bluuebunny/crossref_metadata_2025 huggingface dataset:
K‐PSO: An improved PSO‐based container scheduling algorithm for big data applications
Authors: Liu Bo , Li Jiawei , Lin Weiwei , Bai Weihua , Li Pengfei , Gao Qian
Published: January 2020

In recent years, Docker container technology is being applied in the field of cloud computing at an explosive speed. The scheduling of Docker container resources has gradually become a research hotspot. Existing big data computing and storage platforms apply with traditional virtual machine technology, which often results in low resource utilization, a long time for flexible scaling and expanding clusters. In this paper, we propose an improved container scheduling algorithm for big data applications named Kubernetes‐based particle swarm optimization(K‐PSO). Experimental results show that the proposed K‐PSO algorithm converges faster than the basic PSO algorithm, and the running time of the algorithm is cut in about half. The K‐PSO container scheduling algorithm and algorithm experiment for big data applications are implemented in the Kubernetes container cloud system. Our experimental results show that the node resource utilization rate of the improved scheduling strategy based on K‐PSO algorithm is about 20% higher than that of the Kube‐scheduler default strategy, balanced QoS priority strategy, ESS strategy, and PSO strategy, while the average I/O performance and average computing performance of Hadoop cluster are not degraded.
Taboo and Descent in the Articulation of Gender Relations: An Eastern Indonesian Case
Authors: Forth Gregory
Published: January 2020

In the Lio region of Flores Island patrilineal groups coexist with taboos on animals and plants inherited through females, a combination previously interpreted as reflecting a system of double unilineal descent. Drawing on ethnography from the Lio district of Mego, maternal taboos are shown to accompany similar prohibitions conceived as a property of patriclans, most of which, however, are incumbent not on male clansmen but on their wives. As is further demonstrated, both sorts of taboo reflect ideas about female bodies and blood, particularly as women and their children are transformed through marriage into members of patrilineal groups dominated by men. Also discussed is whether variability in the way taboos are currently inherited in Mego may reflect recent social change, and how matrilineally inherited Lio prohibitions can be seen as an instance of complementary female and male principles equally operative in the social life of other eastern Indonesian societies.
Association between shared medical appointments and weight loss outcomes and anti‐obesity medication use in patients with obesity
Authors: Shibuya Kelly , Ji Xinge , Pfoh Elizabeth R. , Milinovich Alex , Weng Wayne , Bauman Janine , Ganguly Rahul , Misra‐Hebert Anita D. , Hobbs Todd M. , Kattan Michael W. , Pantalone Kevin M. , Ramasamy Abhilasha , Burguera Bartolome
Published: January 2020

Objective

In shared medical appointments (SMAs), multiple patients with a similar clinical diagnosis are seen by a multidisciplinary team for interactive group sessions. Very few studies have specifically studied SMAs and weight loss in patients with obesity. This study compared weight loss outcomes and anti‐obesity medication (AOM) access between patients with obesity managed through (SMAs) versus individual appointments.

Methods

Retrospective study of adults seen for obesity between September 2014 and February 2017 at Cleveland Clinic Institute of Endocrinology and Metabolism. Percent weight loss from baseline was compared between two propensity score‐matched populations: patients who attended ≥1 SMA and patients managed with individual medical appointments.

Results

From all eligible patients identified (n=310 SMA, n=1,993 non‐SMA), 301 matched pairs were evaluated for weight loss. The SMA group (n=301) lost a mean of 4.2%, 5.2% and 3.8% of baseline weight over 6, 12 and 24 months; the non‐SMA group (n=301) lost significantly less weight (1.5%, 1.8% and 1.6%, respectively) (paired t‐test, P<.05). All patients were eligible for US Food and Drug Administration‐approved AOMs based on obesity diagnosis; however, 49.8% (150/301) of matched SMA patients were prescribed an AOM versus 12.3% (37/301) of matched non‐SMA patients.

Conclusion

This study suggests that SMAs may offer a promising alterative for obesity management and one that may facilitate greater utilization of AOMs. In propensity score‐matched cohorts, SMAs were associated with greater weight loss outcomes when compared to usual care facilitated through individual medical appointments alone.
Pharmacy hydroxyurea education materials for patients with sickle cell disease: An environmental scan and assessment of accuracy
Authors: Cervi Andrea , Diamantouros Artemis , Azzam Mona , Lane Shannon J. , Sapru Hyra , Verhovsek Madeleine
Published: January 2020

Background

Hydroxyurea (HU) remains a cornerstone of sickle cell disease (SCD) therapy; however, its use is limited by poor patient adherence owing to concerns about side effects. Pharmacies routinely provide patients with handouts about HU, which, we hypothesized, contain inaccuracies that may contribute to negative patient perceptions of HU.

Methods

We used a systematic approach to collect and review patient information handouts (PIHs) on HU from pharmacies in Ontario, Canada. PIHs were evaluated according to:

Number of inaccurate statements,

Percentage of essential statements based on comparison with a reference standard PIH developed by the Canadian Haemoglobinopathy Association (CanHaem), and

Reading level.

