bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural prediction of protein interactions and docking using conservation and coevolution
Authors: Andreani Jessica , Quignot Chloé , Guerois Raphael
Published: May 2020

Knowledge of the detailed structure of macromolecular interactions is key to a better understanding and modulation of essential cellular functions and pathological situations. Great efforts are invested in the development of improved computational prediction methods, including binding site prediction and protein–protein docking. These tools should benefit from the inclusion of evolutionary information, since the pressure to maintain functional interactions leads to conservation signals on protein surfaces at interacting sites and coevolution between contacting positions. However, unveiling such constraints and finding the best way to integrate them into computational pipelines remains a challenging area of research. Here, we first introduce evolutionary properties of interface structures, focusing on recent work exploring evolutionary mechanisms at play in protein interfaces and characterizing the complexity of evolutionary signals, such as interface deep mutational scans. Then, we review binding site predictors and interface structure modeling methods that integrate conservation and coevolution as important ingredients to improve predictive capacity, ending with a section dedicated to the prediction of binding modes between a globular protein domain and a short motif located within an intrinsically disordered or flexible region. Throughout the review, we discuss practical applications and recent promising developments, in particular regarding the use of coevolutionary information for interface structural prediction and the integration of these coevolution signals with machine learning and deep learning algorithms.

This article is categorized under:

Structure and Mechanism > Molecular Structures

Structure and Mechanism > Computational Biochemistry and Biophysics

Molecular and Statistical Mechanics > Molecular Interactions
Spacetime fluctuations in AdS/CFT
Authors: Verlinde Erik , Zurek Kathryn M.
Published: May 2020

Abstract

We compute fluctuations in the modular energy of the vacuum associated with a Rindler-wedge in AdS spacetime in the context of AdS/CFT. We discuss the possible effect of these energy fluctuations on the spacetime geometry, and on the traversal time of a light beam propagating from the boundary to the bulk and back.
A near-infrared spectroscopy (NIRS) device unveils oxygenation levels in skeletal muscle and brain of a conscious Harris’s Hawk (Parabuteo unicinctus)
Authors: Doi Kimiaki , Hiwatashi Keisuke , Yokosuka Makoto , Mizuno Risuke
Published: May 2020

We measured the regional saturation of oxygen of hemoglobin (rSO2) and the total hemoglobin index (HbI) in the brain and skeletal muscles of a conscious Harris’s Hawk by a near-infrared spectroscopy device (NIRS). The oxygenation levels of the breast were significantly lower than the cerebral parts. A flight exercise significantly increased the rSO2 and HbI of the breast. The breast surface temperature significantly increased in response to flight training by a thermography. NIRS enabled us to measure changes in the oxygenation levels of brain and skeletal muscles in a conscious Harris’s Hawk before and after a moving task.
Potential of European universities as Marie Curie grantee hosts
Authors: Falk Martin Thomas , Hagsten Eva
Published: May 2020

This study investigates the potential of European universities as hosts for Marie Skłodowska-Curie Actions (MSCA) grantees. Factors explaining both the probability of a university hosting an MSCA grantee and its extent are estimated using a zero-inflated negative binomial regression model. Results reveal that the probability of hosting MSCA grantees increases significantly with excellence (research performance), size and country group of the university. In addition, a deepening of excellence (citations), international orientation and the teaching burden (student-staff ratio) are significant predictors for the extent of grantees. Based on the estimates, the relative performance of a university is identified by use of a frontier production function. This reveals that some universities in the Northwest of Europe host more MSCA grantees than would have been expected given their attributes, and certain top universities host fewer. These results could be related to marketing and support activities that partially offset the importance of research performance or alternative models for financing.
A Twitter-Based Study of the European Internet of Things
Authors: Ustek-Spilda Funda , Vega Davide , Magnani Matteo , Rossi Luca , Shklovski Irina , Lehuede Sebastian , Powell Alison
Published: May 2020

We present a methodology integrating social media data, data from qualitative research and network analysis. Qualitative insights gained from ethnographic fieldwork are used to collect and annotate social network data, and social media data is used as part of the ethnography to identify relevant actors and topics. The methodology is presented in the context of an analysis of the Internet of Things in the European context.
Correction to: Transformative experience and the shark problem
Authors: Campbell Tim , Mosquera Julia
Published: May 2020

The article Transformative experience and the shark problem, written by Tim Campbell and Julia Mosquera, was originally published electronically on the publisher’s Internet portal on 31 January 2020 without open access.
Exploring land-use histories of tree-crop landscapes: a cross-site comparison in the Mediterranean Basin
Authors: Wolpert Franziska , Quintas-Soriano Cristina , Plieninger Tobias
Published: May 2020

