bluuebunny/crossref_metadata_2025_split huggingface dataset:
A vector‐based representation of the chemical bond for predicting competitive and noncompetitive torquoselectivity of thermal ring‐opening reactions
Authors: Azizi Alireza , Momen Roya , Morales‐Bayuelo Alejandro , Xu Tianlv , Kirk Steven R. , Jenkins Samantha 
Published: September 2018

AbstractWe present a new vector‐based representation of the chemical bond referred to as the bond‐path frame‐work set B = {p, q, r}, where p, q, and r represent three paths with corresponding eigenvector‐following paths with lengths H*, H, and the bond‐path length from the quantum theory of atoms in molecules (QTAIM). We find that longer path lengths H of the ring‐opening bonds predict the preference for the transition state inward (TSIC) or transition state outward (TSOC) of thermal ring opening reactions in agreement with experiment for all five reactions R1‐R5. Competitiveness and noncompetitiveness have traditionally been considered using activation energies within transition state theory that is known to fail for thermal ring‐opening reactions. Consequently, we find that the activation energy for R3 does not satisfactorily determine competitiveness or provide consistent agreement with experimental yields. We choose a selection of five competitive and noncompetitive reactions; methyl‐cyclobutene (R1), ethyl‐methyl‐cyclobutene (R2), iso‐propyl‐methyl‐cyclobutene (R3), ter‐butyl‐methyl‐cyclobutene (R4), and phenyl‐methyl‐cyclobutene (R5). Therefore, in this investigation we provide a new criterion, within the QTAIM framework, to determine whether the reactions R1‐R5 are competitive or noncompetitive. We that find R2, R3, and R5 are competitive and R1 and R4 are noncompetitive reactions in contrast to the results from the activation energies, calling into question the reliability of activation energies.
Harnessing CRISPR/Cas 9 System for manipulation of DNA virus genome
Authors: Ebrahimi Saeedeh , Teimoori Ali , Khanbabaei Hashem , Tabasi Maryam 
Published: September 2018

SummaryThe recent development of the Clustered Regularly Interspaced Palindromic Repeat (CRISPR)/CRISPR‐associated protein 9 (Cas9) system, a genome editing system, has many potential applications in virology. The possibility of introducing site specific breaks has provided new possibilities to precisely manipulate viral genomics. Here, we provide diagrams to summarize the steps involved in the process. We also systematically review recent applications of the CRISPR/Cas9 system for manipulation of DNA virus genomics and discuss the therapeutic potential of the system to treat viral diseases.
Electronic data acquisition and operational control system for time‐of‐flight sputtered neutral mass spectrometer
Authors: Bajo Ken‐ichi , Fujioka Osamu , Itose Satoru , Ishihara Morio , Uchino Kiichiro , Yurimoto Hisayoshi 
Published: September 2018

A new electric data acquisition and operational control system was developed for time‐of‐flight sputtered neutral mass spectrometry (TOF‐SNMS). The system is designed for high‐speed data acquisition, data processing, and data streaming. The developed system is constructed on an NI‐PXI platform and provides timing clocks for the TOF‐SNMS operation. The system performs data processing of noise suppression and ion counting while acquiring TOF mass spectrum for 13‐microsecond length at sampling rate of 3 GS/s for every 1 millisecond. In addition, the system acquires and records TOF mass spectrum of 60‐microsecond length at sampling rate of 3 GS/s for every 1 millisecond without data processing. The system detects single ion signals from accumulated TOF mass spectrum of 107 times and counts up to 10 ions accurately from a single event of TOF mass spectrum.
$$ {R}_{D^{\left(*\right)}},{R}_{K^{\left(*\right)}} $$ and neutrino mass in the 2HDM-III with right-handed neutrinos
Authors: Li Shao-Ping , Li Xin-Qiang , Yang Ya-Dong , Zhang Xin 
Published: September 2018

Abstract

Given that the two-Higgs-doublet model of type III (2HDM-III) has the potential to address the

$$ {R}_{D^{\left(*\right)}} $$

R

D

*

anomalies while the resolution to the

$$ {R}_{K^{\left(*\right)}} $$

R

K

*

deficits requires new degrees of freedom within this framework, we consider in this paper a unified scenario where the low-scale type-I seesaw mechanism is embedded into the 2HDM-III, so as to accommodate the

$$ {R}_{D^{\left(*\right)}} $$

R

D

*

and

$$ {R}_{K^{\left(*\right)}} $$

R

K

*

anomalies as well as the neutrino mass. We first revisit the

$$ {R}_{D^{\left(*\right)}} $$

R

D

*

anomalies and find that the current world-averaged results can be addressed at 2σ level without violating the bound from the branching ratio

$$ \mathrm{\mathcal{B}}\left({B}_c^{-}\to {\tau}^{-}\overline{\nu}\right) $$

ℬ

B
c
−

→

τ
−

ν
¯

≤ 30%. The scenario predicts two sub-eV neutrino masses based on a decoupled heavy Majorana neutrino and two nearly degenerate Majorana neutrinos with mass around the electroweak scale. For the

$$ {R}_{K^{\left(*\right)}} $$

R

K

*

anomalies, the same scenario can generate the required Wilson coefficients in the direction C
9
μ

