is fundamental to how we understand our world and develop new technologies. Many applied mathematicians see new challenges as an opportunity to expand their mathematical horizon, and in our rapidly changing society, such new challenges abound. ‘Where are we going? Networks and the brain’ considers recent developments in applied mathematics such as network theory, used in modelling the internet and for studying epidemiology, and its use in studying the brain, an organ of extreme complexity. Applied mathematics is being used to create a mathematical theory of the brain, which is crucial for understanding of a host of neurological conditions.
Improved genomic island predictions with IslandPath-DIMOB
Authors: Bertelli Claire , Brinkman Fiona S L 
Published: February 2018

Abstract

Motivation
Genomic islands (GIs) are clusters of genes of probable horizontal origin that play a major role in bacterial and archaeal genome evolution and microbial adaptability. They are of high medical and industrial interest, due to their enrichment in virulence factors, some antimicrobial resistance genes and adaptive metabolic pathways. The development of more sensitive but precise prediction tools, using either sequence composition-based methods or comparative genomics, is needed as large-scale analyses of microbial genomes increase.

Results
IslandPath-DIMOB, a leading GI prediction tool in the IslandViewer webserver, has now been significantly improved by modifying both the decision algorithm to determine sequence composition biases, and the underlying database of HMM profiles for associated mobility genes. The accuracy of IslandPath-DIMOB and other major software has been assessed using a reference GI dataset predicted by comparative genomics, plus a manually curated dataset from literature review. Compared to the previous version (v0.2.0), this IslandPath-DIMOB v1.0.0 achieves 11.7% and 5.3% increase in recall and precision, respectively. IslandPath-DIMOB has the highest Matthews correlation coefficient among individual prediction methods tested, combining one of the highest recall measures (46.9%) at high precision (87.4%). The only method with higher recall had notably lower precision (55.1%). This new IslandPath-DIMOB v1.0.0 will facilitate more accurate studies of GIs, including their key roles in microbial adaptability of medical, environmental and industrial interest.

Availability and implementation
IslandPath-DIMOB v1.0.0 is freely available through the IslandViewer webserver {{http://www.pathogenomics.sfu.ca/islandviewer/}} and as standalone software {{https://github.com/brinkmanlab/islandpath/}} under the GNU-GPLv3.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms
Authors: Zhou Zilu , Wang Weixin , Wang Li-San , Zhang Nancy Ruonan 
Published: February 2018

Abstract

Motivation
Copy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large-scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous single-nucleotide polymorphism (SNP)-array data are available. An integrated cross-platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele-specific reads.

Results
We propose a statistical framework, integrated CNV (iCNV) detection algorithm, which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform-specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a hidden Markov model. We compare integrated two-platform CNV detection using iCNV to naïve intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only and show that the utilization of allele-specific reads improve CNV detection accuracy compared to existing methods.

Availability and implementation
https://github.com/zhouzilu/iCNV

Supplementary information
Supplementary data are available at Bioinformatics online.
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts
Authors: Swainston Neil , Dunstan Mark , Jervis Adrian J , Robinson Christopher J , Carbonell Pablo , Williams Alan R , Faulon Jean-Loup , Scrutton Nigel S , Kell Douglas B 
Published: February 2018

Abstract

Motivation
Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. PartsGenie is introduced to facilitate the computational design of such synthetic biology parts, bridging the gap between optimization tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language, and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimization algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimization and dissemination of reusable synthetic biology parts through an integrated application.

Availability and implementation
PartsGenie is freely available at https://parts.synbiochem.co.uk.
The Sophists
Authors: McKirahan Richard D. 
Published: February 2018