Agroforestry landscapes in the Mediterranean Basin have emerged in a co-evolution between humans and nature and provide numerous ecosystem services to society. Tree crops are iconic elements of these landscapes and have frequently been managed in a sustainable way over centuries, shaping multifunctional landscapes and local people’s cultural identities. However, many Mediterranean tree-crop landscapes are undergoing substantial land-use changes, threatening important ecosystem services as a result. The overarching goal of this study is to explore common and diverging patterns of land-use change across different tree crops (oaks, chestnuts, olives) and contrasting landscapes in the Mediterranean Basin over a 200-year period. Specifically, we aim to: (1) describe the dominant land-use change processes across these three crop types using three exemplary sites per crop; and (2) identify and classify the main drivers that determine these landscapes’ land change histories. We find a general acceleration of landscape dynamics and identify expansion, continuity, polarisation, intensification, abandonment and renaissance as dominant processes. Although each landscape history is contextualised, we observe a general trend from multifunctional tree-crop landscapes (expansion) towards intensification or abandonment in the last 70 years. The landscapes of the southern fringe of the Mediterranean Basin show predominant trends towards intensification, while the northern landscapes evolve towards abandonment. The driving forces identified are diverse and interrelated, comprising sets of socio-cultural, political, technical, economic and natural factors. We offer some key lessons for sustainable landscape management in highlighting the undervalued potential of tree crops, the inherent complexity of landscapes, the interdependencies of drivers and the importance of economic and socio-cultural driving forces.
A revision of the genus Gouania (Rhamnaceae) in the Philippines and Sundaland
Authors: Cahen Daniel , Stenn Kurt S. , Utteridge Timothy M. A.
Published: May 2020

The climbing genusGouania(Rhamnaceae) is revised in western Malesia. Five species are recognised for the Philippines and Sundaland using morphological evidence, including a new species from the Philippines:Gouania longipedunculata. A taxonomic treatment, including a preliminary IUCN conservation status assessment, is presented for each species.
Wearable Battery-Free Perspiration Analyzing Sites Based on Sweat Flowing on ZnO Nanoarrays
Authors: Zhang Wanglinhan , Guan Hongye , Zhong Tianyan , Zhao Tianming , Xing Lili , Xue Xinyu
Published: May 2020

We fabricated wearable perspiration analyzing sites for actively monitoring physiological status during exercises without any batteries or other power supply. The device mainly consists of ZnO nanowire (NW) arrays and flexible polydimethylsiloxane substrate. Sweat on the skin can flow into the flow channels of the device through capillary action and flow along the channels to ZnO NWs. The sweat flowing on the NWs (with lactate oxidase modification) can output a DC electrical signal, and the outputting voltage is dependent on the lactate concentration in the sweat as the biosensing signal. ZnO NWs generate electric double layer (EDL) in sweat, which causes a potential difference between the upper and lower ends (hydrovoltaic effect). The product of the enzymatic reaction can adjust the EDL and influence the output. This device can be integrated with wireless transmitter and may have potential application in constructing sports big data. This work promotes the development of next generation of biosensors and expands the scope of self-powered physiological monitoring system.
A generalized many-facet Rasch model and its Bayesian estimation using Hamiltonian Monte Carlo
Authors: Uto Masaki , Ueno Maomi
Published: May 2020

Performance assessments, in which raters assess examinee performance for given tasks, have a persistent difficulty in that ability measurement accuracy depends on rater characteristics. To address this problem, various item response theory (IRT) models that incorporate rater characteristic parameters have been proposed. Conventional models partially consider three typical rater characteristics: severity, consistency, and range restriction. Each are important to improve model fitting and ability measurement accuracy, especially when the diversity of raters increases. However, no models capable of simultaneously representing each have been proposed. One obstacle for developing such a complex model is the difficulty of parameter estimation. Maximum likelihood estimation, which is used in most conventional models, generally leads to unstable and inaccurate parameter estimations in complex models. Bayesian estimation is expected to provide more robust estimations. Although it incurs high computational costs, recent increases in computational capabilities and the development of efficient Markov chain Monte Carlo (MCMC) algorithms make its use feasible. We thus propose a new IRT model that can represent all three typical rater characteristics. The model is formulated as a generalization of the many-facet Rasch model. We also develop a Bayesian estimation method for the proposed model using No-U-Turn Hamiltonian Monte Carlo, a state-of-the-art MCMC algorithm. We demonstrate the effectiveness of the proposed method through simulation and actual data experiments.
On elliptic partial differential equations in bioimpedance
Authors: Jargal Ariungerel , Seo Jin Keun , Kwon Hyeuknam
Published: May 2020

This paper deals with mathematical models in electrical bioimpedance fields that are described by means of elliptic partial differential equations (PDEs). To find solutions that have practical significance and value, it is necessary to gain a deep understanding of the underlying physical phenomena with the parameter details of PDE models as well as the data acquisition systems. This paper describes practical details of boundary conditions and effective coefficients of elliptic PDEs occurring in bioimpedance.
Chromosome-scale assembly of the Kandelia obovata genome
Authors: Hu Min-Jie , Sun Wei-Hong , Tsai Wen-Chieh , Xiang Shuang , Lai Xing-Kai , Chen De-Qiang , Liu Xue-Die , Wang Yi-Fan , Le Yi-Xun , Chen Si-Ming , Zhang Di-Yang , Yu Xia , Hu Wen-Qi , Zhou Zhuang , Chen Yan-Qiong , Zou Shuang-Quan , Liu Zhong-Jian
Published: May 2020

