bluuebunny/crossref_metadata_2025 huggingface dataset:
Software-based Detection of Acute Rejection Changes in Face Transplant
Authors: Dorante Miguel I. , Kollar Branislav , Bittner Marian , Wang Alice , Diehm Yannick , Foroutanjazi Sina , Parikh Neil , Haug Valentin , den Uyl Tim M. , Pomahac Bohdan
Published: September 2021

Background An objective, non-invasive method for redness detection during acute allograft rejection in face transplantation (FT) is lacking.

Methods A retrospective cohort study was performed with 688 images of 7 patients with face transplant (range, 1 to 108 months post-transplant). Healthy controls were matched to donor age, sex, and had no prior facial procedures. Rejection state was confirmed via tissue biopsy. An image-analysis software developed alongside VicarVision (Amsterdam, Netherlands) was used to produce R, a measure of differences between detectable color and absolute red. R is inversely proportional to redness, where lower R values correspond to increased redness. Linear mixed models were used to study fixed effect of rejection state on R values. Estimated marginal means of fitted models were calculated for pairwise comparisons.

Results Of 688 images, 175, 170, 202, and 141 images were attributable to Banff Grade 0,1,2, and 3, respectively. Estimated change in R value of facial allografts decreased with increasing Banff Grade (p = 0.0001). The mean R value of clinical rejection (Banff Grade ⅔) (16.67, 95% Confidence Interval [CI] 14.79–18.58) was lower (p = 0.005) than non-rejection (Banff Grade 0/1) (19.38, 95%CI 17.43–21.33). Both clinical and non-rejection mean R values were lower (p = 0.0001) than healthy controls (24.12, 95%CI 20.96–27.28).

Conclusion This proof-of-concept study demonstrates that software-based analysis can detect and monitor acute rejection changes in FT. Future studies should expand on this tool's potential application in telehealth and as a screening tool for allograft rejection.
Traumatic Brachial Plexus Injury in Indonesia: An Experience from a Developing Country
Authors: Suroto Heri , Antoni Irene , Siyo Angelina , Steendam Tawatha C. , Prajasari Tabita , Mulyono Herlambang Budi , De Vega Brigita
Published: September 2021

Background Brachial plexus injuries (BPI) cause severe physical disability and major psycho-socioeconomic burden. Although various countries have reported BPI incidence, the data from Indonesia as the fourth most populated country in the world remains unknown. We aim to assess the distribution of traumatic BPI, patients' characteristics, and treatment modalities in Indonesia.

Methods A retrospective investigation was performed comprising 491 BPI patients at a tertiary referral hospital in Indonesia from January 2003 to October 2019. Demographic and outcomes data were retrieved from medical records.

Results The average BPI patients' age was 27.3 ± 11.6 years old, with a male/female ratio of 4.6:1. Motorcycle accidents caused the majority (76.1%) of all BPI cases. Concomitant injuries were present in 62.3% of patients, dominated by fractures (57.1%) and brain injuries (25.4%). BPI lesion type was classified into complete (C5-T1, observed in 70% patients), upper (C5-C6, in 15% patients), extended upper (C5-C7, in 14% patients), and lower type (C8-T1, in 1% patients). The average time to surgery was 16.8 months (range 1–120 months), with the majority (76.6%) of the patients was operated on six months after the trauma. Free functional muscle transfer (FFMT) was the most common procedure performed (37%). We also analyzed the functional outcomes (active range of motion (AROM) and muscle power), DASH (Disabilities of the Arm, Shoulder, and Hand) score, and VAS (Visual Analogue Scale) across four most frequent procedures involving nerve reconstruction (FFMT, nerve transfer, external neurolysis, and nerve grafting). We found that FFMT was significantly better than nerve transfer in terms of DASH score and VAS (p = 0.000 and p = 0.016, respectively) in complete BPI (C5-T1). Moreover, we also found that nerve grafting resulted in a significantly better shoulder abduction AROM than nerve transfer and external neurolysis in extended upper BPI (C5-C7) (p = 0.033 and p = 0.033, respectively). Interestingly, no significant differences were observed in other measurements.