Results

PIHs were collected from 98% of chain and community pharmacies registered in Ontario. All PIHs contained inaccurate statements, most frequently relating to the risk of developing cancer. Only 33% of PIHs identified SCD as an indication for HU use. Pharmacy PIHs contained 45% of the essential statements present within the CanHaem HU PIH, neglecting to mention use of HU for management of SCD and benefits of HU in preventing SCD complications. Moreover, the reading level across pharmacy PIHs was 1.8 grades higher than that advised for written patient education materials.

Conclusion

Patients who are prescribed HU are likely to be provided with PIHs that contain inaccuracies that are weighted toward the risks of HU therapy and run contrary to published literature. This study identifies a gap in the care of patients with SCD and an opportunity to improve the quality of HU PIHs to help patients make well‐informed decisions about their health.
Mendelian susceptibility to mycobacterial disease—Challenges in hematopoietic stem cell transplantation
Authors: Patel Shivani , Uppuluri Ramya , Vellaichamy Swaminathan Venkateswaran , Ravichandran Nikila , Melarcode Ramanan Kesavan , Raj Revathi
Published: January 2020

We present our experience in the hematopoietic stem cell transplantation (HSCT) in two children diagnosed with Mendelian susceptibility to mycobacterial diseases. The first child underwent a haploidentical HSCT with posttransplant cyclophosphamide using a reduced intensity conditioning following which he had primary graft failure. He was subsequently found to have interferon‐γ1 receptor deficiency. He had immune reconstitution and is on antitubercular therapy. The second child diagnosed with IL12RB1 gene mutation underwent matched sibling donor HSCT with myeloablative conditioning following pretransplant immunosuppression with fludarabine and dexamethasone. He is 13 months post‐HSCT with complete and remains disease free.
Social anhedonia and social functioning: Loneliness as a mediator
Authors: Tan Melody , Shallis Amy , Barkus Emma
Published: January 2020

Social anhedonia is associated with reduced social functioning and diminished reward from social interactions. Individuals expressing social anhedonia are likely to experience reduced social connectedness and feel lonely. Loneliness is also associated with reduced social functioning. Therefore, loneliness could account for the relationship between social anhedonia and social functioning. We aimed to determine whether loneliness mediates the relationship between social anhedonia and reduced social functioning. In total, 824 young adults (M age = 21.03, SD = 5.59; 72.3% female) completed the Revised‐Social Anhedonia Scale (RSAS), University of California Los Angeles (UCLA) Loneliness Scale, and the Social Functioning Scale (SFS). Scores on thee SFS were summed into six subscales: Social Withdrawal, Relationships, Social Activities, Recreational Activities, Independence (Competence), and Independence (Performance). Negative affect (Depression, Anxiety and Stress Scales‐21 [DASS] total score) was included as a covariate. Both the RSAS and the UCLA Loneliness Scale were negatively correlated with overall and all social functioning subscales. The DASS‐21 positively correlated with all variables of interest. Mediation analyses revealed that loneliness partially mediated the relationship between social anhedonia and the social functioning subscales, with the exception of Recreational Activities. However, loneliness was a full mediator for the relationship between social anhedonia and overall social functioning. The study findings suggest that targeting loneliness in interventions may be important for improving various aspects of social functioning in those individuals who express social anhedonia.
Improving measurement of binary covariates in claims data: A simulation study
Authors: Connolly John G. , Glynn Robert J. , Schneeweiss Sebastian , Gagne Joshua J.
Published: January 2020

Purpose

When investigators have two claims‐based definitions for a binary confounder, it is unclear whether to prefer the more sensitive or more specific definition. Our objective was to compare adjusting for the sensitive or specific definition alone vs two novel approaches combining both definitions: a “two‐algorithm indicator” and a “two‐algorithm restriction” approach.

Methods

Each simulated patient had a binary exposure, outcome, and confounder. We created two nested, misclassified versions of the confounder using validated heart failure definitions. The sensitive definition had a sensitivity/specificity of 0.98/0.83, while the specific definition had a sensitivity/specificity of 0.77/0.99. Patients were classified into 3 groups: group 0 did not meet either definition, group 1 met the sensitive but not specific definition, and group 2 met both. The two‐algorithm indicator approach adjusted using indicators for groups 1 and 2, while the two‐algorithm restriction approach excluded patients in group 1 and adjusted using an indicator for group 2. Adjusted exposure odds ratios (ORs) were estimated for each approach using logistic regression.

Results

The crude OR was 1.33 (95% CI, 1.07‐1.63). Adjusting for the specific or sensitive definitions resulted in ORs of 1.09 (95% CI, 0.87‐1.35) and 1.14 (95% CI, 0.91‐1.40). The two‐algorithm indicator method returned an OR of 1.07 (95% CI, 0.86‐1.33). The two‐algorithm restriction approach returned an OR of 1.02 (95% CI, 0.79‐1.29) but excluded 20% of the cohort.