The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.
An in situ formed LiF protective layer on a Li metal anode with solvent-less cross-linking
Authors: Kim Hyunjin , Kim Youn Sang , Yoo Jeeyoung
Published: May 2020

The artificial SEI layer that includes LiF can be fabricated simply through thermal curing of an F rich material on the surface of Li metal. The proposed artificial SEI layer design offers an alternative strategy for stabilizing the surface of Li metal.
Energy analysis for internet of things software: A simulator approach
Authors: Zhu Lingyu , Lin Qingyin , Liu Fang
Published: May 2020

This Letter reports a method to obtain fine‐grained energy consumption analysis of programs running on the low‐power internet of things (IoT) devices. In the energy estimation domain, most state‐of‐the‐art solutions focus on the coarse‐grained approach to monitor the energy consumption of a device or an application. However, few solutions addressed energy monitoring to analyse fine‐grained energy consumption of a program, especially for IoT appliances. Therefore, the authors present a fine‐grained gem5‐based energy profiling tool to help developers to evaluate the energy efficiency of hot spots in their programs. The authors demonstrate its usability by applying it to profiling garbage collection and property lookup in Jerryscript, a JavaScript engine specifically designed for resource‐constrained IoT devices, and discover that these two operations are consuming, as they account for 17.67 and 12.26% of total energy, respectively. Therefore, this tool can aid the developers to gain insight into the energy efficiency of their software.
Hierarchical conditional random field model for multi‐object segmentation in gastric histopathology images
Authors: Sun Changhao , Li Chen , Zhang Jinghua , Kulwa Frank , Li Xiaoyan
Published: May 2020

In this Letter, a hierarchical conditional random field (HCRF) model‐based gastric histopathology image segmentation (GHIS) method is proposed, which can localise abnormal (cancer) regions in gastric histopathology images to assist histopathologists in medical work. First, to obtain pixel‐level segmentation information, the authors retrain a convolutional neural network (CNN) to build up their pixel‐level potentials. Then, to obtain abundant spatial segmentation information in patch level, they fine tune another three CNNs to build up their patch‐level potentials. Thirdly, based on the pixel‐ and patch‐level potentials, their HCRF model is structured. Finally, a graph‐based post‐processing is applied to further improve their segmentation performance. In the experiment, a segmentation accuracy of is achieved on a haematoxylin and eosin stained gastric histopathological dataset with 560 images, showing the effectiveness and future potential of the proposed GHIS method.
Research on control strategy of MMC DC power electronic transformer based on DAB mode
Authors: Shi Shuhuai , Zhuo Fang , Zhu Yanlin , Cheng Sheng , Wang Feng
Published: May 2020

High‐power DC power electronic transformer (DC PET) is becoming the key equipment in the DC power network. Face‐to‐Face (F2F) DC transformers based on modular multilevel converter (MMC) have the modular structure and can flexibly design systems based on different voltage and power levels. Previous studies show that the control strategy of the F2F topology regulates the MMCs separately. Moreover, the voltage ratio of the DC sides depends on the intermediate AC transformer. In the current study, a new control strategy is proposed, which can change the DC voltage ratio by turning on/off submodules of each MMC bridge flexibly and set relevant parameters with different application scenarios. The algorithm enables the DC PET with F2F topology to operate in a dual active bridge (DAB) circuit mode. Thereby reducing the overall system size and meeting different demands of medium and high voltage application scenarios. According to the control strategy used, a submodule capacitor voltage equalization method is proposed to eliminate the capacitance voltage deviation and reduce the capacitance voltage stress. At the same time, the current characteristics of the AC conversion part in the DC transformer are analyzed. Finally, the feasibility of the proposed method is verified by simulation and experiments.
Core form transformer topological duality based transient model validation for exciting current calculation within DC bias
Authors: Li Jinlong , Li Jinzhong
Published: May 2020

Transformer topological duality‐based transient model (TDuM) has been widely used in the electromagnetic transient (EMT) simulation to consider the impact of core non‐linear features and windings arrangement on exciting current. In this study, the transformer TDuMs that specialized for geomagnetically induced current events studying were validated. After a summary of the transformer TDuMs' derivation and their parameters estimation methodologies, the numerical experiments were carried out to investigate the transformer TDuMs and their related key issues such as core's material types, loss factor of hysteresis model, linear leakage inductance, tank wall with EMT analysis software. The numerical results show a good agreement with the measured data in the field experiments with DC bias applied, which mean that using the transformer TDuM to calculate the exciting current under DC bias condition is feasible. Besides, some practical tips were proposed based on the parameters sensitivity analysis for estimating the transformer TDuMs' parameters to study the transformers' dynamics under DC bias condition.
Effect of accurate modelling of converter interfaced generation on a practical bulk power system
Authors: Huang Qiuhua , Ramasubramanian Deepak , Vittal Vijay , Keel Brian , Silva Jose
Published: May 2020

