bluuebunny/crossref_metadata_2025_split huggingface dataset:
On a Discretization of Confocal Quadrics. A Geometric Approach to General Parametrizations
Authors: Bobenko Alexander I , Schief Wolfgang K , Suris Yuri B , Techter Jan 
Published: November 2018

Abstract
We propose a discretization of classical confocal coordinates. It is based on a novel characterization thereof as factorizable orthogonal coordinate systems. Our geometric discretization leads to factorizable discrete nets with a novel discrete analog of the orthogonality property. A discrete confocal coordinate system may be constructed geometrically via polarity with respect to a sequence of classical confocal quadrics. Various sequences correspond to various discrete parametrizations. The coordinate functions of discrete confocal quadrics are computed explicitly. The theory is illustrated with a variety of examples in two and three dimensions. These include confocal coordinate systems parametrized in terms of Jacobi elliptic functions. Connections with incircular nets and a generalized Euler–Poisson–Darboux system are established.
Neutron transfer reactions in accreting neutron stars
Authors: Chugunov A I 
Published: November 2018

ABSTRACT
I suggest a novel type of nuclear reactions in accreting neutron stars – neutron transfer, which is quantum tunnelling of weakly bounded neutron from one nucleus to another. I estimate the rate of this process for fixed nuclei separation and then average the result over realistic distribution of nuclei to get the rate value for astrophysical conditions. The neutron transfer can modify reaction chains in accreting neutron stars, thus affecting their heating and cooling. In particular, it can suppress cooling by URCA pairs of nuclei, which is supposed to be crucial for the hottest neutron stars.
Combined Transpetrosal Approach With Preservation of Superior Petrosal Vein Drainage for a Cerebellopontine Angle Epidermoid Cyst Extending Into Meckel's Cave: 3-Dimensional Operative Video
Authors: Matsushima Ken , Kohno Michihiro , Nakajima Nobuyuki , Ichimasu Norio 
Published: November 2018

Abstract
The combined transpetrosal approach enables wide exposure around the petroclival region by cutting the tentorium and superior petrosal sinus. We often choose this approach for removal of tumors ventral to the facial and vestibulocochlear nerves, such as petroclival meningioma and epidermoid cyst, because complete removal of the tumor under direct visualization is required to prevent its later recurrence, especially in young patients. Recent reports revealed anatomical variations of the drainage of the superior petrosal sinus, and dural incision considering preservation of the superior petrosal vein was proposed.
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This 3-dimensional video shows a patient with an epidermoid cyst, which was surgically treated using the combined transpetrosal approach, with consideration of the variation of the superior petrosal sinus and preservation of the drainage route of the superior petrosal vein. The video was reproduced after informed consent of the patient. The patient is a 31-yr-old woman who presented with a left cerebellopontine angle epidermoid cyst extending into Meckel's cave. The superior petrosal sinus was of the lateral type, draining only laterally into the transverse–sigmoid junction without medial connection with the cavernous sinus.
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The combined transpetrosal approach was performed with cutting of the superior petrosal sinus medial to the entry point of the superior petrosal vein, in order to preserve its drainage into the transverse–sigmoid junction. Meckel’ cave was opened along its lateral margin, and tumor removal was accomplished, leaving only a minute part of the capsule strongly adhering to the neurovascular structures. The patient had no new permanent neurological deficits during follow-up.
The figures in the video were modified from Matsushima et al
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by permission of the Congress of Neurological Surgeons.
The Impact of Endoscopic Retrograde Cholangiopancreatography on Islet Cell Yield During Total Pancreatectomy With Islet Autotransplantation
Authors: LaBarre Nicolas T. , Morgan Katherine A. , Adams David B. , Waljee Akbar K. , Coté Gregory A. , Elmunzer B. Joseph 
Published: November 2018

Objectives
Many patients with recurrent acute and chronic pancreatitis who are candidates for total pancreatectomy and islet cell autotransplantation (TPIAT) undergo endoscopic retrograde cholangiopancreatography (ERCP). However, little is known on the impact of ERCP on TPIAT outcomes. We aimed to explore the effect of antecedent ERCP on islet yield and postoperative insulin requirement after TPIAT.

