bluuebunny/crossref_metadata_2025 huggingface dataset:
Usability Evaluation of a Distributed User Interface Application for Visuomotor Organization Assessment
Authors: Cuerda Cristian , Romero-Ayuso Dulce , Gallud Jose A. , Morales Carmen , Tesoriero Ricardo , Triviño-Juarez Jose-Matias , Fardoun Habib M.
Published: September 2020

Background This article describes the development and evaluation of a distributed user interface (DUI) application to assess visuomotor organization ability. This application enables therapists to evaluate the acquired brain injury (ABI) on patients, and patients, to perform the assessment on a touch screen while therapists can observe the assessment process in real time on a separated monitor without interfering patients during the process as in traditional methodologies employing physical elements.

Objectives The main goal of this research is the evaluation of the quality in use of DUIs in the Pegboard Construction assessment with patients with ABI from the therapist perspective in the area of occupational therapy.

Methods To evaluate our system, we have performed a usability evaluation following the ISO/IEC 25010 and ISO/IEC 25062 standards to evaluate software usability and quality and it was conducted in collaboration with therapists and psychologists that have previously worked with people with ABI in diagnostic and assessment tasks.

Results We show the results of the evaluation collected in a table that shows the completeness rate for each user for both, assisted (i.e., the percentage of tasks where participants performed with test director assistance) and unassisted tasks (i.e., the percentage of tasks where participants completed tasks autonomously), the total time participants required to complete proposed tasks, the number of mistakes participants performed during the session, and the number of assists they required to finish proposed tasks. In addition, we also evaluated the user satisfaction regarding our application using the system usability scale.

Conclusion The use of information technologies in this field enables therapists to perform these evaluations in a simpler, efficient, and automated way. This proposal enables patients to perform the assessment as it is performed traditionally using paper providing them with a touch screen in which they can easily insert a set of pins into the holes. The usability evaluation of the proposal meets the appropriate design standards for applications of this type, and this is demonstrated by the high degree of satisfaction of the participants.
Enhancing Traceability in Clinical Research Data through a Metadata Framework
Authors: Hume Samuel , Sarnikar Surendra , Noteboom Cherie
Published: September 2020

Background The clinical research data lifecycle, from data collection to analysis results, functions in silos that restrict traceability. Traceability is a requirement for regulated clinical research studies and an important attribute of nonregulated studies. Current clinical research software tools provide limited metadata traceability capabilities and are unable to query variables across all phases of the data lifecycle.

Objectives To develop a metadata traceability framework that can help query and visualize traceability metadata, identify traceability gaps, and validate metadata traceability to improve data lineage and reproducibility within clinical research studies.

Methods This research follows the design science research paradigm where the objective is to create and evaluate an information technology (IT) artifact that explicitly addresses an organizational problem or opportunity. The implementation and evaluation of the IT artifact demonstrate the feasibility of both the design process and the final designed product.

Results We present Trace-XML, a metadata traceability framework that extends standard clinical research metadata models and adapts graph traversal algorithms to provide clinical research study traceability queries, validation, and visualization. Trace-XML was evaluated using analytical and qualitative methods. The analytical methods show that Trace-XML accurately and completely assesses metadata traceability within a clinical research study. A qualitative study used thematic analysis of interview data to show that Trace-XML adds utility to a researcher's ability to evaluate metadata traceability within a study.

Conclusion Trace-XML benefits include features that (1) identify traceability gaps in clinical study metadata, (2) validate metadata traceability within a clinical study, and (3) query and visualize traceability metadata. The key themes that emerged from the qualitative evaluation affirm that Trace-XML adds utility to the task of creating and assessing end-to-end clinical research study traceability.
Reconsidering NMIHBA Core Features: Macrocephaly Is Not a So Unusual Sign in PRUNE1-Related Encephalopathy
Authors: Battini Roberta , Bertini Enrico , Milone Roberta , Aiello Chiara , Pasquariello Rosa , Rubegni Anna , Santorelli Filippo Maria
Published: September 2020

PRUNE1-related disorders manifest as severe neurodevelopmental conditions associated with neurodegeneration, implying a differential diagnosis at birth with static encephalopathies, and later with those manifesting progressive brain damage with the involvement of both the central and the peripheral nervous system.

Here we report on another patient with PRUNE1 (p.Asp106Asn) recurrent mutation, whose leukodystrophy, inferior olives hyperintensity, and macrocephaly led to the misleading clinical suspicion of Alexander disease. Clinical features, together with other recent descriptions, suggest avoiding the term “microcephaly” in defining this disorder that could be renamed “neurodevelopmental disorder with progressive encephalopathy, hypotonia, and variable brain anomalies” (NPEHBA).
Impact of Income on Perceived Stress, Coping, and Family Functioning in Indian Females with Pseudoseizures
Authors: Mehta Richa , Mittal Anuj , Singh Dweep , Patel Chirag
Published: September 2020

Background Pseudoseizures are paroxysmal alterations in behavior that resemble epileptic seizures but are without any organic cause. Stress, coping, and family functioning are contributing factors in the development and maintenance of pseudoseizures. Literature has found patients with pseudoseizures to belong to lower economic strata; however, no study has directly looked at the impact of income on the core contributing and maintaining factors of pseudoseizures.