With increased penetration of converter interfaced generation (CIG) in power systems, the suitability of modelling approaches and models dependent on the system conditions has to be studied. However, their suitability has yet to be systematically analysed. In this study, the authors first develop a methodology for identifying the maximum penetration of aggregated rooftop sources that can be represented as negative loads in both the steady state and dynamic analysis. Then they verify the suitability of a positive‐sequence performance‐based model and a detailed electromagnetic transient (EMT) model for utility‐scale photovoltaic (PV) plants under different fault conditions. Based on the results, they perform dynamic simulations on a large practical system with both positive‐sequence transient stability (TS) and EMT‐TS hybrid simulation. This study shows that positive‐sequence performance based PV plant model is more suitable for study cases with faults relatively far away from the point of connection. In addition, the results indicate that positive‐sequence models and TS simulation approach can produce comparable results with reference to the EMT‐TS hybrid simulation with EMT detailed models for normally‐cleared single‐line‐to‐ground faults, but the inadequacy of positive‐sequence based model and simulation approach becomes obvious for prolonged‐tripping of unbalanced faults in the proximity of the PV plants.
Novel estimation method of utility harmonic impedance based on short‐term impedance minimum variance criterion
Authors: Shu Qin , Zhao Siliang , Xu Fangwei
Published: May 2020

For harmonic control of a power grid, it is prerequisite to accurately estimate and follow the utility harmonic impedance at the point of common coupling (PCC). The existing estimation methods generally consider that the utility harmonic impedance is constant, which causes the estimation error and fail in tracking of impedance fluctuations, since the utility harmonic impedance is fluctuant in practice. Actually, the harmonic impedance fluctuations will lead to the transient variation of the harmonic voltage and current which is bad for harmonic control. In this study, to follow the harmonic impedance fluctuations, a longer observation period is divided into a series of shorter period, and the fluctuations of the utility harmonic impedance over a short period are regarded as a stationary random process. Then, for each short period, the utility harmonic impedance is estimated by minimizing the fluctuation variance of the utility harmonic impedance. Besides the high estimation precision and good tracking performance of impedance fluctuations, other advantages of the proposed method are not limited by the traditional assumptions, such as the background harmonics are stable and small, the customer harmonic impedance is much larger than the utility, and the harmonic sources of both sides are independent, and so on.
Compact CPW‐fed circular patch flexible antenna for super‐wideband applications
Authors: Hasan Md. Rabiul , Riheen Manjurul Ahsan , Sekhar Praveen , Karacolak Tutku
Published: May 2020

This study proposes a coplanar waveguide‐fed circular monopole antenna that is designed by ink‐jetting conductive silver particle ink on photo paper. The antenna comprises a slotted circular patch and a reduced symmetrically slotted ground plane that is etched rectangularly. The slotted circular patch and ground plane provide the design flexibility with a broad bandwidth, substantial gain over 1.66–56.1 GHz frequency band, and relatively consistent radiation pattern. The fractional bandwidth (%BW) of this antenna is 188.5% that is covering industrial, scientific, and medical (ISM) bands, ultra‐wideband, wireless local area network (WLAN) band, worldwide interoperability for microwave access (WiMAX) band, and various frequencies of upcoming fifth‐generation technology. The total size of the antenna is only 34 × 25 mm2, with an electrical dimension of 0.18 λ × 0.13 λ at 1.66 GHz. The bandwidth ratio (BR) is 33.81:1, and the bandwidth dimension ratio (BDR) is 7462, which is the highest among the flexible super‐wideband antennas reported so far. It is a low profile, lightweight, and low‐cost antenna that is accommodating a broad frequency spectrum for extended wideband communication. The measured results show good agreement with the simulations.
Vf‐constrained ηρ‐pareto optimisation of medium frequency transformers in ISOP‐DAB converters
Authors: Beiranvand Hamzeh , Rokrok Esmaeel , Liserre Marco
Published: May 2020

This study deals with (efficiency‐power density) pareto optimisation of medium frequency transformers (MFTs) with considerations of voltage and frequency (Vf) constraints of semiconductors for mega‐watt range input‐series output‐parallel (ISOP) connected dual‐active bridges (DABs). A simple design methodology to include the Litz wire configuration in the optimisation process is proposed. Based on the presented design methodology, the effects of the semiconductors blocking voltage and switching frequency on the ‐pareto optimisation are evaluated. First, an idealised optimisation is carried out to understand the general behaviour of the optimum point. Second, brute‐force optimisation is utilised to find the practical optimum solution based on the market availability of MFT components. Designing MFTs for a 1 MW 10 kV/600 V ISOP‐DAB converter is the subject of numerical studies. The best trade‐off between is selected as the final optimal solution and its design correctness is validated using three‐dimensional finite‐element analysis. Experimental tests on a 3 kW downscaled MFT prototype show that the proposed method is valid in practice.
Sliding mode controller‐based voltage source inverter for power quality improvement in microgrid
Authors: Rajakumar Vinifa , Anbukumar Kavitha , Selwynraj A Immanuel
Published: May 2020