NP
= − C
10
μ

NP
< 0, with

$$ \mathcal{O}(1) $$

O

1

Yukawa couplings for the muon and the top quark.
Media studies to enhance the production of verticillins facilitated by in situ chemical analysis
Authors: Amrine Chiraz Soumia M , Raja Huzefa A , Darveaux Blaise A , Pearce Cedric J , Oberlies Nicholas H 
Published: September 2018

Abstract
Verticillins are a group of epipolythiodioxopiperazine alkaloids that have displayed potent cytotoxicity. To evaluate their potential further, a larger supply of these compounds was needed for both in vivo studies and analogue development via semisynthesis. To optimize the biosynthesis of these secondary metabolites, their production was analyzed in two different fungal strains (MSX59553 and MSX79542) under a suite of fermentation conditions. These studies were facilitated by the use of the droplet-liquid microjunction-surface sampling probe (droplet probe), which enables chemical analysis in situ directly from the surface of the cultures. These experiments showed that the production of verticillins was greatly affected by growth conditions; a significantly higher quantity of these alkaloids was noted when the fungal strains were grown on an oatmeal-based medium. Using these technologies to select the best among the tested growth conditions, the production of the verticillin analogues was increased while concomitantly decreasing the time required for fermentations from 5 weeks to about 11 days. Importantly, where we could previously supply 5–10 mg every 6 weeks, we are now able to supply 50–150 mg quantities of key analogues per month via laboratory scale fermentation.

Graphical abstract
Poverty dynamics and graduation from conditional cash transfers: a transition model for Mexico’s Progresa-Oportunidades-Prospera program
Authors: Villa Juan M. , Niño-Zarazúa Miguel 
Published: September 2018

AbstractThe effects of conditional cash transfers (CCTs) on poverty and well-being have been widely studied. However, there is limited knowledge on how a CCT should respond to the dynamics of poverty. How should program administrators treat beneficiaries that exit poverty in period t-1, but exhibit a high probability of falling into poverty in period t? This is a relevant, yet unanswered question. This paper provides an analysis of the implications of poverty dynamics in the implementation of graduation strategies of CCTs, taking Mexico’sProgresa-Oportunidades-Prospera(POP) program as reference case. We propose a Markovian transition model that allows to control for unobserved heterogeneity, state dependence, and attrition. The model provides a framework for a generic graduation condition that can be applied to cash transfer programs that follow well-defined eligibility income thresholds. Overall, we find that only one-third of program beneficiaries that were poor in 2002 exhibited low probabilities of becoming poor in 2009–12 and therefore could be regarded as true ‘graduates’ of the program. We also find that the ‘recertification’ process of POP—which takes place every three years—would be more efficient if it took place every 3.7 and 5.1 years in urban and rural areas, respectively.
Prevalence of Burnout among Canadian Radiologists and Radiology Trainees
Authors: Zha Nanxi , Patlas Michael N. , Neuheimer Nick , Duszak Richard 
Published: September 2018

Purpose Physician burnout is on the rise compared to the average population, and radiology burnout rates are ranked high compared to other specialties. We aim to assess radiologist and radiology trainee burnout in Canada. Methods A survey using the abbreviated 7-item Maslach Burnout Inventory that characterizes burnout symptoms into personal accomplishment, emotional exhaustion, and depersonalization was sent to all eligible members of the Canadian Association of Radiologists in January 2018. The anonymous survey was hosted on SurveyMonkey for 1 month. A reminder e-mail was sent halfway through the survey period. Results Overall, 262 of 1401 invited radiology trainees and radiologists completed the survey (response rate 18.7%). With regards to personal accomplishment, we observed that (1) burnout in this domain improved with increased years worked and (2) milder symptoms were observed in community radiologists compared with their academic counterparts. In comparison with other studies of radiologist burnout, we found mild burnout symptoms in personal accomplishment, but severe symptoms in the burnout domains of both emotional exhaustion and depersonalization. Conclusions Canadian radiologists and radiology trainees reported above average burnout symptoms with regard to both emotional exhaustion and depersonalization. Future research directions include exploring etiologies of burnout and implementation of treatment strategies based on these identified problem areas.
DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning
Authors: Xie Yubin , Luo Xiaotong , Li Yupeng , Chen Li , Ma Wenbin , Huang Junjiu , Cui Jun , Zhao Yong , Xue Yu , Zuo Zhixiang , Ren Jian 
Published: September 2018