Aim This article studies the impact of income on perceived stress, coping, and family functioning in females with pseudoseizures.

Materials and Methods Ninety-one females with pseudoseizures were recruited from the psychiatry department of a tertiary care hospital in New Delhi, India. Each participant completed the Perceived Stress Scale, Ways of Coping Questionnaire, and McMasters Family Assessment Device–General Functioning Scale. Other sociodemographic variables including per capita family monthly income, level of education, area of residence, and employment status were also recorded.

Results Planful Problem Solving and Positive Reappraisal were positively associated with per capita income, while escape-avoidance coping was found to be negatively associated with per capita income. Results also showed a statistically significant negative relationship between perceived stress scores, family functioning, and per capita family income, with income having the highest contribution to family functioning in females with dissociative convulsions.

Conclusion Income was a significant contributor to perceived stress, coping processes, and family functioning. Therefore, high levels of perceived stress, greater familial dysfunction, and maladaptive coping had negative impacts on the outcome of female patients with pseudoseizures belonging to lower income group.
Supraclavicular Flap for Large Anterior Chest Wall Defects–A Road Less Travelled
Authors: More Amrita , Sivakumar Anoop , Gaurav Gupta K
Published: September 2020

Large upper central chest wall defects are a reconstructive challenge. The commonly described flaps for this area do not provide very large skin paddle, and free tissue transfer remains the only option for large skin defects. Supraclavicular flap as a local flap is widely used for head and neck reconstruction and has been described for upper chest wall defects earlier. We have used nonislanded supraclavicular flap for reconstruction of two cases of large chest wall defects, which would otherwise need free tissue transfer, single flap in one case and bilateral flaps in the other. It is easy to do and has minimal morbidity. Supraclavicular flap offers a simple solution for large skin defects of the upper central chest wall and is especially useful in patients with high-operative risk and guarded prognosis.
Mutation Spectrum of Tuberous Sclerosis Complex Patients in Indian Population
Authors: Sudarshan Shruthi , Kumar Atin , Gupta Arun , Bhari Neetu , Sethuraman Gomathy , Kaushal Tanuja , Pradhan Ankita , Sapra Savita , Gupta Neerja , Kaur Punit , Gulati Sheffali , Chakrawarty Biswaroop , Danda Sumita , Bhatt Meenakshi , Kapoor Seema , Girisha Katta M. , Sankhyan Naveen , Kabra Madhulika , Chowdhury Madhumita Roy
Published: September 2020

Tuberous sclerosis complex (TSC) is a multiorgan disorder characterized by formation of hamartomas and broad phenotypic spectrum including seizures, mental retardation, renal dysfunction, skin manifestations and brain tubers. It is inherited in an autosomal dominant pattern, caused due to mutation in either TSC1 or TSC2 genes. Seizures are one of the major presenting symptoms of TSC that helps in early diagnosis. The present study describes the mutation spectrum in TSC1 and TSC2 genes in TSC patients and their association with neurocognitive-behavioral phenotypes. Ninety-eight TSC patients were enrolled for TSC genetic testing after detailed clinical and neurobehavioral assessment. Large genomic rearrangement testing was performed by multiplex ligation-dependent probe amplification (MLPA) technique for all cases and Sanger sequencing was performed for MLPA negative cases. Large rearrangements were identified in approximately 1% in TSC1 and 14.3% in TSC2 genes. The present study observed the presence of duplications in two (2%) cases, both involving TSC2/PKD1 contiguous genes which to the best of our knowledge is reported for the first time. 8.1% of small variants were identified in the TSC1 gene and 85.7% in TSC2 gene, out of which 23 were novel variations and no variants were found in six (6.1%) cases. This study provides a representative picture of the distribution of variants in the TSC1 and TSC2 genes in Indian population along with the detailed assessment of neurological symptoms. This is the largest cohort study from India providing an overview of comprehensive clinical and molecular spectrum.
Mapping the community: use of research evidence in policy and practice
Authors: Farley-Ripple Elizabeth N. , Oliver Kathryn , Boaz Annette
Published: September 2020

The use of research evidence (URE) in policy and practice is relevant to many academic disciplines, as well as policy and practice domains. Although there has been increased attention to how such evidence is used, those engaged in scholarship and practice in this area face challenges in advancing the field. This paper attempts to “map the field” with the objective of provoking conversation about where we are and what we need to move forward. Utilizing survey data from scholars, practitioners, and funders connected to the study of the use of research evidence, we explore the extent to which URE work span traditional boundaries of research, practice, and policy, of different practice/policy fields, and of different disciplines. Descriptive and network analyses point to the boundary spanning and multidisciplinarity of this community, but also suggest exclusivity, as well as fragmentation among disciplines and literatures on which this work builds. We conclude with opportunities for to improve the connectedness, inclusiveness, relationship to policy and practice, and sustainability of URE scholarship.
Preparation and Structures of Rare Earth 3-Benzoylpropanoates and 3-Phenylpropanoates
Authors: Thomas Nicholas C. , Beaumont Owen A. , Deacon Glen B. , Gaertner Cornelius , Forsyth Craig M. , Somers Anthony E. , Junk Peter C.
Published: September 2020