Sophistês (from sophos, “wise”) originally designated epic poets, prophets, sages, Presocratic philosophers and others with wisdom beneficial to society. Sometime after c. 450 bce it was applied to a new kind of wise people. These men were professional showmen and teachers, the first to provide education beyond the traditional basic subjects—music, poetry, physical training, and arithmetic. They were entrepreneurs, rivals, and competitors who expected to be paid. They traveled from city to city, charging fees for teaching and for their public performances. Each Sophist taught whatever subjects he wished, subjects ranging from mathematics and astronomy to grammar and literary criticism. Many Sophists had interests in language and taught techniques of reasoning, argument, and public speaking that could be useful in public and private life. They came from different cities in the Greek world. They were regarded as attractive and fascinating, but suspicious and dangerous, attitudes reflected in literature, most prominently in Plato’s writings. Plato contrasts individual Sophists with Socrates and sophistry with philosophy. The negative connotations of “sophistry,” “sophism,” and “sophist” are due ultimately to Plato’s influence and should not lead us to suppose that the Sophists engaged in and taught nothing but how to reason badly and construct misleading arguments. They were important in many areas. To them is due the beginnings of the study of language and speech, which stands at the origins of grammar and rhetoric. Others puzzled about the gods and the origins of religion. Some contributed to mathematics. Most importantly, they stand at the origins of moral, political and social philosophy, anthropology, and political theory. Plato’s negative portrayal dominated until the 20th century and the few exceptions interpreted the Sophists uncritically as forerunners of their own philosophical views. Study of the Sophists requires access to information about them, not just to the interpretations of others. This information falls into three sorts: (1) Actual words of the Sophists—complete works and excerpts from works that do not survive in their entirety; (2) summaries and paraphrases of their works; (3) reports in ancient authors of their views and other information about them; and (4) interpretations by ancient and modern authors. The first three sorts form the basis of valid research. They were collected for the first time in 1903 by Diels—Die Fragmente der Vorsokratiker, 6th ed. (1952)—which remains the basic reference point. The Sophists have been viewed from many angles which cannot all be represented adequately in this bibliography, which is intended as a guide to books and articles useful for understanding who the Sophists were, their methods, aims, and achievements, how they were viewed in antiquity, and their contributions to philosophical thought.
HEMORRHAGIC OCCLUSIVE RETINAL VASCULITIS AFTER INTRACAMERAL VANCOMYCIN USE IN CATARACT SURGERY AFTER INTRAVENOUS EXPOSURE
Authors: Alasil Tarek , Wong James J.Y. , Adelman Ron A. , Tom David , Coady Patrick A. 
Published: February 2018

Purpose:
To report a case of hemorrhagic occlusive retinal vasculitis after cataract surgery.

Methods:
A 74-year-old woman presented with blurry vision and distorted vision, which started 2 days after an uncomplicated cataract surgery in the left eye. Intracameral vancomycin was injected during the case. The patient reported being treated with systemic vancomycin in the past.

Results:
The visual acuity was 20/80 in the left eye. She had trace cells in the anterior chamber with no hypopyon and intraocular lens implant within the capsular bag in the left eye. Dilated fundus examination revealed no vitritis, There were large patches of peripheral retinal hemorrhages and retinal ischemia. The patient was diagnosed with hemorrhagic occlusive retinal vasculitis likely secondary to hypersensitivity reaction to intracameral vancomycin. The patient was started on oral prednisone, and the topical difluprednate course was escalated. Within 3 weeks, vision improved to 20/30 in the left eye. She underwent pan retinal photocoagulation targeting the ischemic areas in the periphery.

Conclusion:
The patient had previous exposure to systemic vancomycin, which may have sensitized her immune system. Later on, the hypersensitivity reaction took place after exposure to intracameral vancomycin during cataract surgery. Our hemorrhagic occlusive retinal vasculitis case had a favorable visual outcome, and recognition of this entity will ensure that vancomycin will not be used for infection prophylaxis in the fellow eye at the time of cataract surgery.
PROFOUND VISUAL RECOVERY AT 16 MONTHS AFTER RESOLUTION OF SEROUS RETINAL DETACHMENTS SECONDARY TO THROMBOTIC THROMBOCYTOPENIC PURPURA: CASE REPORT AND LITERATURE REVIEW
Authors: Williams Parker J. , Pearce William A. , Smith Jesse M. , Robinson Joshua 
Published: February 2018

Purpose:
To report a unique case of dramatic improvement in objective visual function during the recovery phase, after resolution of thrombotic thrombocytopenic purpura–related serous retinal detachments and to review prognostic trends in reported cases involving the macula.

Methods:
Observational case report and literature review.

Results:
A 36-year-old white woman with thrombotic thrombocytopenic purpura developed vision loss from serous retinal detachments in both eyes. Over a 16-month period, after both retinae remained attached, best-corrected visual acuity improved from 20/400 to 20/50 in both eyes with dramatic improvement on optical coherence tomography and autofluorescence imaging.

Conclusion:
Although thrombotic thrombocytopenic purpura is a life-threatening illness, visual prognosis in patients with macula off serous retinal detachments appears excellent. Most cases reviewed in literature improved to baseline visual acuity, but recovery periods ranged from days to many months. Hyperautofluorescent granularity on autofluorescence photography may be an indicator of chronic retinal detachment and a more delayed visual recovery.
INVERTED INTERNAL LIMITING MEMBRANE–FLAP TECHNIQUE FOR OPTIC DISK PIT MACULOPATHY: MORPHOLOGIC AND FUNCTIONAL ANALYSIS
Authors: Sborgia Giancarlo , Recchimurzo Nicola , Sborgia Luigi , Niro Alfredo , Sborgia Alessandra , Piepoli Marina , Alessio Giovanni 
Published: February 2018

Purpose:
To analyze morphologic and functional changes after inverted internal limiting membrane–flap technique for optic disk pit maculopathy using optical coherence tomography, multifocal electroretinography, and microperimetry.