Conclusions

The two‐algorithm indicator approach may improve adjustment for claims‐based confounders by returning a point estimate at least as unbiased as the better of the two component definitions.
Locally‐Strain‐Induced Heavy‐Hole‐Band Splitting Observed in Mobility Spectrum of p‐Type InAs Grown on GaAs
Authors: Wróbel Jarosław , Umana-Membreno Gilberto A. , Boguski Jacek , Sztenkiel Dariusz , Michałowski Paweł Piotr , Martyniuk Piotr , Faraone Lorenzo , Wróbel Jerzy , Rogalski Antoni
Published: January 2020

High‐quality Be‐doped InAs layer grown by molecular beam epitaxy on GaAs substrate has been examined via magnetotransport measurements and high‐resolution quantitative mobility spectrum analysis (HR‐QMSA) in the range of 5–300 K and up to 15 T magnetic field. The results show four‐channel conductivity and essential splitting of the most populated hole‐like channel below 55 K. It is concluded that origin of such effect results from the locally strain‐induced interlayer, which direct observation is difficult or impossible via alternative techniques. Based on the magnetotransport data analysis, the multilayer model is proposed, which is implemented into nextnano simulation, giving the proof of the argumentation correctness. These results indicate potential usefulness of HR‐QMSA technique even in the degeneration statistic regime.
Should observations be grouped for effective monitoring of multivariate process variability?
Authors: Ajadi Jimoh Olawale , Zwetsloot Inez Maria
Published: January 2020

A multivariate dispersion control chart monitors changes in the process variability of multiple correlated quality characteristics. In this article, we investigate and compare the performance of charts designed to monitor variability on the basis of individual and grouped multivariate observations. We compare one of the most well‐known methods for monitoring individual observations—a multivariate exponentially weighted mean squared deviation (MEWMS) chart—with various charts based on grouped observations. In addition, we compare charts based on monitoring with overlapping and nonoverlapping subgroups. We recommend using charts based on overlapping subgroups when monitoring with subgroup data. The effect of subgroup size is also investigated. Steady‐state average time to signal is used as the performance measure. We show that monitoring methods based on individual observations are the quickest in detecting sustained shifts in the process variability. We use a simulation study to obtain our results and illustrated these with a case study.
Shotgun assembly of random jigsaw puzzles
Authors: Bordenave Charles , Feige Uriel , Mossel Elchanan
Published: January 2020

We consider the shotgun assembly problem for a random jigsaw puzzle, introduced by Mossel and Ross (2015). Their model consists of a puzzle—an n×n grid, where each vertex is viewed as a center of a piece. Each of the four edges adjacent to a vertex is assigned one of q colors (corresponding to “jigs,” or cut shapes) uniformly at random. Unique assembly refers to there being only one puzzle (the original one) that is consistent with the collection of individual pieces. We show that for any ε>0, if q ≥ n1+ε, then unique assembly holds with high probability. The proof uses an algorithm that assembles the puzzle in time nΘ(1/ε).22
Analytical solutions for multiple mode III cracks in a cylindrical bar with an orthotropic coating under dynamic loading
Authors: Karimi M. , Hassani A. R.
Published: January 2020

This study presents an analytical formulation for a cylindrical bar, with an orthotropic layer, containing multiple mode III cracks under time‐dependent torsion. The transient response to a dislocation cut with time‐dependent Burgers vector is obtained in the cross‐section of the cylindrical bar, with an orthotropic layer, with the help of the Fourier and Laplace transform. The dislocation solution is used to drive a group of singular integral equations for the study of circular domains with the orthotropic coating containing smooth radial cracks under transient torsional loading. The singular integral equations are evaluated numerically to calculate the torsional rigidity of the domain, and the dynamic stress intensity factors at the singular crack tips. Finally, there are several examples to illustrate the effect of the orthotropic coating on the dynamic stress intensity factors and torsional rigidity of the domain under consideration.
Embedding Feynman integral (Calabi-Yau) geometries in weighted projective space
Authors: Bourjaily Jacob L. , McLeod Andrew J. , Vergu Cristian , Volk Matthias , von Hippel Matt , Wilhelm Matthias
Published: January 2020

Abstract

It has recently been demonstrated that Feynman integrals relevant to a wide range of perturbative quantum field theories involve periods of Calabi-Yau manifolds of arbitrarily large dimension. While the number of Calabi-Yau manifolds of dimension three or higher is considerable (if not infinite), those relevant to most known examples come from a very simple class: degree-2k hypersurfaces in k-dimensional weighted projective space WP1,...,1,k
. In this work, we describe some of the basic properties of these spaces and identify additional examples of Feynman integrals that give rise to hypersurfaces of this type. Details of these examples at three loops and of illustrations of open questions at four loops are included as supplementary material to this work.
Non-derivative axionic couplings to nucleons at large and small N
Authors: Bigazzi Francesco , Cotrone Aldo L. , Järvinen Matti , Kiritsis Elias
Published: January 2020

Abstract

Among the possible CP-odd couplings of the axion to ordinary matter, the most relevant ones for phenomenology are the Yukawa couplings to nucleons. We analyze such non-derivative couplings within three different approaches: standard effective field theory, the Skyrme model and holographic QCD. In all the cases, the couplings can be related to the CP-odd non-derivative couplings to nucleons of the low-lying mesons and the η′. Using the effective field theory approach we discuss how to derive the expressions for the CP-odd interaction terms as functions of the parameters of the effective Lagrangian at generic number of colors N

c
and flavors N

f

. Then, we compute the CP-odd couplings to nucleons of the axion, the η′ and the pseudo-Goldstone mesons in both the Skyrme and the holographic QCD model with N

f
= 2, 3. We present model-independent expressions for the coefficients of the non-derivative axion-nucleon couplings. This allows us to provide quantitative estimates of these couplings.
The dynamical diquark model: fine structure and isospin
Authors: Giron Jesse F. , Lebed Richard F. , Peterson Curtis T.
Published: January 2020