Methods
Through a prospectively maintained database, we identified patients who underwent TPIAT at our institution between 2009 and 2016. After adjusting for confounders, islet cell yield and postoperative insulin requirement were compared between subjects who did and did not undergo ERCP within 2 years prior to TPIAT.

Results
Data were available on 167 TPIAT patients during the study period; 105 (62.9%) had undergone ERCP within 2 years prior. Prior ERCP was not associated with a reduction in islet equivalents per patient kilogram (odds ratio, 1.37; 95% confidence interval, 0.75–2.5; P = 0.31). Antecedent ERCP was not associated with increased postoperative insulin requirement among patients with no diabetes undergoing TPIAT (odds ratio, 0.85; 95% confidence interval, 0.39–1.83; P = 0.67).

Conclusions
Antecedent ERCP does not appear to have a deleterious impact on islet cell yield during TPIAT. Additional multicenter data are needed to more clearly determine the impact of ERCP in this context.
Perineural Invasion is a Strong Prognostic Moderator in Ampulla of Vater Carcinoma
Authors: Luchini Claudio , Veronese Nicola , Nottegar Alessia , Riva Giulio , Pilati Camilla , Mafficini Andrea , Stubbs Brendon , Simbolo Michele , Mombello Aldo , Corbo Vincenzo , Cheng Liang , Yachida Shinichi , Wood Laura D. , Lawlor Rita T. , Salvia Roberto , Scarpa Aldo 
Published: November 2018

Objective
Ampulla of Vater carcinoma (AVC) has a broad spectrum of different prognoses. As such, new moderators of survival are urgently needed. We aimed at clarifying the prognostic role of perineural invasion in AVC.

Methods
Using PubMed and SCOPUS databases, we conducted the first systematic review and meta-analysis on this topic.

Results
Analyzing 29 articles for a total of 2379 patients, we found that the presence of perineural invasion increased the risk of all-cause mortality more than 2 times (relative risk [RR], 2.07; 95% confidence interval [CI], 1.78–2.42 [P < 0.0001]; hazard ratio [HR], 2.72; 95% CI, 1.86–3.97 [P < 0.0001]), of cancer-specific mortality more than 6 times (RR, 6.12; 95% CI, 3.25–11.54 [P < 0.0001]; HR, 6.59; 95% CI, 2.29–3.49 [P < 0.0001]), and of recurrence more than 2 times (RR, 2.63; 95% CI, 1.89–3.67 [P < 0.0001]; HR, 2.54; 95% CI, 1.24–5.21 [P = 0.01]).

Conclusions
Perineural invasion is strongly associated with a poorer prognosis in AVC, influencing both survival and risk of recurrence. It should be reported in the final pathology report and should be taken into account by future oncologic staging systems, identifying a group of AVC with a more malignant biological behavior.
Expression of Epithelial-Mesenchymal Transition Proteins in Pancreatic Anaplastic (Undifferentiated) Carcinoma
Authors: Ishida Kazuyuki , Yamashita Rina , Osakabe Mitsumasa , Uesugi Noriyuki , Yamada Noriyuki , Nitta Hiroyuki , Fujishima Fumiyoshi , Motoi Fuyuhiko , Suzuki Hiroyoshi , Shimamura Hiromune , Noda Yutaka , Sawai Takashi , Unno Michiaki , Sasano Hironobu , Sasaki Akira , Sugai Tamotsu 
Published: November 2018

Objectives
The aim of this study was to identify an association of pancreatic anaplastic carcinoma (APC) with the epithelial-mesenchymal transition (EMT).

Methods
Resected APCs (n = 24) were examined to assess components of APCs, including carcinomatous, transitional, and sarcomatous regions. Analysis was performed based on the immunoreactivity of E-cadherin and 3 EMT-related proteins: Slug (zinc finger protein SNAI2), Twist (Twist-related protein 1), and Zeb1 (zinc finger E-box–binding homeobox 1). Expression score was determined based on staining intensity and stained area of the target cells. Finally, we performed a hierarchical clustering based on the expression pattern of E-cadherin and EMT-related proteins of the sarcomatous component.