Rare earth (RE) complexes of 3-benzoylpropanoate (bp), [RE(bp)3(H2O)n] (RE=La, n=2; RE=Y, Ce, Pr, Nd, Yb, n=1) and 3-phenylpropanoate (pp), [RE(pp)3] (RE=Y, La, Ce, Nd, Yb), have been prepared by metathesis reactions between the corresponding rare earth chloride and the appropriate sodium carboxylate. Analysis by single-crystal X-ray diffraction finds that both RE bp and pp complexes favour formation of carboxylate-bridged 1-D coordination polymers in the solid state. Here, the former favours heteroleptic 9 or 10-coordinate complexes (splitting between Ce and La) with the carbonyl remaining uncoordinated but participating as a hydrogen bond acceptor with water in the coordination sphere. Lack of bp carbonyl coordination leaves this group available for surface interactions during corrosion inhibition and complex solubilization. The latter pp derivatives form eight-coordinate complexes for Y and Yb and are the first examples of homoleptic RE pp complexes to be reported.
Advanced LIGO squeezer platform for backscattered light and optical loss reduction
Authors: Fernández-Galiana Álvaro , McCuller Lee , Kissel Jeff , Barsotti Lisa , Miller John , Tse Maggie , Evans Matthew , Aston Stuart M , Abbott Richard , Shaffer Thomas J , Pele Arnaud , Romie Janeen H , Weaver Betsy , Fritschel Peter , Mavalvala Nergis , Matichard Fabrice
Published: September 2020

The Advanced LIGO gravitational-wave detectors are limited by optical quantum noise in most of their detection band. To overcome this limit, squeezed vacuum states have been injected into the Advanced LIGO detectors during the third observing run (O3), leading to an increase of their detection rate by about 40% to 50%. Here we present a key element of LIGO’s squeezed vacuum source: the seismic isolation platform that houses core components placed in ultra-high vacuum. This paper describes the architecture of the isolation platform as well as the active control system, tuned to minimize backscattered light that otherwise deteriorates the sensitivity of the detectors. This architecture permits fewer optical Faraday isolators in the optical path of the squeezing system, minimizing optical losses to maximize the quantum noise improvement. The system reliably operated throughout LIGO’s O3 with no evidence of noise from backscattered light. The innovative architecture of this platform makes it ideal for straightforward reshaping and adaptation to other gravitational-wave detector subsystems and low-noise optical instrumentation.
Hölder-logarithmic stability in Fourier synthesis
Authors: Isaev Mikhail , Novikov Roman G
Published: September 2020

We prove a Hölder-logarithmic stability estimate for the problem of finding a sufficiently regular compactly supported function v on

R

d

from its Fourier transform

F
v

given on [−r, r]
d
. This estimate relies on a Hölder stable continuation of

F
v

from [−r, r]
d
to a larger domain. The related reconstruction procedures are based on truncated series of Chebyshev polynomials. We also give an explicit example showing optimality of our stability estimates.
A novel baseline-free defect detection and localization method of welded steel plate based on reciprocity loss
Authors: He Tianhao , Xing Gailan , Li Yong , Li Qinfei , Zhou Shaoping
Published: September 2020

In recent years, ultrasonic Lamb waves have been widely applied to the field of non-destructive testing of plate-like structures as they have outstanding advantages, such as low attenuation, high sensitivity, and wide detection range. Current studies about defect-detection of plate-like structures using Lamb waves mostly focus on non-weld plate-like structures, and defect-detection methods are based on baseline data. This paper proposes a novel baseline-free damage inspection method of welded plate-like structures, which is based on the principle of reciprocity loss and combines the OPTICS and K-means intelligent clustering algorithms to achieve accurate defect localization. In order to verify the location accuracy of the clustering defect localization algorithm, this paper performs comparative experiments between the ellipse imaging algorithm and the clustering algorithm, which use baseline data as health signals. The comparative experimental results show that the single-defect location accuracy of the clustering algorithm is greatly improved compared with the traditional ellipse algorithm. Moreover, in order to verify the validity and feasibility of the baseline-free method, this paper applies this method to obtain characteristic signals and combines the clustering algorithm to locate both single-defect and double-defects. The experimental result of baseline-free method shows that this method can successfully detect and locate multiple defects, which gets rid of the dependence of baseline data.
Apparent differences between single layer molybdenum disulphide fabricated via chemical vapour deposition and exfoliation
Authors: Pollmann Erik , Madauß Lukas , Schumacher Simon , Kumar Uttam , Heuvel Flemming , vom Ende Christina , Yilmaz Sümeyra , Güngörmüs Sümeyra , Schleberger Marika
Published: September 2020