Development of control technologies facilitates the integration of renewable energy sources to the grid through power electronic converters. In this study, the inverter acts as shunt active power filter along with the power conversion operation. Various sliding mode control (SMC) techniques namely relay and signum method, hysteresis method and equivalent control method are implemented to control the real, and reactive power flow between Renewable Energy System (RES), load and grid using an inverter. To reduce the complexity, the control law (ueq) for equivalent control method is derived using a simple single‐phase equivalent circuit of a three‐phase voltage source inverter. In this study, the robustness is enhanced by choosing the integral sliding surface. These controllers are used to reduce the total harmonic distortion (THD) and to ensure unity power factor (PF) in the grid during balanced and unbalanced grid voltage conditions even in the existence of nonlinear loads. The SMC using equivalent control function outperforms the other methods in terms of chattering, THD and PF. To illustrate the effectiveness, three different modes are considered: (i) no RES power, (ii) insufficient RES power and (iii) excess RES power. The performance of controllers is validated by the simulation and experimental results.
Experimental and numerical study of the novel diffuser with a passive adaptive flexible flange for improving the shroud augmented wind turbine
Authors: Hu Jun Feng , Chen Zhou , Yu Su Dong , Zhang Xu Tong , Deng Xi , Xu Ke , Liu Hao Zheng , Liu Yi Ge , Liu De Wei , Shu Wen Long
Published: May 2020

This study proposed a new type of diffuser which can not only accelerate the wind approaching the turbine before wind velocity reaches the rated velocity, but also reduces the wind drag on the diffuser when wind velocity is overrated one. A passive adaptive flexible flange constructed of two flexible cantilevered plates is developed for the diffuser. The flow distribution around the diffuser equipped with a flexible flange, as well as the wind drag on the diffuser, varies with the deformation of the flexible flange under the wind drag. Wind tunnel experiments and numerical analysis are conducted to study the flow distribution around the diffuser and the corresponding wind drag on it at different wind velocities. Experimental results reveal that the drag reduction rate of the diffuser with the passive adaptive flexible flange is 17.9% at the velocity of 20 m/s. Numerical results overall match well with the experimental measurement, such as velocity and pressure distributions, although the simulated values are slightly lower than the experimental ones.
Computerized Tomography-Based Morphometric Analysis of Cervical Spinal Canal in Central Indian Population
Authors: Kumar Ambuj , Sahu Subhash , Sethi Shivank , Ratre Shailendra , Parihar Vijay , Swamy Narayan , Yadav Yad Ram
Published: May 2020

Objective Normal cervical spine canal morphometry is critical for understanding the pathology of certain diseases and for proper preoperative planning. Computerized tomography (CT) scan can replace older conventional radiography techniques by providing more accurate morphometric measurements. This study was aimed to find out various dimensions of the cervical spinal canal of central Indian population.

Materials and Methods A prospective study was conducted including 100 consecutive cervical spine CT scan of asymptomatic adult subjects. The anteroposterior sagittal canal diameter (SCD), transverse canal diameter (TCD), canal surface area (CSA), and Pavlov-Torg Ratio (PTR) from C2 to C7 were calculated.

Statistical Analysis Data were entered in Microsoft Excel Sheet 2007 and statistical analysis was performed by IBM SPSS statistics 2.0 version. p-Value < 0.05 was considered as significant.

Results Age ranged from 18 years to 77 years with mean age 39.5 years. There was no significant difference in all the dimensions (SCD, TCD, CSA) in male and female except at C2 level, where SCD, TCD, and CSA were significant larger in male. The mean SCD, TCD, and CSA is largest at C2 level (14.4 ± 1.63 mm, 21.57 ± 1.59 mm, and 156.20 ± 24.98 mm﻿﻿2, respectively) and smallest at C4 level (12.77 ± 1.48 mm, 20.37 ± 1.72 mm, and 130.42 ± 21.20 mm﻿﻿2). PTR showed very little variation.

Conclusion Normal values of cervical spinal canal could serve as a future reference. CT scan provides more accurate measurement. More studies are needed as there could be variations in dimensions in different regions in India.
Can Cheiromancy Predict Mean Survival or Fatality of a Patient with Amyotrophic Lateral Sclerosis?
Authors: Anand Akshay , Prabhakar Sudesh , Thakur Keshav , Tyagi Rahul , Shastri Vinod , Tripathi Devi Prasad , Sharma Suresh
Published: May 2020

Background The past three decades have seen palmistry as an interface to human health. There have been no previously organized attempts in utilizing this knowledge to predict the state of disease.

Objective Due to unavailability of any biological marker for diagnosing amyotrophic lateral sclerosis (ALS) till date, we attempt to examine whether palmistry could be used for detecting the onset and survival of patient suffering from ALS.