Results
The expression score of E-cadherin decreased in the order of sarcomatous > transitional > carcinomatous components (P < 0.01). Although there were significant differences in the immunohistochemical scores of Slug, Twist, and Zeb1 between carcinomatous and transitional components (P < 0.01), the significant difference in immunohistochemical score of Zeb1 between transitional and sarcomatous components was found (P < 0.05). Furthermore, APCs were divided into 2 subgroups based on the expression patterns of E-cadherin and EMT-related proteins (hierarchical clustering analysis). Consequently, these subgroups were distinguished by Twist expression.

Conclusions
Epithelial-mesenchymal transition plays an essential role in the pathogenesis of APC.
Transient Expression of Interleukin-21 in the Second Hit of Acute Pancreatitis May Potentiate Immune Paresis in Severe Acute Pancreatitis
Authors: Thomson John-Edwin , Nweke Ekene E. , Brand Martin , Nel Marietha , Candy Geoffrey P. , Fonteh Pascaline N. 
Published: November 2018

Objectives
Interleukin-21 (IL-21) is a cytokine associated with tissue inflammation, autoimmune and infectious diseases. Organ dysfunction and death can occur in patients with acute pancreatitis (AP) in two distinct clinical phases. Initially, a systemic inflammatory response syndrome may be followed by systemic sepsis from infected pancreatic necrosis, known as the “second hit.” The expression and possible role of IL-21 in AP has not been established.

Methods
Thirty-six patients with mild, moderate, and severe AP (SAP) were enrolled. Peripheral blood samples of patients were drawn on days 7, 9, 11, and 13. Reverse transcription–polymerase chain reaction and enzyme-linked immunosorbent assay were performed to determine the expression and concentration of IL-21.

Results
Interleukin-21 mRNA levels increased significantly at day 9 in severe (P = 0.002) pancreatitis compared with both the mild and control patient groups. At the protein level, IL-21 was elevated in SAP patients compared with those with mild pancreatitis, although this was not significant. Furthermore, day 9 IL-21 was elevated in septic SAP patients and patients with pancreatic necrosis.

Conclusions
Interleukin-21 is transiently elevated in SAP compared with the mild/moderate group, and hence IL-21 may contribute to the immune imbalance that occurs in AP.
Performance of a Multidisciplinary Pancreatic Cancer Conference in Predicting and Managing Resectable Pancreatic Cancer
Authors: Rao Bharat , Syed Aslam , Singh Shailendra , Gulati Abhishek , Moussiade Ghita , Garg Mrinal , Sharma Manav , Morrissey Suzanne , Williams Harry , Atkinson Donald , Schiffman Suzanne , Monga Dulabh , Lupetin Anthony , Kirichenko Alexander , Mitre Marcia , Tang Amy , Dhawan Manish , Kulkarni Abhijit , Thakkar Shyam 
Published: November 2018

Objectives
Surgery is the curative treatment for pancreatic ductal adenocarcinoma (PDA). Guidelines recommend utilizing a multidisciplinary pancreatic cancer conference (MDPC) in treatment; however, data are limited. The objective of this study was to assess the accuracy of an MDPC.

Methods
Patients with PDA presented at an MDPC were prospectively collected from April 2013 to August 2016. Patients were included if the MDPC predicted them to have resectable PDA and underwent upfront surgery. Secondary aims were to compare differences in tumor characteristics, time to surgery, and resection rates with patients prior to MDPC implementation (pre-MDPC).

Results
A total of 278 patients were presented at the MDPC. After excluding borderline and nonresectable cases, 91 patients were predicted as resectable on evaluation, and 70 were fit for surgery. The MDPC predicted resection in 91.4%. The MDPC had larger tumor size (32.6 vs 24.0 mm), greater proportion of stage II tumor, and a shorter time from diagnosis to resection (27.3 vs 35.5 days) compared with the pre-MDPC. Microscopically negative resections were similar between MDPC and pre-MDPC (85.9% vs 88.0%) despite advanced tumor size and stage.