Innovative applications based on two-dimensional solids require cost-effective fabrication processes resulting in large areas of high quality materials. Chemical vapour deposition is among the most promising methods to fulfill these requirements. However, for 2D materials prepared in this way it is generally assumed that they are of inferior quality in comparison to the exfoliated 2D materials commonly used in basic research. In this work we challenge this assumption and aim to quantify the differences in quality for the prototypical transition metal dichalcogenide MoS2. To this end single layers of MoS2 prepared by different techniques (exfoliation, grown by different chemical vapour deposition methods, transfer techniques and as vertical heterostructure with graphene) are studied by Raman and photoluminescence spectroscopy, complemented by atomic force microscopy. We demonstrate that as-prepared MoS2, directly grown on SiO2, differs from exfoliated MoS2 in terms of higher photoluminescence, lower electron concentration and increased strain. As soon as a water film is intercalated (e.g. by transfer) underneath the grown MoS2, in particular the (opto)electronic properties become practically identical to those of exfoliated MoS2. A comparison of the two most common precursors shows that the growth with MoO3 causes greater strain and/or defect density deviations than growth with ammonium heptamolybdate. As part of a heterostructure directly grown MoS2 interacts much stronger with the substrate and in this case an intercalated water film does not lead to the complete decoupling, which is typical for exfoliation or transfer. Our work shows that the supposedly poorer quality of grown 2D transition metal dichalcogenides is indeed a misconception.
Coupling between structural properties and charge transport in nano-crystalline and amorphous graphitic carbon films, deposited by electron-beam evaporation
Authors: Brus V V , Ilashchuk M I , Orletskyi I G , Solovan M M , Parkhomenko G P , Babichuk I S , Schopp N , Andrushchak G O , Mostovyi A I , Maryanchuk P D
Published: September 2020

Nano-crystalline and amorphous films of graphitized carbon were deposited by electron-beam evaporation of bulk graphite. Structural properties and the size of graphite nanoclusters (L ≈ 1.2–5 nm) in the films were determined from the analysis of their Raman spectra. Electrical properties of the bulk nano-crystalline graphite reference sample and the deposited graphitic carbon films were measured by means of the Hall effect technique within the temperature range from 290 to 420 K. The electrical conductivity σ and Hall mobility μH
of all samples exhibited exponential temperature dependences, indicating on the non-metallic behavior. Electrical properties of the amorphous graphitic carbon thin films, deposited at low substrate temperatures (620 and 750 K) were analyzed in the scope of the hopping charge transport mechanism via localized states. We have shown that the charge transport in the bulk and thin film (920 K) nano-crystalline graphite samples is carried out via the tunneling and thermionic emission over potential barriers at the grain boundaries.This paper contributes towards better understanding of coupling between structural and electrical properties of graphitic carbon thin films.
Excitation of electrostatic solitary waves during neutralization of ion beam pulse by plasma
Authors: Lan C , Dong P , Li J
Published: September 2020

The possibility of exciting electrostatic solitary waves (ESWs) during the neutralization of ion beam pulses by plasmas is investigated using a two-dimensional (2D) electrostatic particle-in-cell (PIC) code. The simulation results show that if an axial magnetic field is applied, an ESW can be excited when the ion beam enters the plasma. The ESW is caused by the phase space vortex motion of electrons in the potential well formed by the plasma and the ion beam. The ESW is very stable and has a very long lifetime when it propagates in the plasma and the ion beam. The ESW has a 2D space structure, with about 3 cm length and more than twice the width of the ion beam. The splitting of the ESW is observed when it encounters a potential drop. The excitation conditions of the ESW are also discussed.
Entropy production at criticality in a nonequilibrium Potts model
Authors: Martynec Thomas , Klapp Sabine H L , Loos Sarah A M
Published: September 2020

Understanding nonequilibrium systems and the consequences of irreversibility for the system’s behavior as compared to the equilibrium case, is a fundamental question in statistical physics. Here, we investigate two types of nonequilibrium phase transitions, a second-order and an infinite-order phase transition, in a prototypical q-state vector Potts model which is driven out of equilibrium by coupling the spins to heat baths at two different temperatures. We discuss the behavior of the quantities that are typically considered in the vicinity of (equilibrium) phase transitions, like the specific heat, and moreover investigate the behavior of the entropy production (EP), which directly quantifies the irreversibility of the process. For the second-order phase transition, we show that the universality class remains the same as in equilibrium. Further, the derivative of the EP rate with respect to the temperature diverges with a power-law at the critical point, but displays a non-universal critical exponent, which depends on the temperature difference, i.e., the strength of the driving. For the infinite-order transition, the derivative of the EP exhibits a maximum in the disordered phase, similar to the specific heat. However, in contrast to the specific heat, whose maximum is independent of the strength of the driving, the maximum of the derivative of the EP grows with increasing temperature difference. We also consider entropy fluctuations and find that their skewness increases with the driving strength, in both cases, in the vicinity of the second-order transition, as well as around the infinite-order transition.
Communication tasks in operational theories
Authors: Heinosaari Teiko , Kerppo Oskari , Leppäjärvi Leevi
Published: September 2020

We investigate the question which communication tasks can be accomplished within a given operational theory. The concrete task is to find out which communication matrices have a prepare-and-measure implementation with multiple states and a single measurement from a given theory, without using shared randomness. To set a general framework for this question we develop the ultraweak matrix majorization in the set of communication matrices. This preorder gives us means to determine when one communication task is more difficult than another. Furthermore, we introduce several monotones which can be used to compare and characterize the communication matrices. We observe that not only do the monotones allow us to compare communication matrices, but also their maximal values in a given theory are seen to relate to some physical properties of the theory. The maximal values can then be thought as ‘dimensions’, allowing us to compare different theories to each other. We analyse the introduced monotones one by one and demonstrate how the set of implementable communication matrices is different in several theories with the focus being mainly on the difference between classical and quantum theories of a given dimension.
Integrals whose saddle-point expansions terminate
Authors: Berry M V
Published: September 2020