Abstract

We incorporate fine-structure corrections into the dynamical diquark model of multiquark exotic hadrons. These improvements include effects due to finite diquark size, spin-spin couplings within the diquarks, and most significantly, isospin-dependent couplings in the form of pionlike exchanges assumed to occur between the light quarks within the diquarks. Using a simplified two-parameter interaction Hamiltonian, we obtain fits in which the isoscalar J
PC = 1++ state — identified as the X (3872) — appears naturally as the lightest exotic (including all states that are predicted by the model but have not yet been observed), while the closed-charm decays of Z

c
(3900) and Z

c
(4020) prefer J/𝜓 and h

c
modes, respectively, in accord with experiment. We explore implications of this model for the excited tetraquark multiplets and the pentaquarks.
Anomalies of QFTs from M-theory and holography
Authors: Bah Ibrahima , Bonetti Federico , Minasian Ruben , Nardoni Emily
Published: January 2020

Abstract

We describe a systematic way of computing the ’t Hooft anomalies for continuous symmetries of Quantum Field Theories in even dimensions that can be geometrically engineered from M5-branes. Our approach is based on anomaly inflow, and characterizes the anomaly polynomial of the QFT in terms of the geometric definition of the field theory. In particular, when the QFT admits a holographic dual, the topological data of the solution is sufficient to compute the anomalies of the dual field theory, including finite terms in N. We study several classes of examples in four and six dimensions, with or without known M5-brane probe configurations.
Malnutrition and its effects in severely injured trauma patients
Authors: Dijkink Suzan , Meier Karien , Krijnen Pieta , Yeh D. Dante , Velmahos George C. , Schipper Inger B.
Published: January 2020

Purpose

In hospitalized patients, malnutrition is associated with adverse outcomes. However, the consequences of malnutrition in trauma patients are still poorly understood. This study aims to review the current knowledge about the pathophysiology, prevalence, and effects of malnutrition in severely injured patients.

Methods

A systematic literature review in PubMed and Embase was conducted according to PRISMA-guidelines.

Results

Nine review articles discussed the hypermetabolic state in severely injured patients in relation to malnutrition. In these patients, malnutrition negatively influenced the metabolic response, and vice versa, thereby rendering them susceptible to adverse outcomes and further deterioration of nutritional status. Thirteen cohort studies reported on prevalences of malnutrition in severely injured patients; ten reported clinical outcomes. In severely injured patients, the prevalence of malnutrition ranged from 7 to 76%, depending upon setting, population, and nutritional assessment tool used. In the geriatric trauma population, 7–62.5% were malnourished at admission and 35.6–60% were at risk for malnutrition. Malnutrition was an independent risk factor for complications, mortality, prolonged hospital length of stay, and declined quality of life.

Conclusions

Despite widespread belief about the importance of nutrition in severely injured patients, the quantity and quality of available evidence is surprisingly sparse, frequently of low-quality, and outdated. Based on the malnutrition-associated adverse outcomes, the nutritional status of trauma patients should be routinely and carefully monitored. Trials are required to better define the optimal nutritional treatment of trauma patients, but a standardized data dictionary and reasonable outcome measures are required for meaningful interpretation and application of results.
Experimental tail shortening affects feeding rate depending on original tail length in female barn swallows Hirundo rustica gutturalis
Authors: Hasegawa Masaru , Arai Emi , Nakamura Masahiko
Published: January 2020

Long tail feathers of the barn swallowHirundo rusticaare a classic example of an intersexually selected trait, but previous aerodynamic analyses indicate that the tail feather is only 10–12 mm longer than the aerodynamic optimum even in the nominate subspecies with long tails. Here, by experimentally shortening female tail length, we studied the feeding cost of long tail feathers in Japanese barn swallows,Hirundo rustica gutturalis, which have ca. 10 mm shorter tails than the nominate subspecies. Female feeding rate was explained by the interaction between treatment and original female tail length: feeding rate decreased with decreasing original female tail length in control, but not in tail-shortened females. Because the interaction term was far from significant in the analysis of female incubation investment, the observed pattern would be specific to feeding rate, which is greatly affected by the aerodynamic properties associated with tail length. Differential allocation of paternal feeding investment was not observed in the current data set. Long tails would be costly at least in short-tailed females, supporting differential costs of ornamentation as predicted by sexual selection theory. Female outermost tail feathers are costly ornamentation in short-tailed Japanese barn swallows.
Testing individual baroreflex responses to hypoxia-induced peripheral chemoreflex stimulation
Authors: Kronsbein Hendrik , Gerlach Darius A. , Heusser Karsten , Hoff Alex , Hoffmann Fabian , Diedrich André , Ehmke Heimo , Jordan Jens , Tank Jens
Published: January 2020

Introduction

Baroreflexes and peripheral chemoreflexes control efferent autonomic activity making these reflexes treatment targets for arterial hypertension. The literature on their interaction is controversial, with suggestions that their individual and collective influence on blood pressure and heart rate regulation is variable. Therefore, we applied a study design that allows the elucidation of individual baroreflex–chemoreflex interactions.