Conclusions
The MDPC demonstrates a high resection rate. Compared with a pre-MDPC, MDPC provides shorter time to surgery and selects for advanced tumors.
Using insect natural history collections to study global change impacts: challenges and opportunities
Authors: Kharouba Heather M. , Lewthwaite Jayme M. M. , Guralnick Rob , Kerr Jeremy T. , Vellend Mark 
Published: November 2018

Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species’ ecological and evolutionary responses to rapid, widespread global changes.
This article is part of the theme issue ‘Biological collections for understanding biodiversity in the anthropocene’.
Systems Biology Theory Clarification of a Controversy in Pancreatic Beta Cell Regeneration
Authors: Cai Haoran , Cheng Runtan , Yuan Ruoshi , Zhu Xiaomei , Ao Ping 
Published: November 2018

ABSTRACTWhether new pancreatic beta-cells arise via pre-existing beta-cells or from differentiation of precursor cells − a question of fundamental importance for diabetic therapy − has long been debated. Recent experiments suggest that multipotent precursors from adult mouse pancreas, that give rise to beta-cells, do exist. However, such a finding is at odds with prior evidence that beta-cell expansions occurs exclusively through self-replication. Here we show that these two observations can be partially compatible. We use a systems biology approach to analyze the dynamics of the endogenous molecular-cellular network in the pancreas. Our results show that self-replicating ‘beta-cells’ can themselves be multipotent precursors. In addition, our model predicts heterogeneity in beta-cell regeneration and suggests various differentiation paths of precursors. This work therefore provides a means of reconciling an apparent contradiction in the field, but also sheds light on possible paths of beta-cell regeneration from a systems biology perspective.
Concurrent Multisensory Integration and Segregation with Complementary Congruent and Opposite Neurons
Authors: Zhang Wen-Hao , Wang He , Chen Aihua , Gu Yong , Lee Tai Sing , Wong K. Y. Michael , Wu Si 
Published: November 2018

AbstractOur brain perceives the world by exploiting multiple sensory modalities to extract information about various aspects of external stimuli. If these sensory cues are from the same stimulus of interest, they should be integrated to improve perception; otherwise, they should be segregated to distinguish different stimuli. In reality, however, the brain faces the challenge of recognizing stimuli without knowing in advance whether sensory cues come from the same or different stimuli. To address this challenge and to recognize stimuli rapidly, we argue that the brain should carry out multisensory integration and segregation concurrently with complementary neuron groups. Studying an example of inferring heading-direction via visual and vestibular cues, we develop a concurrent multisensory processing neural model which consists of two reciprocally connected modules, the dorsal medial superior temporal area (MSTd) and the ventral intraparietal area (VIP), and that at each module, there exists two distinguishing groups of neurons, congruent and opposite neurons. Specifically, congruent neurons implement cue integration, while opposite neurons compute the cue disparity, both optimally as described by Bayesian inference. The two groups of neurons provide complementary information which enables the neural system to assess the validity of cue integration and, if necessary, to recover the lost information associated with individual cues without re-gathering new inputs. Through this process, the brain achieves rapid stimulus perception if the cues come from the same stimulus of interest, and differentiates and recognizes stimuli based on individual cues with little time delay if the cues come from different stimuli of interest. Our study unveils the indispensable role of opposite neurons in multisensory processing and sheds light on our understanding of how the brain achieves multisensory processing efficiently and rapidly.Significance StatementOur brain perceives the world by exploiting multiple sensory cues. These cues need to be integrated to improve perception if they come from the same stimulus and otherwise be segregated. To address the challenge of recognizing whether sensory cues come from the same or different stimuli that are unknown in advance, we propose that the brain should carry out multisensory integration and segregation concurrently with two different neuron groups. Specifically, congruent neurons implement cue integration, while opposite neurons compute the cue disparity, and the interplay between them achieves rapid stimulus recognition without information loss. We apply our model to the example of inferring heading-direction based on visual and vestibular cues and reproduce the experimental data successfully.
Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster
Authors: Betancourt Nicolas J. , Rajpurohit Subhash , Durmaz Esra , Fabian Daniel K. , Kapun Martin , Flatt Thomas , Schmidt Paul 
Published: November 2018