The saddle-point expansion for integrals with integrand exp(−kf(x)) is a series in powers of 1/k. Usually this series diverges, but there is a family of exponent functions f(x), defining a family of canonical integrals, for which the series terminates and the saddle-point expansion is exact. For this family, the transformation x → X such that f(x) = X
2 possesses a Jacobian that is a polynomial in X, whose coefficients parameterise the canonical integrals.
Evaluation of surface properties and shear bond strength of zirconia substructure after sandblasting and acid etching
Authors: Zhang Qingqing , Yao Chun , Yuan Chunping , Zhang Hao , Liu Lin , Zhang Yue , Bai Jing , Tang Chunbo
Published: September 2020

To compare the effects of different surface treatment methods on the surface characteristics of yttria-stabilized tetragonal zirconia (Y-TZP) and relevant shear bond strength (SBS) between zirconia and composite resin. Forty-eight Y-TZP ceramics were randomly divided into four groups based on the specific surface treatments: Group C (blank treatment), Group Sand (sandblasting with 80 μm Al2O3 particles), Group HF (etched with 40% hydrofluoric acid for 10 min), and Group H2SO4 (etched with hot sulfuric acid for 10 min). Surface characteristics of the treated specimens, including morphology, roughness, wettability, chemical composition and crystalline structure were analyzed. SBS was tested by bonding ceramics to resin cement in the same group. Kruskal-Wallis test followed by pair wise comparison was conducted for statistical processing. A significance level of α = 0.05 was set. Three kinds of surface structures with different widths and heights in roughness were obtained, including micron-scale pit/peak size by sandblasting, nano-scale pit/peak size by hydrofluoric acid etching and middle submicron-scale pit/peak size by hot sulfuric acid etching. By comparison, the specimens of Group HF showed the most favorable wettability, the highest SBS and the lowest phase transformation than those of other groups. Therefore, HF etching was considered as a promising surface treatment to promote resin–zirconia bonding without excessive surface damage. The height, width, frequency and regularity of roughness altogether affected the shear strength.
Improvement the efficacy of Al/CuPc/n-Si/Al Schottky diode based on strong light absorption and high photocarriers response
Authors: Elgazzar Elsayed
Published: September 2020

Copper phthalocyanine has been prepared by simple chemical approach and its structural and optical properties were investigated. X-ray diffraction pattern exhibits a notable peak at

2
θ
=
6.75
°

assigned to the

α
−

phase of CuPc. SEM images show the particles distributed in nanospheres with average size at about 50 nm. The linear optical constants like optical band gap

(

E

g

)

and dielectric constants (

ε
′
,
ε
″

) were estimated from transmittance and reflectance spectra in the wavelength range from 250 to 900 nm. The energy gap was found to be 1.62 and 2.90 eV dependent on the incident photon energy. Al/CuPc/n-Si/Al Schottky diode has been fabricated using thermal evaporation technique. The electronic parameters such as the ideality factor

(
n
)
,

series resistance

(

R

s

)

,

and barrier height (

ϕ

b

) were evaluated in dark by applying the (I–V), Cheung-Chung, and Norde models. At various illumination intensities, the photocurrent sensitivity was studied based on the response of trapped charge carriers. At 1 Mhz, the built-in voltage

(

V

b
i

)

and donor concentration

(

N

d

)

were calculated from (C–V) measurements. The findings revealed that CuPc/n-type Si can be used as photodiode in optoelectronic applications.
Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
Authors: Lanchantin Jack , Qi Yanjun
Published: September 2020

Motivation

Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial structure of DNA, is highly influential in the chromatin profile. Deep neural networks have achieved state of the art performance on chromatin profile prediction by using short windows of DNA sequences independently. These methods, however, ignore the long-range dependencies when predicting the chromatin profiles because modeling the 3D genome is challenging.

Results

In this work, we introduce ChromeGCN, a graph convolutional network for chromatin profile prediction by fusing both local sequence and long-range 3D genome information. By incorporating the 3D genome, we relax the independent and identically distributed assumption of local windows for a better representation of DNA. ChromeGCN explicitly incorporates known long-range interactions into the modeling, allowing us to identify and interpret those important long-range dependencies in influencing chromatin profiles. We show experimentally that by fusing sequential and 3D genome data using ChromeGCN, we get a significant improvement over the state-of-the-art deep learning methods as indicated by three metrics. Importantly, we show that ChromeGCN is particularly useful for identifying epigenetic effects in those DNA windows that have a high degree of interactions with other DNA windows.

Availability and implementation

https://github.com/QData/ChromeGCN.