Methods

We studied nine healthy young men who breathed either normal air (normoxia) or an air–nitrogen–carbon dioxide mixture with decreased oxygen content (hypoxia) for 90 min, with randomization to condition, followed by a 30-min recovery period and then exposure to the other condition for 90 min. Multiple intravenous phenylephrine bolus doses were applied per condition to determine phenylephrine pressor sensitivity as an estimate of baroreflex blood pressure buffering and cardiovagal baroreflex sensitivity (BRS).

Results

Hypoxia reduced arterial oxygen saturation from 98.1 ± 0.4 to 81.0 ± 0.4% (p < 0.001), raised heart rate from 62.9 ± 2.1 to 76.0 ± 3.6 bpm (p < 0.001), but did not change systolic blood pressure (p = 0.182). Of the nine subjects, six had significantly lower BRS in hypoxia (p < 0.05), two showed a significantly decreased pressor response, and three showed a significantly increased pressor response to phenylephrine in hypoxia, likely through reduced baroreflex buffering (p < 0.05). On average, hypoxia decreased BRS by 6.4 ± 0.9 ms/mmHg (19.9 ± 2.0 vs. 14.12 ± 1.6 ms/mmHg; p < 0.001) but did not change the phenylephrine pressor response (p = 0.878).

Conclusion

We applied an approach to assess individual baroreflex–chemoreflex interactions in human subjects. A subgroup exhibited significant impairments in baroreflex blood pressure buffering and BRS with peripheral chemoreflex activation. The methodology may have utility in elucidating individual pathophysiology and in targeting treatments modulating baroreflex or chemoreflex function.
Length-Change Patterns of the Collateral Ligaments During Functional Activities After Total Knee Arthroplasty
Authors: Hosseini Nasab S. H. , Smith C. R. , Schütz P. , Damm P. , Trepczynski A. , List R. , Taylor W. R.
Published: January 2020

This study aimed to quantify the elongation patterns of the collateral ligaments following TKA during functional activities of daily living. Using mobile video-fluoroscopy to capture radiographic images of the knee in a group of six patients, each with an ultra-congruent knee implant, tibiofemoral kinematics were reconstructed throughout complete cycles of level gait, downhill walking, stair descent, and squat activities. Kinematic data were then used to drive subject-specific multibody knee models to estimate length-change patterns of the LCL as well as three bundles of the MCL. In addition, a sensitivity analysis examined the role of the attachment site in the elongation patterns. Our data indicate a slackening of the LCL but non-uniform length-change patterns across the MCL bundles (ranging from lengthening of the anterior fibers to shortening of the posterior fibers) with increasing knee flexion angle. Near-isometric behavior of the intermediate fibers was observed throughout the entire cycle of the studied activities. These length-change patterns were found to be largely consistent across different activities. Importantly, length-change patterns were critically sensitive to the location of the femoral attachment points relative to the femoral component. Thus, in TKA with ultra-congruent implants, implantation of the femoral component may critically govern post-operative ligament function.
2D:4D Suggests a Role of Prenatal Testosterone in Gender Dysphoria
Authors: Sadr Mostafa , Khorashad Behzad S. , Talaei Ali , Fazeli Nasrin , Hönekopp Johannes
Published: January 2020

Gender dysphoria (GD) reflects distress caused by incongruence between one’s experienced gender identity and one’s natal (assigned) gender. Previous studies suggest that high levels of prenatal testosterone (T) in natal females and low levels in natal males might contribute to GD. Here, we investigated if the 2D:4D digit ratio, a biomarker of prenatal T effects, is related to GD. We first report results from a large Iranian sample, comparing 2D:4D in 104 transwomen and 89 transmen against controls of the same natal sex. We found significantly lower (less masculine) 2D:4D in transwomen compared to control men. We then conducted random-effects meta-analyses of relevant studies including our own (k = 6, N = 925 for transwomen and k = 6, N = 757 for transmen). In line with the hypothesized prenatal T effects, transwomen showed significantly feminized 2D:4D (d ≈ 0.24). Conversely, transmen showed masculinized 2D:4D (d ≈ − 0.28); however, large unaccounted heterogeneity across studies emerged, which makes this effect less meaningful. These findings support the idea that high levels of prenatal T in natal females and low levels in natal males play a part in the etiology of GD. As we discuss, this adds to the evidence demonstrating the convergent validity of 2D:4D as a marker of prenatal T effects.
Targeting the undruggable: exploiting neomorphic features of fusion oncoproteins in childhood sarcomas for innovative therapies
Authors: Knott Maximilian M. L. , Hölting Tilman L. B. , Ohmura Shunya , Kirchner Thomas , Cidre-Aranaz Florencia , Grünewald Thomas G. P.
Published: January 2020