Methods Patients suffering from ALS attending the neurology outpatient department at Postgraduate Institute of Medical Education and Research, India were selected for study. Palm photographs were obtained from all patients including controls after their consent. Patients suffering from other comorbidities such as diabetes, hypertension, migraine, as well as smokers and nonsmokers were included in the study. Twenty-six ALS patients, 30 neurological controls, and 34 healthy age matched controls were recruited in the study. Retrospective analysis of the palm pictures based on blinding method was performed by academically qualified palmists.

Results The results demonstrated the need for further studies in the subject even though the observations made were independent by both the palmists.

Conclusion This study opens new vistas for cheiromancy to be further explored for analysis in larger samples.
Study of Knowledge, Attitude, and Practice among Epilepsy Patients in North India
Authors: Sethi Arshdeep Kaur , Singh Vineeta , Chaurasia Rameshwar Nath , Joshi Deepika , Pathak Abhishek , Rath Shivani , Mishra Ashutosh , Mishra Vijay Nath
Published: May 2020

Background Religious and sociocultural beliefs influence the nature of treatment and care received by people with epilepsy.

Objective This study aimed to study knowledge, attitude, and practice (KAP) among epilepsy patients in north India.

Materials and Methods In this study, 201 patients attending the outpatient and inpatient services of the neurology department of Sir Sunderlal Hospital, Banaras Hindu University, were asked to fill a questionnaire comprising 25 questions assessing the KAPs in English or Hindi, whichever the patient was proficient with. The same questionnaire was also given to 200 patients without epilepsy for the control group. Responses were recorded as yes/no/do not know.

Results Approximately, 67% of the patients consisted of a young population, of which 64.7% were males and 35.3% were females. Around 25.9% of patients had studied up to 10th class, 96.5% of patients had heard of epilepsy, and 89.05% thought it was treatable by modern drugs. Out of all patients, 80.1% of patients believed that epilepsy was not contagious, 87.6% believed that they can work, 93.5% believed that they can marry, 66.5% did not feel discriminated by batchmates, and 78.5% did not feel discriminated by teachers. Of all patients, 41.8% said that they would disclose the epileptic condition of their daughters before marriage and 96.01% knew epilepsy patients should be taken to hospital.

Conclusion Poor knowledge, negative attitude, and malpractices regarding epilepsy are still prevalent in North India. Epilepsy patients have better knowledge than normal people about this disease. There is still a need to educate people about epilepsy.
Phenytoin-Induced Gingival Overgrowth with Predominant Involvement of Hard Palate and Floor of Oral Cavity: A Case Report and Review of Literature
Authors: Sharma Rajeev , Das Prasenjit , Kairo Arvind , Kale Shashank S.
Published: May 2020

Drug-induced gingival overgrowth (DIGO) secondary to chronic phenytoin intake for seizure control is a well-recognized phenomenon. Phenytoin-induced gingival overgrowth (PIGO) usually resolves gradually following cessation of phenytoin intake. It is usually seen throughout the dentate regions of the maxillary and mandibular dental arches, but more severely affect their anterior portions exposed to atmosphere. We report a rare case of PIGO predominantly involving hard palate and floor of oral cavity, which has not been reported in English literature till date.
Painless Legs and Moving Toes Presenting as a Tardive Phenomenon: Case Report and Review of the Literature
Authors: Nagarajan Elanagan , Digala Lakshmi P , Bollu Pradeep C
Published: May 2020

Painless legs and moving toes syndrome is a rare movement disorder. Various conditions like spinal cord trauma, lumbar radiculopathy, peripheral neuropathy, neuroleptic treatment, or traumatic lesions of the soft tissues of the foot can present with this disorder. In our case report, we aim to report a case of a young woman who developed painless legs and moving toes in the setting of chronic neuroleptic usage, which improved after the discontinuation of antipsychotics and treatment with clonazepam. We describe in detail her presentation and clinical examination, along with the review of the literature.
Mesenchymal Chondrosarcoma of the Brain with Metastasis: A Case Report with Literature Review
Authors: Bhardwaj Sandeep , Sharma Ashish , Sharma Akangsha
Published: May 2020

Mesenchymal chondrosarcoma of the brain is one of the rarest tumors with dismal prognosis. A 26-year-old man presented with headache, vomiting, and diplopia. On evaluation, a moderately enhancing extra-axial lesion was seen in right temporal region involving right greater wing of sphenoid, adjacent right maxillary sinus, and lateral wall of right orbit. Patient underwent magnetic resonance imaging of the spine and computed tomography (CT) of the chest for possible metastasis which showed lesion in lumbar vertebrae and left lung. Patient was planned for CT-guided lung biopsy which proved inconclusive. The patient was further planned for craniotomy and underwent craniotomy with microscopic excision of the mass. Histoimmunochemistry was suggestive of extraskeletal mesenchymal chondrosarcoma. Mesenchymal chondrosarcoma of the brain is highly aggressive tumors which are difficult to differentiate radiologically. Radical excision followed by chemoradiotherapy is optimal treatment of choice.
Inequity in Distribution of Psychiatry Trainee Seats and Institutes Across Indian States: A Critical Analysis
Authors: Ransing Ramdas S. , Agrawal Girish , Bagul Koustubh , Pevekar Krishna
Published: May 2020

Background The delivery of mental health services largely depends on the adequacy of human resources. In India, the deficit of psychiatrists is more than 90% and is one of the major challenges that needs to be tackled to address the huge burden of mental illness. Psychiatry trainee institutes play a vital role in reducing human resource deficit and inequality in delivering mental health care. However, the distribution pattern of psychiatry trainee seats and institutes across Indian states is unknown. Therefore, we estimated the number of psychiatry trainee seats and institutes in each Indian state and union territory (UT).