Abstract
Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases. Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively, demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%−42% improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http://deepnitro.renlab.org.
GAAD: A Gene and Autoimmiune Disease Association Database
Authors: Lu Guanting , Hao Xiaowen , Chen Wei-Hua , Mu Shijie 
Published: September 2018

Abstract
Autoimmune diseases (ADs) arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations between 49 ADs and 4249 genes from public databases and MEDLINE documents. We manually verified the associations to ensure the quality and credibility. We reconstructed and recapitulated the relationships among ADs using their shared genes, which further validated the quality of our data. We also provided a list of significantly co-occurring gene pairs among ADs; with embedded tools, users can query gene co-occurrences and construct customized co-occurrence network with genes of interest. To make GAAD more straightforward to experimental biologists and medical scientists, we extracted additional information describing the associations through text mining, including the putative diagnostic value of the associations, type and position of gene polymorphisms, expression changes of implicated genes, as well as the phenotypical consequences, and grouped the associations accordingly. GAAD is freely available at http://gaad.medgenius.info.
Meta-analysis – perineural invasion as prognostic factor in rectal cancer
Authors: Murugesan Jothi Rajasekaran , Murugesan Shenthil Prabhu , Yip Jim , Hitos Kerry , Fulham Stephen , Engel Alexander 
Published: September 2018

AbstractObjectives The aim of this analysis was to determine prognostic value of perineural invasion in rectal cancer.Methods Medline (PubMed, Ovid), Embase and Cochrane Library were searched for relevant reports published from January 1980 up to December 2017. All clinical trials which studied perineural invasion in rectal cancer, prospective observational studies, clinical registry data and retrospective case series which reported perineural invasion as an outcome were included. Case reports, abstracts, letters and comments were excluded. hazard ratio (HR) with 95% confidence interval (CI) was used to determine the prognostic value.Results Nineteen studies comprising 6438 patients with rectal cancer were analysed. The results indicate that perineural invasion is a negative prognostic factor as evident from the overall survival (HR = 1.30, 95% CI 1.13–1.50, p < 0.01) and disease-free survival (HR = 2.14, 95% CI 2.06–2.22, p < 0.01).Conclusion This study shows that presence of perineural invasion is associated with poor prognosis in rectal cancer.
Exoskeleton and End‐Effector Robots for Upper and Lower Limbs Rehabilitation: Narrative Review
Authors: Molteni Franco , Gasperini Giulio , Cannaviello Giovanni , Guanziroli Eleonora 
Published: September 2018

AbstractRecovery of upper and lower limbs function is essential to reach independence in daily activities in patients with upper motor neuron syndrome (UMNS). Rehabilitation can provide a guide for motor recovery influencing the neurobiology of neuronal plasticity providing controlled, repetitive, and variable patterns. Increasing therapy dosage, intensity, number of repetition, execution of task‐oriented exercises, and combining top‐down and bottom‐up approaches can promote plasticity and functional recovery. Robotic exoskeletons for upper and lower limbs, based on the principle of motor learning, have been introduced in neurorehabilitation. In this narrative review, we provide an overview of literature published on exoskeleton devices for upper and lower limb rehabilitation in patients with UMNS; we summarized the available current research evidence and outlined the new challenges that neurorehabilitation and bioengineering will have to face in the upcoming years. Robotic treatment should be considered a rehabilitation tool useful to generate a more complex, controlled multisensory stimulation of the patient and useful to modify the plasticity of neural connections through the experience of movement. Efficacy and efficiency of robotic treatment should be defined starting from intensity, complexity, and specificity of the robotic exercise, that are related to human‐robot interaction in terms of motion, emotion, motivation, meaning of the task, feedback from the exoskeleton, and fine motion assistance. Duration of a single session, global period of the treatment, and the timing for beginning of robotic treatment are still open questions. There is the need to evaluate and individualize the treatment according to patient's characteristics. Robotic devices for upper and lower limbs open a window to define therapeutic modalities as possible beneficial drug, able to boost biological, neurobiological, and epigenetic changes in central nervous system. We need to implement large and innovative research programs to answer these issues in the near future.
Duress as a tort law defence?
Authors: Murphy John 
Published: September 2018