While sarcomas account for approximately 1% of malignant tumors of adults, they are particularly more common in children and adolescents affected by cancer. In contrast to malignancies that occur in later stages of life, childhood tumors, including sarcoma, are characterized by a striking paucity of somatic mutations. However, entity-defining fusion oncogenes acting as the main oncogenic driver mutations are frequently found in pediatric bone and soft-tissue sarcomas such as Ewing sarcoma (EWSR1-FLI1), alveolar rhabdomyosarcoma (PAX3/7-FOXO1), and synovial sarcoma (SS18-SSX1/2/4). Since strong oncogene-dependency has been demonstrated in these entities, direct pharmacological targeting of these fusion oncogenes has been excessively attempted, thus far, with limited success. Despite apparent challenges, our increasing understanding of the neomorphic features of these fusion oncogenes in conjunction with rapid technological advances will likely enable the development of new strategies to therapeutically exploit these neomorphic features and to ultimately turn the “undruggable” into first-line target structures. In this review, we provide a broad overview of the current literature on targeting neomorphic features of fusion oncogenes found in Ewing sarcoma, alveolar rhabdomyosarcoma, and synovial sarcoma, and give a perspective for future developments.
Semi-automatic construction of word-formation networks
Authors: Lango Mateusz , Žabokrtský Zdeněk , Ševčíková Magda
Published: January 2020

The article presents a semi-automatic method for the construction of word-formation networks focusing particularly on derivation. The proposed approach applies a sequential pattern mining technique to construct useful morphological features in an unsupervised manner. The features take the form of regular expressions and later they are used to feed a machine-learned ranking model. The network is constructed by applying the learned model to sort the lists of possible base words and selecting the most probable ones. This approach, besides relatively small training set and a lexicon, does not require any additional language resources such as a list of vowel and consonant alternations, part-of-speech tags etc. The proposed approach is evaluated on lexeme sets of four languages, namely Polish, Spanish, Czech, and French. The conducted experiments demonstrate the ability of the proposed method to construct linguistically adequate word-formation networks from small training sets. Furthermore, the performed feasibility study shows that the method can further benefit from the interaction with a human language expert within the active learning framework.
The ea22 gene of lambdoid phages: preserved prolysogenic function despite of high sequence diversity
Authors: Dydecka Aleksandra , Bloch Sylwia , Necel Agnieszka , Topka Gracja , Węgrzyn Alicja , Tong Jinge , Donaldson Logan W. , Węgrzyn Grzegorz , Nejman-Faleńczyk Bożena
Published: January 2020

The exo-xis region of lambdoid phages contains open reading frames and genes that appear to be evolutionarily important. However, this region has received little attention up to now. In this study, we provided evidence that ea22, the largest gene of this region, favors the lysogenic pathway over the lytic pathway in contrast to other characterized exo-xis region genes including ea8.5, orf61, orf60a, and orf63. Our assays also suggest some functional analogies between Ea22 and the phage integrase protein (Int). While it is unsurprising that Ea22 operates similarly in both λ and Stx phages, we have observed some distinctions that may arise from considerable sequence dissimilarity at the carboxy termini of each protein.
Psychometric Properties of the Italian Version of the Smartphone Application-Based Addiction Scale (SABAS)
Authors: Soraci Paolo , Ferrari Ambra , Antonino Urso , Griffiths Mark D.
Published: January 2020

The aim of the present study was to test the psychometric properties of the Italian version of the Smartphone Application-Based Addiction Scale (SABAS; Csibi et al., International Journal of Mental Health and Addiction, 16, 393–403, 2018), a short and easy to use six-item tool for screening the risk of addiction to smartphone-based applications. A further goal was to explore the impact on smartphone addiction of several variables related to smartphone use habits, perceived quality of life, and sociability measures. The data were collected online from 205 Italian-speaking volunteers (128 males and 77 females aged 18 to 99 years). The psychometric instruments included in the study were the SABAS and the Nomophobia Questionnaire (NMP-Q). Psychometric testing showed that the six items included in the SABAS comprised a unidimensional factor with good reliability (Cronbach’s alpha = .890). Therefore, the SABAS appears to be a reliable instrument to assess the risk of addiction to smartphone apps. Moreover, longer daily time spent using the smartphone was found to be positively correlated with the total SABAS and NMP-Q scores, while perceived quality of life and self-reported sociability were found to be negatively correlated with such scores.
What Research Institutions Can Do to Foster Research Integrity
Authors: Bouter Lex
Published: January 2020

In many countries attention for fostering research integrity started with a misconduct case that got a lot of media exposure. But there is an emerging consensus that questionable research practices are more harmful due to their high prevalence. QRPs have in common that they can help to make study results more exciting, more positive and more statistically significant. That makes them tempting to engage in. Research institutions have the duty to empower their research staff to steer away from QRPs and to explain how they realize that in a Research Integrity Promotion Plan. Avoiding perverse incentives in assessing researchers for career advancement is an important element in that plan. Research institutions, funding agencies and journals should make their research integrity policies as evidence-based as possible. The dilemmas and distractions researchers face are real and universal. We owe it to society to collaborate and to do our utmost best to prevent QRPs and to foster research integrity.
Diagnostic performance of a computer-assisted diagnostic system: sensitivity of BONENAVI for bone scintigraphy in patients with disseminated skeletal metastasis is not so high
Authors: Koizumi Mitsuru , Motegi Kazuki , Koyama Masamichi , Ishiyama Mitsutomi , Togawa Takashi , Makino Tomoko , Arisaka Yukiko , Terauchi Takashi
Published: January 2020

Purpose

Bone scintigraphy (BS) of disseminated skeletal metastasis is sometimes misinterpreted as normal. The use of computer-assisted diagnosis (CAD) may resolve this problem. We investigated the performance of a CAD system, BONENAVI, in the diagnosis of disseminated skeletal metastasis.