Materials and Methods In this cross-sectional study, psychiatry trainee seats and institutes were searched on the official web sites of Medical Council of India and National Board of Examinations. The data available on these web sites until December 2019 were included. State-wise data were compared using proportion and percentages. The psychiatry trainee index (PTI) was calculated and compared across Indian states and UTs.

Results Among 221 Indian psychiatry trainee institutes considered in the present study, 116 (52.48%) were private institutes and 105 (47.51%) were government institutes. Overall, more psychiatry trainee seats were reported in government institutes (n= 565, 65.89%) than in private institutes. National PTI was considered fair (0.06), and based on their PTIs, Indian states and UTs were classified as follows: worst (n= 9), poor (n= 8), fair (n= 9), average (n= 7), good (n= 1), and excellent (n= 2).

Conclusion A huge deficit of psychiatry trainees and institutes exists in more than two-thirds of Indian states and UTs, along with a huge maldistribution of seats. PTI and its distribution across the states and UTs are a crucial indicator of the need to improve the access and equity of mental health care.
Is a nondemolition measurement of the quantum state vector collapse of a remote localised system possible?
Authors: Belinsky A.V.
Published: May 2020

By the example of an experiment that implements, according to its authors, Wigner friends’ paradox, the impossibility of measuring the state vector collapse of a remote localised system is shown. It is also found that the objectivity of the results of quantum measurements is not violated in this case.
Quantum channel capacities
Authors: Holevo A.S.
Published: May 2020

A brief general review is presented of the theory of information transmission capacities of quantum communication channels, which is a development of the classical Shannon theory. Unlike a classical communication channel, a quantum channel is characterised by a whole set of different capacities, which depend on the type of transmitted information (classical or quantum) and on additional resources used during transmission. The main characteristics of a quantum channel are considered: classical capacity, capacity assisted by entanglement between the channel input and output, quantum capacity and secret classical capacity. The unique role of the quantum entanglement property, which manifests itself, in particular, in a nonclassical phenomenon of capacity superadditivity, is emphasised.
Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network
Authors: Friedmann Drew , Pun Albert , Adams Eliza L. , Lui Jan H. , Kebschull Justus M. , Grutzner Sophie M. , Castagnola Caitlin , Tessier-Lavigne Marc , Luo Liqun
Published: May 2020

The projection targets of a neuronal population are a key feature of its anatomical characteristics. Historically, tissue sectioning, confocal microscopy, and manual scoring of specific regions of interest have been used to generate coarse summaries of mesoscale projectomes. We present here TrailMap, a three-dimensional (3D) convolutional network for extracting axonal projections from intact cleared mouse brains imaged by light-sheet microscopy. TrailMap allows region-based quantification of total axon content in large and complex 3D structures after registration to a standard reference atlas. The identification of axonal structures as thin as one voxel benefits from data augmentation but also requires a loss function that tolerates errors in annotation. A network trained with volumes of serotonergic axons in all major brain regions can be generalized to map and quantify axons from thalamocortical, deep cerebellar, and cortical projection neurons, validating transfer learning as a tool to adapt the model to novel categories of axonal morphology. Speed of training, ease of use, and accuracy improve over existing tools without a need for specialized computing hardware. Given the recent emphasis on genetically and functionally defining cell types in neural circuit analysis, TrailMap will facilitate automated extraction and quantification of axons from these specific cell types at the scale of the entire mouse brain, an essential component of deciphering their connectivity.
Increased variability but intact integration during visual navigation in Autism Spectrum Disorder
Authors: Noel Jean-Paul , Lakshminarasimhan Kaushik J. , Park Hyeshin , Angelaki Dora E.
Published: May 2020

Autism Spectrum Disorder (ASD) is a common neurodevelopmental disturbance afflicting a variety of functions. The recent computational focus suggesting aberrant Bayesian inference in ASD has yielded promising but conflicting results in attempting to explain a wide variety of phenotypes by canonical computations. Here, we used a naturalistic visual path integration task that combines continuous action with active sensing and allows tracking of subjects’ dynamic belief states. Both groups showed a previously documented bias pattern by overshooting the radial distance and angular eccentricity of targets. For both control and ASD groups, these errors were driven by misestimated velocity signals due to a nonuniform speed prior rather than imperfect integration. We tracked participants’ beliefs and found no difference in the speed prior, but there was heightened variability in the ASD group. Both end point variance and trajectory irregularities correlated with ASD symptom severity. With feedback, variance was reduced, and ASD performance approached that of controls. These findings highlight the need for both more naturalistic tasks and a broader computational perspective to understand the ASD phenotype and pathology.
Renewable energy engineering solutions
Authors: Hojiev J N , Morkovkin D E , Starovoitov V G , Gibadullin A A , Dubrovsky A V , Boldyreva I A
Published: May 2020