Methods:
One case report.

Results:
A 30-year-old woman presented us with decreased visual acuity (20/63) in the left eye because of retinoschisis and serous macular detachment associated with optic disk pit. Optical coherence tomography did not localize the source of intraretinal and subretinal fluid. A partial flattening of serous detachment after vitrectomy with internal limiting membrane peeling, inverted internal limiting membrane–flap technique, and gas tamponade was reported. Visual acuity and multifocal electroretinography improved while retinal sensitivity decreased at microperimetry during 3 months of follow-up.

Conclusion:
Optical coherence tomography is helpful to assess the effectiveness of surgical maneuvers to treat optic disk pit maculopathy. Multifocal electroretinography and microperimetry might offer additional tools for follow-up analysis of retinal function after surgery.
Impact of 3D virtual planning on reconstruction of mandibular and maxillary surgical defects in head and neck oncology
Authors: Witjes Max J.H. , Schepers Rutger H. , Kraeima Joep 
Published: February 2018

Purpose of review
This review describes the advances in 3D virtual planning for mandibular and maxillary reconstruction surgical defects with full prosthetic rehabilitation. The primary purpose is to provide an overview of various techniques that apply 3D technology safely in primary and secondary reconstructive cases of patients suffering from head and neck cancer.

Recent findings
Methods have been developed to overcome the problem of control over the margin during surgery while the crucial decision with regard to resection margin and planning of osteotomies were predetermined by virtual planning. The unlimited possibilities of designing patient-specific implants can result in creative uniquely applied solutions for single cases but should be applied wisely with knowledge of biomechanical engineering principles.

Summary
The high surgical accuracy of an executed 3D virtual plan provides tumor margin control during ablative surgery and the possibility of planned combined use of osseus free flaps and dental implants in the reconstruction in one surgical procedure. A thorough understanding of the effects of radiotherapy on the reconstruction, soft tissue management, and prosthetic rehabilitation is imperative in individual cases when deciding to use dental implants in patients who received radiotherapy.
Magnetization Transfer Ratio in Peripheral Nerve Tissue
Authors: Kollmer Jennifer , Kästel Thorsten , Jende Johann M.E. , Bendszus Martin , Heiland Sabine 
Published: February 2018

Background and Purpose
Magnetization transfer contrast imaging provides indirect information on the concentration of “bound” water protons and their interactions with “free” water molecules. The purpose of this study is to analyze location- and age-dependent changes in the magnetization transfer ratio (MTR) of lower extremity nerves.

Materials and Methods
Ten younger (20–32 years) and 5 older (50–63 years) healthy volunteers underwent magnetization transfer contrast imaging at 3 Tesla Two 3-dimensional gradient echo sequences with and without an off-resonance saturation pulse (repetition time: 58 milliseconds; echo time: 2.46 milliseconds; band width: 530 Hz/Px; flip angle: α = 7°) were acquired at 3 different locations covering the proximal thigh to the distal lower leg in the group of younger volunteers and at 2 different locations covering the proximal to distal thigh in the group of older volunteers. Sciatic and tibial nerve regions of interest (ROIs) were manually drawn and additional ROIs were placed in predetermined muscles. Magnetization transfer ratios were extracted from respective ROIs and calculated for each individual and location.

Results
In young volunteers, mean values of nerve and muscle MTR were not different between the proximal thigh (nerve: 20.34 ± 0.91; muscle: 31.71 ± 0.29), distal thigh (nerve: 19.90 ± 0.98; P = 0.76; muscle: 31.53 ± 0.69; P = 0.87), and lower leg (nerve: 20.82 ± 1.07; P = 0.73; muscle: 32.44 ± 1.11; P = 0.51). An age-dependent decrease of sciatic nerve MTR was observed in the group of older volunteers (16.95 ± 1.2) compared with the group of younger volunteers (20.12 ± 0.65; P = 0.019). Differences in muscle MTR were not significant between older (31.01 ± 0.49) and younger (31.62 ± 0.37; P = 0.20) volunteers.