Methods

Cases of disseminated skeletal metastasis were selected from a BS log. These patients’ BSs were analyzed by BONENAVI to obtain an artificial neural network (ANN) and bone scan index (BSI). Clinical features (type of primary cancer, CT type, and BS type) were compared with the BONENAVI (ANN and BSI) results. The BS findings (diffuse increased axial skeleton uptake, inhomogeneity of uptake, proximal extremity contrast, and degree of renal uptake) and ANN or BSI were evaluated. Then, negative ANN patients were presented.

Results

Fifty-four patients were diagnosed as having disseminated skeletal metastasis. Regarding the primary cancers, 12 had prostate cancer, 16 gastric cancers, 16 breast cancers, and 10 miscellaneous cancers. Total sensitivity of ANN (≥ 0.5) was 76% (41/54). ANN values correlated with the BS type among clinical features. Diffuse increased axial skeleton uptake was mostly correlated with ANN of the BS findings.

Conclusion

The BONENAVI CAD system was partially helpful in diagnosing disseminated skeletal metastasis, but the sensitivity of BONENAVI was not sufficient and underestimated the disseminated skeletal metastasis. Further improvement of this CAD system is necessary to improve the detectability of disseminated skeletal metastasis.
CFD analysis and field observation of tool erosion caused by abrasive waterjet fracturing
Authors: Sheng Mao , Huang Zhong-Wei , Tian Shou-Ceng , Zhang Yi , Gao Shi-Wang , Jia Yun-Peng
Published: January 2020

Abrasive waterjet (AWJ) fracturing has become an accepted horizontal multistage stimulation technique due to its flexibility and high efficiency of extensive fracture placement. The downhole tool failure of AWJ fracturing becomes an issue in the massive hydraulic fracturing because of high velocity and proppant erosion. This paper proposed a 3D computational fluid dynamics (CFD)-based erosion model by considering high-velocity waterjet impact, proppant shear erosion, and specific inner structure of hydra-jet tool body. The discrete phase approach was used to track the proppant transport and its concentration distribution. Field observation provides strong evidence of erosion patterns and mechanisms obtained from CFD simulation. The results show that the erosion rate has a space dependence in the inner wall of the tool body. The severe erosion areas are primarily located at the entries of the nozzle. Evident erosion patterns are found including a ‘Rabbit’s ear’ erosion at the upper-layer nozzles and a half bottom loop erosion at the lower-layer nozzles. Erosion mechanisms attribute to high flow velocity at the entry of nozzles and the inertia force of proppant. Sensitivity analysis demonstrates that the pumping rate is a primary factor contributing to erosion intensity.
Correction to: Self-Reported Sleep and Exercise Patterns in Patients with Schizophrenia: A Cross-Sectional Comparative Study
Authors: Kiwan Nancy , Mahfoud Ziyad , Ghuloum Suhaila , Chamali Rifka , Yehya Arij , Hammoudeh Samer , Hani Yahya , Amro Iman , Al-Amin Hassen
Published: January 2020

The article Self-Reported Sleep and Exercise Patterns in Patients with Schizophrenia: a Cross-Sectional Comparative Study written by Nancy Kiwan, Ziyad Mahfoud, Suhaila Ghuloum, Rifka Chamali, Arij Yehya, Samer Hammoudeh, Yahya Hani, Iman Amro, and Hassen Al-Amin
Control and Ownership of Neuroprosthetic Speech
Authors: Maslen Hannah , Rainey Stephen
Published: January 2020

Implantable brain-computer interfaces (BCIs) are being developed to restore speech capacity for those who are unable to speak. Patients with locked-in syndrome or amyotrophic lateral sclerosis could be able to use covert speech – vividly imagining saying something without actual vocalisation – to trigger neural controlled systems capable of synthesising speech. User control has been identified as particularly pressing for this type of BCI. The incorporation of machine learning and statistical language models into the decoding process introduces a contribution to (or ‘shaping of’) the output that is beyond the user’s control. Whilst this type of ‘shared control’ of BCI action is not unique to speech BCIs, the automated shaping of what a user ‘says’ has a particularly acute ethical dimension, which may differ from parallel concerns surrounding automation in movement BCIs. This paper provides an analysis of the control afforded to the user of a speech BCI of the sort under development, as well as the relationships between accuracy, control, and the user’s ownership of the speech produced. Through comparing speech BCIs with BCIs for movement, we argue that, whilst goal selection is the more significant locus of control for the user of a movement BCI, control over process will be more significant for the user of the speech BCI. The design of the speech BCI may therefore have to trade off some possible efficiency gains afforded by automation in order to preserve sufficient guidance control necessary for users to express themselves in ways they prefer. We consider the implications for the speech BCI user’s responsibility for produced outputs and their ownership of token outputs. We argue that these are distinct assessments. Ownership of synthetic speech concerns whether the content of the output sufficiently represents the user, rather than their morally relevant, causal role in producing that output.
Identifying viruses from metagenomic data using deep learning
Authors: Ren Jie , Song Kai , Deng Chao , Ahlgren Nathan A. , Fuhrman Jed A. , Li Yi , Xie Xiaohui , Poplin Ryan , Sun Fengzhu
Published: January 2020

Background

The recent development of metagenomic sequencing makes it possible to massively sequence microbial genomes including viral genomes without the need for laboratory culture. Existing reference‐based and gene homology‐based methods are not efficient in identifying unknown viruses or short viral sequences from metagenomic data.