AbstractThis paper addresses a straightforward question: ‘Should tort law recognise a defence of duress?’ Previous scholarship concerning this issue is thin on the ground, and the answers it supplies are demonstrably inadequate. Those who have favoured the development of a duress defence in tort have done so by analogy with criminal law where duress is, of course, well established. The rival school of thought has sought to highlight the fact that excuse defences are out of place in tort and that, therefore, there is no room for duress in tort. This paper rejects both approaches. It accepts that the criminal law is a poor source of analogy, but rejects the idea that duress must be seen as an excuse (and hence the idea that there can be no space for it in tort). It offers a fresh start based on the role of duress within tort law's sibling, the law of contract. It identifies three possible conceptions of duress in contract and then asks whether these conceptions could be used to ground a comparable defence of duress in tort by analogy. It concludes that a plausible case can be made in respect of each conception, but – given that the paper has primarily theoretical ambitions – it stops short of advocating any one conception in particular.
Forging a Women's United Front: Chinese elite women's networks for national salvation and resistance, 1932–1938
Authors: GUO VIVIENNE XIANGWEI 
Published: September 2018

AbstractFocusing on Chinese elite women who gravitated towards national affairs in the pre-war urban sites of eastern China and who migrated to Wuhan after the outbreak of the War of Resistance (1937–1945), this article analyses the emergence, development, and integration of their sociopolitical networks for the purpose of promoting women's participation in national salvation, against a backdrop of the deepening national crisis in the 1930s. I argue that two years before the Second Kuomintang-Chinese Communist Party (KMT-CCP) United Front was officially formed, these elite women, hailing from diverse social and political backgrounds and different professions, had already established their own leadership during the national salvation movement and called for a women's united front. Therefore, rather than being simply political rhetoric enhanced under the auspices of the KMT-CCP alliance, the women's united front served as an important institution with which Chinese elite women identified and through which they empowered themselves at a local and then national level, across and beyond geopolitical boundaries. I conclude that the birth and evolution of this women's united front, which have been neglected in the historiography of China's War of Resistance, are crucial to an understanding of unsettling negotiations, communication, and cooperation between the various forces signed up to the cause of national salvation in the 1930s, and to the interpretation of popular resistance before the war.
First assessment of the conservation status of the jaguarPanthera oncain the Sierra Madre de Chiapas, Mexico
Authors: De La Torre J. Antonio , Rivero Marina , Camacho Gamaliel , Álvarez-Márquez Luis Arturo , Medellín Rodrigo A. 
Published: September 2018

AbstractAlthough the Near Threatened jaguarPanthera oncaranges from the south-west USA to central Argentina, populations outside Amazonia are generally small and isolated. One such area, the Sierra Madre de Chiapas in the state of Chiapas, Mexico, is potentially an important area for jaguar conservation but information on the species in this region is limited and its conservation status is unknown. In this study we documented the occurrence and abundance of jaguars in the Sierra Madre de Chiapas complex. We compiled all available records of the species within the region and conducted a camera-trap survey during August 2015–December 2016. Interviews were conducted to determine the perception of the jaguar by cattle owners and to obtain information on any livestock predation. We found that jaguars still occur throughout the Sierra Madre de Chiapas landscape, including the plains on the Pacific Coast of Chiapas, but its abundance in the region is low. On the basis of our findings we have incorporated the Sierra Madre de Chiapas in Mexico's National Jaguar Conservation Strategy, and recommend that international organizations include this area in their priorities for jaguar conservation. To improve coexistence between jaguars and the communities of the Sierra Madre de Chiapas, strategies need to be developed, in collaboration with the local communities, to improve livestock practices for reduction of predation by jaguars, to strengthen government conservation policies and to implement educational and communication programmes about the importance of this species in the region.
Modelling, trajectory optimisation and prototyping of sequentially actuated manipulators
Authors: Harton David , Laliberté Thierry , Gosselin Clément 
Published: September 2018

SUMMARYThis paper presents a concept of sequentially actuated multi-degree-of-freedom (DOF) robot with only one motor. A switching mechanism allowing to actuate sequentially the different joints–or combinations of the joints–of the robot is also proposed. Potential actuation schemes (joint combinations) are presented and their properties are discussed. Cartesian pick-and-place trajectories are then considered using different actuation schemes. An optimisation algorithm is presented in order to provide the best possible sequence by minimising the amplitude of the joint rotations for a given actuation combination. A simple planar two-DOF and the SCARA architectures are used to illustrate the concept. Finally, a prototype is developed with the aim of demonstrating the sequentially actuated manipulator concept.