AbstractThe insulin insulin-like growth factor signaling pathway has been hypothesized as a major determinant of life history profiles that vary adaptively in natural populations. InDrosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includesfoxo, a conserved gene that regulates insulin signaling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation atfoxounderlies genetic variance for traits that vary with latitude and reflect local adaptation. To evaluate this, we generated recombinant outbred populations in which the focalfoxoallele was homozygous and fixed for either the allele common at high latitude or low latitude and the genomic background was randomized across 20 inbred lines. After eight generations of recombination, experimental populations were phenotyped for a series of traits related to gene function. Our results demonstrate that natural allelic variation atfoxohas major and predictable effects on body size and starvation tolerance, but not on development time. These patterns mirror those observed in natural populations collected across the latitudinal gradient in the eastern U.S.: clines were observed for starvation tolerance and body size, but development time exhibited no association with latitude. Furthermore, differences in size betweenfoxogenotypes were equivalent to those observed between populations sampled from the latitudinal extremes, although contribution to the genetic variance for starvation tolerance was less pronounced. These results suggest that allelic variation atfoxois a major contributor to adaptive patterns of life history variation in natural populations of this genetic model.
A study on the protective effects of CpG ODN-induced mucosal immunity against lung injury in a mouse ARDS model
Authors: Wang Guan , Liu Zong-Jian , Liu Xuan , Liu Feng-Ge , Li Yan , Weng Yi-Bing , Zhou Jian-Xin 
Published: November 2018

AbstractThis study aims to determine the feasibility of using oligodeoxynucleotides with unmethylated cytosine-guanine dinucleotide sequences (CpG ODN) as an immunity protection strategy for a mouse model of acute respiratory distress syndrome (ARDS). This is a prospective laboratory animal investigation. 20-week old BALB/c mice in Animal research laboratory were randomized into groups. An ARDS model was induced in mice using lipopolysaccharides. CpG ODN was intranasally and transrectally immunized before or after the 3rdand 7thday of establishing the ARDS model. Mice were euthanized on day seven after the 2ndimmunization. Then, retroorbital bleeding was carried, out and the chest was rapidly opened to collect the trachea and tissues from both lungs for testing. CpG ODN significantly improved the pathologic impairment in mice lung, especially after the intranasal administration of 50 ug. This resulted in the least severe lung tissue injury. Furthermore, IL-6 and IL-8 concentrations were lower, which was second to mice treated with the rectal administration of 20 μg CpG ODN. In contrast, the nasal and rectal administration of CpG ODN in BALB/c mice before LPS immunization did not appear to exhibit any significant protective effects. In conclusion, the intranasal administration of CpG ODN may be is a potential treatment approach to ARDS. More studies are needed to further determine the protective mechanism of CpG ODN.
Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs
Authors: Yan Zhangming , Huang Norman , Wu Weixin , Chen Weizhong , Jiang Yiqun , Chen Jingyao , Huang Xuerui , Wen Xingzhao , Xu Jie , Jin Qiushi , Zhang Kang , Chen Zhen , Chien Shu , Zhong Sheng 
Published: November 2018

AbstractFusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common features have been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, non-cancerous cell types (using iMARGI, an enhanced version of the MARGI [Mapping RNA-Genome Interactions assay]). Among the top 10 most significant RNA-DNA interactions in normal cells, 5 co-localized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed these in a validation cohort of 96 lung cancer samples using RNA-seq. 37 out of 42 fusion transcripts in the validation cohort were found to exhibit RNA-DNA interactions in normal cells. Finally, by combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with EML4-ALK fusion RNA without forming the EML4-ALK fusion gene. Collectively, these data suggest a novel RNA-poise model, where spatial proximity of RNA and DNA could poise for the creation of fusion transcripts.