Methods

Here we developed a reference‐free and alignment‐free machine learning method, DeepVirFinder, for identifying viral sequences in metagenomic data using deep learning.

Results

Trained based on sequences from viral RefSeq discovered before May 2015, and evaluated on those discovered after that date, DeepVirFinder outperformed the state‐of‐the‐art method VirFinder at all contig lengths, achieving AUROC 0.93, 0.95, 0.97, and 0.98 for 300, 500, 1000, and 3000 bp sequences respectively. Enlarging the training data with additional millions of purified viral sequences from metavirome samples further improved the accuracy for identifying virus groups that are under‐represented. Applying DeepVirFinder to real human gut metagenomic samples, we identified 51,138 viral sequences belonging to 175 bins in patients with colorectal carcinoma (CRC). Ten bins were found associated with the cancer status, suggesting viruses may play important roles in CRC.

Conclusions

Powered by deep learning and high throughput sequencing metagenomic data, DeepVirFinder significantly improved the accuracy of viral identification and will assist the study of viruses in the era of metagenomics.
Machine Learning to Analyze Single-Case Data: A Proof of Concept
Authors: Lanovaz Marc J. , Giannakakos Antonia R. , Destras Océane
Published: January 2020

Visual analysis is the most commonly used method for interpreting data from single-case designs, but levels of interrater agreement remain a concern. Although structured aids to visual analysis such as the dual-criteria (DC) method may increase interrater agreement, the accuracy of the analyses may still benefit from improvements. Thus, the purpose of our study was to (a) examine correspondence between visual analysis and models derived from different machine learning algorithms, and (b) compare the accuracy, Type I error rate and power of each of our models with those produced by the DC method. We trained our models on a previously published dataset and then conducted analyses on both nonsimulated and simulated graphs. All our models derived from machine learning algorithms matched the interpretation of the visual analysts more frequently than the DC method. Furthermore, the machine learning algorithms outperformed the DC method on accuracy, Type I error rate, and power. Our results support the somewhat unorthodox proposition that behavior analysts may use machine learning algorithms to supplement their visual analysis of single-case data, but more research is needed to examine the potential benefits and drawbacks of such an approach.
Social and economic flows across multimodal transportation networks in the Greater Tokyo Area
Authors: Bramson Aaron , Hori Megumi , Zha Bingran , Inamoto Hirohisa
Published: January 2020

We model the flow of human capital and resources across multimodal transportation networks throughout the Greater Tokyo Area. Our transportation networks include trains, buses, and roads integrated with a walking network among a geographically grounded hexagonal grid and connecting nodes of different modes. The hexagonal grid holds data on both the working population and number of jobs from which we built probability distributions for the origins and destinations of commuting trips. Using both the network simplex method and stochastically generated origin-destination trips we estimate the population flows necessary to satisfy this demand. Rather than micro-simulations of actual commuting patterns, congestion, or route planning, our approach aims to uncover patterns in the aggregate flow of human resources to and from economic opportunities. We describe the details of the socioeconomic data, network generation, and the results of our exploratory analysis, then discuss the implications of these findings for transportation usage and future work.
Effect of Sieving on Ex Situ Soil Respiration of Soils from Three Land Use Types
Authors: Adekanmbi Adetunji Alex , Shaw Liz J. , Sizmur Tom
Published: January 2020

This study aims to investigate the effect of sieving on ex situ soil respiration (CO2 flux) measurements from different land use types. We collected soils (0–10 cm) from arable, grassland and woodland sites, allocated them to either sieved (4-mm mesh, freshly sieved) or intact core treatments and incubated them in gas-tight jars for 40 days at 10 °C. Headspace gas was collected on days 1, 3, 17, 24, 31 and 38 and CO2 analysed. Our results showed that sieving (4 mm) did not significantly influence soil respiration measurements, probably because micro aggregates (< 0.25 mm) remain intact after sieving. However, soils collected from grassland soil released more CO2 compared with those collected from woodland and arable soils, irrespective of sieving treatments. The higher CO2 from grassland soil compared with woodland and arable soils was attributed to the differences in the water holding capacity and the quantity and stoichiometry of the organic matter between the three soils. We conclude that soils sieved prior to ex situ respiration experiments provide realistic respiration measurements. This finding lends support to soil scientists planning a sampling strategy that better represents the inhomogeneity of field conditions by pooling, homogenising and sieving samples, without fear of obtaining unrepresentative CO2 flux measurements caused by the disruption of soil architecture.