Supplementary information

Supplementary data are available at Bioinformatics online.
An efficient framework to identify key miRNA–mRNA regulatory modules in cancer
Authors: Mokhtaridoost Milad , Gönen Mehmet
Published: September 2020

Motivation

Micro-RNAs (miRNAs) are known as the important components of RNA silencing and post-transcriptional gene regulation, and they interact with messenger RNAs (mRNAs) either by degradation or by translational repression. miRNA alterations have a significant impact on the formation and progression of human cancers. Accordingly, it is important to establish computational methods with high predictive performance to identify cancer-specific miRNA–mRNA regulatory modules.

Results

We presented a two-step framework to model miRNA–mRNA relationships and identify cancer-specific modules between miRNAs and mRNAs from their matched expression profiles of more than 9000 primary tumors. We first estimated the regulatory matrix between miRNA and mRNA expression profiles by solving multiple linear programming problems. We then formulated a unified regularized factor regression (RFR) model that simultaneously estimates the effective number of modules (i.e. latent factors) and extracts modules by decomposing regulatory matrix into two low-rank matrices. Our RFR model groups correlated miRNAs together and correlated mRNAs together, and also controls sparsity levels of both matrices. These attributes lead to interpretable results with high predictive performance. We applied our method on a very comprehensive data collection by including 32 TCGA cancer types. To find the biological relevance of our approach, we performed functional gene set enrichment and survival analyses. A large portion of the identified modules are significantly enriched in Hallmark, PID and KEGG pathways/gene sets. To validate the identified modules, we also performed literature validation as well as validation using experimentally supported miRTarBase database.

Availability and implementation

Our implementation of proposed two-step RFR algorithm in R is available at https://github.com/MiladMokhtaridoost/2sRFR together with the scripts that replicate the reported experiments.

Supplementary information

Supplementary data are available at Bioinformatics online.
PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
Authors: Zhang Fuhao , Shi Wenbo , Zhang Jian , Zeng Min , Li Min , Kurgan Lukasz
Published: September 2020

Motivation

Knowledge of protein-binding residues (PBRs) improves our understanding of protein−protein interactions, contributes to the prediction of protein functions and facilitates protein−protein docking calculations. While many sequence-based predictors of PBRs were published, they offer modest levels of predictive performance and most of them cross-predict residues that interact with other partners. One unexplored option to improve the predictive quality is to design consensus predictors that combine results produced by multiple methods.

Results

We empirically investigate predictive performance of a representative set of nine predictors of PBRs. We report substantial differences in predictive quality when these methods are used to predict individual proteins, which contrast with the dataset-level benchmarks that are currently used to assess and compare these methods. Our analysis provides new insights for the cross-prediction concern, dissects complementarity between predictors and demonstrates that predictive performance of the top methods depends on unique characteristics of the input protein sequence. Using these insights, we developed PROBselect, first-of-its-kind consensus predictor of PBRs. Our design is based on the dynamic predictor selection at the protein level, where the selection relies on regression-based models that accurately estimate predictive performance of selected predictors directly from the sequence. Empirical assessment using a low-similarity test dataset shows that PROBselect provides significantly improved predictive quality when compared with the current predictors and conventional consensuses that combine residue-level predictions. Moreover, PROBselect informs the users about the expected predictive quality for the prediction generated from a given input protein.

Availability and implementation

PROBselect is available at http://bioinformatics.csu.edu.cn/PROBselect/home/index.

Supplementary information

Supplementary data are available at Bioinformatics online.
At 50, Janzen–Connell Has Come of Age
Authors: Terborgh John
Published: September 2020

Fifty years ago, Janzen (1970) and Connell (1971) independently published a revolutionary idea to explain the hyperdiverse tree communities of the tropics. The essential observations were that seedfall is concentrated in the vicinity of fruiting trees, whereas saplings recruit at a distance from reproductive conspecifics. These observations were encapsulated in a simple focal-tree model constructed of intersecting curves for seedfall and escape from host-specific enemies postulated to attack propagules (seeds and seedlings) in the vicinity of reproductive conspecifics. In conflict with the thinking of the times, the mechanism operates from the top down rather than from the bottom up. A deterrent to broad acceptance has been the giant intuitive leap required to generalize the focal tree model to an entire forest community. Recent theoretical and empirical results have succeeded in bridging the gap between the focal tree model and its community-level implications. With these new findings, Janzen–Connell has come of age.
Comparison of Surface Area and Cortical Thickness Asymmetry in the Human and Chimpanzee Brain
Authors: Xiang Li , Crow Timothy J , Hopkins William D , Roberts Neil
Published: September 2020

Comparative study of the structural asymmetry of the human and chimpanzee brain may shed light on the evolution of language and other cognitive abilities in humans. Here we report the results of vertex-wise and ROI-based analyses that compared surface area (SA) and cortical thickness (CT) asymmetries in 3D MR images obtained for 91 humans and 77 chimpanzees. The human brain is substantially more asymmetric than the chimpanzee brain. In particular, the human brain has 1) larger total SA in the right compared with the left cerebral hemisphere, 2) a global torque-like asymmetry pattern of widespread thicker cortex in the left compared with the right frontal and the right compared with the left temporo-parieto-occipital lobe, and 3) local asymmetries, most notably in medial occipital cortex and superior temporal gyrus, where rightward asymmetry is observed for both SA and CT. There is also 4) a prominent asymmetry specific to the chimpanzee brain, namely, rightward CT asymmetry of precentral cortex. These findings provide evidence of there being substantial differences in asymmetry between the human and chimpanzee brain. The unique asymmetries of the human brain are potential neural substrates for cognitive specializations, and the presence of significant CT asymmetry of precentral gyrus in the chimpanzee brain should be further investigated.
Functional Connectivity Hypersynchronization in Relatives of Alzheimer’s Disease Patients: An Early E/I Balance Dysfunction?
Authors: Ramírez-Toraño F , Bruña R , de Frutos-Lucas J , Rodríguez-Rojo I C , Marcos de Pedro S , Delgado-Losada M L , Gómez-Ruiz N , Barabash A , Marcos A , López Higes R , Maestú F
Published: September 2020