Conclusion
The MTR of lower extremity nerves shows no proximal-to-distal gradient in young healthy volunteers but decreases with age. For future studies using MTR in peripheral nerve disorders, these findings suggest that referencing magnetization transfer contrast values in terms of age, but not anatomical nerve location is required.
Early Heterogenic Response of Renal Microvasculature to Hemorrhagic Shock/Resuscitation and the Influence of NF-κB Pathway Blockade
Authors: Yan Rui , van Meurs Matijs , Popa Eliane R. , Li Ranran , Zwiers Peter J. , Zijlstra Jan G. , Moser Jill , Molema Grietje 
Published: February 2018

ABSTRACT
Hemorrhagic shock (HS) is associated with low blood pressure due to excessive loss of circulating blood and causes both macrocirculatory and microcirculatory dysfunction. Fluid resuscitation after HS is used in the clinic to restore tissue perfusion. The persistent microcirculatory damage caused by HS and/or resuscitation can result in multiple organ damage, with the kidney being one of the involved organs. The kidney microvasculature consists of different segments that possess a remarkable heterogeneity in functional properties. The aim of this study was to investigate the inflammatory responses of these different renal microvascular segments, i.e., arterioles, glomeruli, and postcapillary venules, to HS and resuscitation (HS/R) in mice and to explore the effects of intervention with a nuclear factor-kappa B (NF-κB) inhibitor on these responses. We found that HS/R disturbed the balance of the angiopoietin-Tie2 ligand-receptor system, especially in the glomeruli. Furthermore, endothelial adhesion molecules, proinflammatory cytokines, and chemokines were markedly upregulated by HS/R, with the strongest responses occurring in the glomerular and postcapillary venous segments. Blockade of NF-κB signaling during the resuscitation period only slightly inhibited HS/R-induced inflammatory activation, possibly because NF-κB p65 nuclear translocation already occurred during the HS period. In summary, although all three renal microvascular segments were activated upon HS/R, responses of endothelial cells in glomeruli and postcapillary venules to HS/R, as well as to NF-κB inhibition were stronger than those in arterioles. NF-κB inhibition during the resuscitation phase does not effectively counteract NF-κB p65 nuclear translocation initiating inflammatory gene transcription.
Aurora B-mediated exclusion of HP1a from latesegregating chromatin prevents formation of micronuclei
Authors: Warecki Brandt , Sullivan William 
Published: February 2018

ABSTRACTLate-segregating acentric chromosomes pose a serious risk to genomic integrity when they are excluded from dividing daughter nuclei and form damage-prone micronuclei. Insight into the cellular mechanisms that prevent the formation of micronuclei from acentrics come from studies demonstrating that acentrics reincorporate into daughter telophase nuclei by passing through Aurora B kinase-dependent channels in the nuclear envelope ofDrosophilaneuroblasts. Here, we uncover a mechanism of nuclear envelope channel formation in which localized concentrations of Aurora B preferentially phosphorylate H3(S10) on heterochromatic acentrics and their associated DNA tethers. This phosphorylation event prevents HP1a from associating with heterochromatin and results in localized inhibition of nuclear envelope reassembly on endonuclease- and X-irradiation-induced acentrics and the main daughter nuclei at the sites of acentric entry to promote the formation of channels. Finally, we find that HP1a also specifies initiation sites of nuclear envelope reassembly on undamaged chromatin. Taken together, these results demonstrate that Aurora B-mediated regulation of HP1a-chromatin interactions plays a key role maintaining genome integrity by locally preventing nuclear envelope assembly and facilitating incorporation of late-segregating acentrics into daughter nuclei.
Ubiquitous abundance distribution of non-dominant plankton across the world’s ocean
Authors: Ser-Giacomi Enrico , Zinger Lucie , Malviya Shruti , De Vargas Colomban , Karsenti Eric , Bowler Chris , De Monte Silvia 
Published: February 2018

AbstractSpecies Abundance Distributions (SADs) bear the imprint of ecological processes that shape biological communities, and are therefore used to discriminate among different scenarios of community assembly. Even though empirical distributions appear to follow a handful of qualitative laws, it is still unclear if and how quantitative variation in SADs reflects peculiar features of the communities and their environmental context. Here, we use the extensive dataset generated by theTaraOceans expedition for marine microbial eukaryotes (protists) and an adaptive algorithm to explore how SADs vary across plankton communities in the global ocean. We show that the decay in abundance of non-dominant OTUs, comprising over 99% of local richness, is commonly governed by a power-law. The power-law exponent varies by less than 10% across locations and shows no biogeographical signature, but is weakly modulated by cell size. Our findings suggest that large-scale ubiquitous ecological processes govern the assembly of non-dominant plankton throughout the global ocean.