As part of the study, engineering solutions in the field of creating power plants based on renewable energy sources were analyzed. The work revealed that in Russia the level of development of renewable energy sources is ten times lower than in the world, and renewable energy potential is not used. An engineering solution was proposed in the work, which consists of the stages of analysis, design, construction and commissioning of a power plant based on renewable energy sources. At the end of the study, a scheme was proposed for introducing wind power plants into the energy system in order to maintain the stability and reliability of power supply to consumers and meet the demand for electric energy.
Sampling and summarizing transmission trees with multi-strain infections
Authors: Sashittal Palash , El-Kebir Mohammed
Published: May 2020

Motivation

The combination of genomic and epidemiological data holds the potential to enable accurate pathogen transmission history inference. However, the inference of outbreak transmission histories remains challenging due to various factors such as within-host pathogen diversity and multi-strain infections. Current computational methods ignore within-host diversity and/or multi-strain infections, often failing to accurately infer the transmission history. Thus, there is a need for efficient computational methods for transmission tree inference that accommodate the complexities of real data.

Results

We formulate the direct transmission inference (DTI) problem for inferring transmission trees that support multi-strain infections given a timed phylogeny and additional epidemiological data. We establish hardness for the decision and counting version of the DTI problem. We introduce Transmission Tree Uniform Sampler (TiTUS), a method that uses SATISFIABILITY to almost uniformly sample from the space of transmission trees. We introduce criteria that prioritize parsimonious transmission trees that we subsequently summarize using a novel consensus tree approach. We demonstrate TiTUS’s ability to accurately reconstruct transmission trees on simulated data as well as a documented HIV transmission chain.

Availability and implementation

https://github.com/elkebir-group/TiTUS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Molecular and cellular correlates of human nerve regeneration: ADCYAP1/PACAP enhance nerve outgrowth
Authors: Baskozos Georgios , Sandy-Hindmarch Oliver , Clark Alex J , Windsor Katherine , Karlsson Pall , Weir Greg A , McDermott Lucy A , Burchall Joanna , Wiberg Akira , Furniss Dominic , Bennett David L H , Schmid Annina B
Published: May 2020

We only have a rudimentary understanding of the molecular and cellular determinants of nerve regeneration and neuropathic pain in humans. This cohort study uses the most common entrapment neuropathy (carpal tunnel syndrome) as a human model system to prospectively evaluate the cellular and molecular correlates of neural regeneration and its relationship with clinical recovery. In 60 patients undergoing carpal tunnel surgery [36 female, mean age 62.5 (standard deviation 12.2) years], we used quantitative sensory testing and nerve conduction studies to evaluate the function of large and small fibres before and 6 months after surgery. Clinical recovery was assessed with the global rating of change scale and Boston Carpal Tunnel Questionnaire. Twenty healthy participants provided normative data [14 female, mean age 58.0 (standard deviation 12.9) years]. At 6 months post-surgery, we noted significant recovery of median nerve neurophysiological parameters (P < 0.0001) and improvements in quantitative sensory testing measures of both small and large nerve fibre function (P < 0.002). Serial biopsies revealed a partial recovery of intraepidermal nerve fibre density [fibres/mm epidermis pre: 4.20 (2.83), post: 5.35 (3.34), P = 0.001], whose extent correlated with symptom improvement (r = 0.389, P = 0.001). In myelinated afferents, nodal length increased postoperatively [pre: 2.03 (0.82), post: 3.03 (1.23), P < 0.0001] suggesting that this is an adaptive phenomenon. Transcriptional profiling of the skin revealed 31 differentially expressed genes following decompression, with ADCYAP1 (encoding pituitary adenylate cyclase activating peptide, PACAP) being the most strongly upregulated (log2 fold-change 1.87, P = 0.0001) and its expression was associated with recovery of intraepidermal nerve fibres. We found that human induced pluripotent stem cell-derived sensory neurons expressed the receptor for PACAP and that this peptide could significantly enhance axon outgrowth in a dose-dependent manner in vitro [neurite length PACAP 1065.0 µm (285.5), vehicle 570.9 μm (181.8), P = 0.003]. In conclusion, carpal tunnel release is associated with significant cutaneous reinnervation, which correlates with the degree of functional improvement and is associated with a transcriptional programme relating to morphogenesis and inflammatory processes. The most highly dysregulated gene ADCYAP1 (encoding PACAP) was associated with reinnervation and, given that this peptide signals through G-protein coupled receptors, this signalling pathway provides an interesting therapeutic target for human sensory nerve regeneration.