Alzheimer’s disease (AD) studies on animal models, and humans showed a tendency of the brain tissue to become hyperexcitable and hypersynchronized, causing neurodegeneration. However, we know little about either the onset of this phenomenon or its early effects on functional brain networks. We studied functional connectivity (FC) on 127 participants (92 middle-age relatives of AD patients and 35 age-matched nonrelatives) using magnetoencephalography. FC was estimated in the alpha band in areas known both for early amyloid accumulation and disrupted FC in MCI converters to AD. We found a frontoparietal network (anterior cingulate cortex, dorsal frontal, and precuneus) where relatives of AD patients showed hypersynchronization in high alpha (not modulated by APOE-ε4 genotype) in comparison to age-matched nonrelatives. These results represent the first evidence of neurophysiological events causing early network disruption in humans, opening a new perspective for intervention on the excitation/inhibition unbalance.
Magnetic Polydopamine Modified with Choline-Based Deep Eutectic Solvent for the Magnetic Solid-Phase Extraction of Sulfonylurea Herbicides in Water Samples
Authors: Wang Dan-Dan , Lu Zhi-Heng , Guan Xiao-yu , Yang Mei-Nan Ou , Guo Hao-Ming , Yang Zhong-Hua
Published: September 2020

A novel magnetic solid-phase extraction technique coupled to ultraperformance liquid chromatography has been developed for separation and preconcentration of four sulfonylurea herbicides (sulfosulfuron, bensulfuron-methyl, pyrazosulfuron-ethyl and halosulfuro-methyl) in aqueous samples. The key point of this method was the application of a novel magnetic nanomaterial that composed of a low eutectic solvent as a shell coated on the magnetic core modified by polydopamine. The extensive active sites outside the low eutectic solvent can effectively adsorb the target herbicide in the extraction process. The obtained magnetic adsorbent was characterized with fourier transform infrared spectrometry, scanning electron microscopy and vibrating sample magnetometer. The influence parameters relevant to this method were optimized. Under the optimum conditions, good linearities could be obtained within the range of 1.0–200 μg L−1 for all analytes, with correlation coefficients ≥0.9908. The limit of detections of the method was between 0.0074 and 0.0100 μg L−1 and the relative standard deviations were 1.1–3.6%. The enrichment factor is 66.6. In the final experiment, the proposed method was successfully applied to the analysis of sulfonylurea herbicides residue in environment and drinking-water samples, and the obtained recoveries were between 70.6% and 109.4%.
Management of Drug Toxicity in Mycobacterium avium Complex Pulmonary Disease: An Expert Panel Survey
Authors: van Ingen Jakko , Aliberti Stefano , Andrejak Claire , Chalmers James D , Codecasa Luigi R , Daley Charles L , Hasegawa Naoki , Griffith David E , Hoefsloot Wouter , Huitt Gwen , Jarand Julie , Jhun Byung Woo , Loebinger Michael R , Marras Theodore K , Morimoto Kozo , Polverino Eva , Ringshausen Felix C , Santin Miguel , Thomson Rachel , Wagner Dirk , Wallace Richard J , Winthrop Kevin L , Yim Jae-Joon
Published: September 2020

Adverse events are frequent in nontuberculous mycobacteria pulmonary disease treatment, but evidence to support their management is scarce. An expert panel survey on management of adverse events shows consistent opinions on management of hepatoxicity, ocular toxicity, ototoxicity, tinnitus, and gastrointestinal upset. These opinions can provide assistance in individual patient management decisions.
The Conditional Reliability Evaluation of Data Center Network BCDC
Authors: Lv Mengjie , Cheng Baolei , Fan Jianxi , Wang Xi , Zhou Jingya , Yu Jia
Published: September 2020

As the number of servers in a data center network (DCN) increases, the probability of server failures is significantly increased. Traditional connectivity is an important metric to measure the reliability of DCN. However, the traditional connectivity of a DCN based on the condition of arbitrary faulty servers is generally lower. Therefore, it is important to increase the connectivity of a DCN by adding some limited conditions for the faulty server set. As a result, $g$-restricted connectivity and $h$-extra connectivity, which are two crucial subjects for a DCN’s ability to tolerate faulty servers, were proposed in the literature. In this paper, we study the $g$-restricted connectivity and $h$-extra connectivity of a new server-centric DCN, called BCDC, based on crossed cube with excellent performance. We prove that the $g$-restricted connectivity of BCDC is 4 for $n=3$ and $2n+g(n-2)-2$ for $n\geq 4$, where $0\leq g\leq n-3$, and the $h$-extra connectivity of BCDC is 4 for $n=3$ and $2n+h(n-2)-2$ for $n\geq 4$, where $0\leq h\leq n-3$.
Market heterogeneity and the distributional incidence of soft-drink taxes: evidence from France
Authors: Etilé Fabrice , Lecocq Sébastien , Boizot-Szantai Christine
Published: September 2020

Market heterogeneity may affect the distributional incidence of nutritional taxes if households sort by income across markets with different characteristics. We use scanner data to analyse the distributional incidence of the 2012 French soda tax on Exact Price Indices that measure consumer welfare from the price and availability of soft-drinks at a local level. While the average pass-through was small—about 45 per cent—, tax incidence was significantly higher in low-income and less-competitive markets. Market heterogeneity ultimately has substantial distributional effects: it accounts for at least 33 per cent of the difference in welfare variation between low- and high-income consumers.
The domestic consumption of firewood in preindustrial Seville, 1518–1775. An intensive bias driven by the Mediterranean diet
Authors: Bartolomé Rodríguez Isabel , González-Mariscal Manuel
Published: September 2020

Fuelwood was the main domestic fuel in the Mediterranean Basin during the early modern age, although the consumption level was lower than in other latitudes. The calculation of annual real prices and per capita household consumption figures in Seville from 1518 to 1775 reveals a complex evolution connected to a European-wide scenario. As expected, low levels of domestic fuelwood use were maintained in accordance with climate and heating requirements, but contrary to prior assumptions, a substantial increase is evidenced as of 1630. The growing supply of firewood from tree-crops, leading to a decrease in real prices, ran parallel to an early diet shift to pulses and the corresponding extension of cooking times.
Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana
Authors: Hamilton John P , Godden Grant T , Lanier Emily , Bhat Wajid Waheed , Kinser Taliesin J , Vaillancourt Brieanne , Wang Haiyan , Wood Joshua C , Jiang Jiming , Soltis Pamela S , Soltis Douglas E , Hamberger Bjoern , Buell C Robin
Published: September 2020

Background

Plants exhibit wide chemical diversity due to the production of specialized metabolites that function as pollinator attractants, defensive compounds, and signaling molecules. Lamiaceae (mints) are known for their chemodiversity and have been cultivated for use as culinary herbs, as well as sources of insect repellents, health-promoting compounds, and fragrance.

Findings

We report the chromosome-scale genome assembly of Callicarpa americana L. (American beautyberry), a species within the early-diverging Callicarpoideae clade of Lamiaceae, known for its metallic purple fruits and use as an insect repellent due to its production of terpenoids. Using long-read sequencing and Hi-C scaffolding, we generated a 506.1-Mb assembly spanning 17 pseudomolecules with N50 contig and N50 scaffold sizes of 7.5 and 29.0 Mb, respectively. In all, 32,164 genes were annotated, including 53 candidate terpene synthases and 47 putative clusters of specialized metabolite biosynthetic pathways. Our analyses revealed 3 putative whole-genome duplication events, which, together with local tandem duplications, contributed to gene family expansion of terpene synthases. Kolavenyl diphosphate is a gateway to many of the bioactive terpenoids in C. americana; experimental validation confirmed that CamTPS2 encodes kolavenyl diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak), a member of the Tectonoideae clade of Lamiaceae known for exceptionally strong wood resistant to insects, revealed 963 collinear blocks and 21,297 C. americana syntelogs.

Conclusions

Access to the C. americana genome provides a road map for rapid discovery of genes encoding plant-derived agrichemicals and a key resource for understanding the evolution of chemical diversity in Lamiaceae.
Water weaponization in the Syrian conflict: strategies of domination and cooperation
Authors: Daoudy Marwa
Published: September 2020

How do actors weaponize water in intrastate conflicts? Existing typologies of water weaponization make deterministic differentiations between state and non-state actors and invoke opaque labels like ‘terrorism’. Furthermore, these typologies ignore how various actors engaged in violent conflict also cooperate over water, and whether water weaponization occurs beyond war. I propose a new typology for water weaponization in an analysis of the case of Syria, drawing on the leaked ‘ISIS papers’ as well as primary sources and interviews. The study begins by charting how the Ba'athist regime used water as a weapon of domination and legitimacy against its Kurdish population with infrastructure that would later facilitate the Islamic State of Iraq and Syria's (ISIS) ability to take hold of northeast Syria. I then turn to how non-state armed groups like ISIS and the Kurdish Democratic Union Party (PYD) have adopted strategies of water weaponization similar to the Syrian government by targeting and channelling water systems with major tactical implications. Finally, I show how enemy parties such as ISIS and the al-Assad regime weaponized cooperative water agreements to advance their mutual interests with violent implications for civilians. As such, I sort strategies of water weaponization into four categories: domination and legitimacy, military tools, military targets, and cooperation. In doing so, this new typology makes three main contributions, by: 1) accounting for how water is weaponized in state-society relations outside conflict; 2) refining existing definitions of water as a military tool and target; and 3) appraising the weapon-like effects of water cooperation.