Conclusion This study provides an overview of traumatic BPI patients in a single tertiary trauma center in Indonesia, expressing the profile of their characteristics and functional outcomes after surgical procedures.
Intermittency of Riemann’s non-differentiable function through the fourth-order flatness
Authors: Boritchev Alexandre , Eceizabarrena Daniel , Vilaça Da Rocha Victor
Published: September 2021

Riemann’s non-differentiable function is one of the most famous examples of continuous but nowhere differentiable functions, but it has also been shown to be relevant from a physical point of view. Indeed, it satisfies the Frisch–Parisi multifractal formalism, which establishes a relationship with turbulence and implies some intermittent nature. It also plays a surprising role as a physical trajectory in the evolution of regular polygonal vortices that follow the binormal flow. With this motivation, we focus on one more classic tool to measure intermittency, namely, the fourth-order flatness, and we refine the results that can be deduced from the multifractal analysis to show that it diverges logarithmically. We approach the problem in two ways: with structure functions in the physical space and with high-pass filters in the Fourier space.
Existence of least energy positive and nodal solutions for a quasilinear Schrödinger problem with potentials vanishing at infinity
Authors: Figueiredo Giovany , Neto Sandra Moreira , Ruviaro Ricardo
Published: September 2021

In this paper, we prove the existence of at least two nontrivial solutions for a class of quasilinear problems with two non-negative and continuous potentials. Thanks to the geometries of these potentials, we are able to prove compact embeddings in some weighted Sobolev spaces, and by a minimization argument, we find a positive and a nodal (or sign-changing) (weak) solution with two nodal domains or that changes the sign exactly once in RN for such problems. The nonlinearity in this problem satisfies suitable growth and monotonicity conditions, which allow this result to complement the classical results due to Liu, Wang, and Wang [Commun. Partial Differ. Equations 29, 879–901 (2004)].
Bidirectional reflectance measurement of tungsten samples to assess reflection model in WEST tokamak
Authors: Ben Yaala M. , Aumeunier M.-H. , Steiner R. , Schönenberger M. , Martin C. , Le Bohec M. , Talatizi C. , Marot L. , Meyer E.
Published: September 2021

This paper presents the measurement of the bidirectional reflectance distribution function of tungsten (W) samples and the resulting reflection models in the nuclear fusion device WEST (tokamak). For this, an experimental gonio-spectrophotometer was developed to fully characterize the material’s optical and thermal-radiative properties of metallic samples with different roughnesses. Ray-tracing photonic simulation was then carried out to predict the photon behavior in a fully metallic environment as a function of reflectance measurement. Low emissivity (0.1 at 4 μm) and highly specular reflectance (fitting with a Gaussian distribution around the specular direction with a small width lower than 10°) are found for W samples. These measurements have been used as input for the photonic simulation, and the resulting synthetic image reproduced the reflection features well on the upper divertor, detected in WEST infrared experimental images.
On predictability of solar irradiance
Authors: Yang Xiaoyi , Yang Dazhi , Bright Jamie M. , Yagli Gokhan Mert , Wang Peng
Published: September 2021

Fair forecast comparisons are exceedingly rare in the literature of solar forecasting. Since many published works have been operating under the condition “the proposed methods outperform the benchmarks,” it is unlikely that the actual advancement in solar forecasting science is indeed successive in that the latter works supersede the former. It follows that one must hold fast to skepticism on those model superiority claims until they can be truly justified. In order to quantify the real progress, one needs to not only employ formal verification methods but also make inquiries on predictability, which, even in the field of statistics, is a controversial topic. Although predictability on its own is hard to define, let alone to quantify, one logically attractive proxy is to examine the performance of a short-range forecasting method relative to that of an optimal long-range forecasting method. This strategy is reasonable on the account that a climatological forecast in the short-range horizon marks the worst-case scenario, by which the relative improvement due to an alternative forecasting method can be gauged: situations with high predictability correspond to large relative improvements, and that with low predictability correspond to low relative improvements. If this argument can be considered admissible, the remaining task is to examine what properties ought the short-range forecasting method possess. This paper proposes, in this regard, a new measure of predictability for solar irradiance.
Influence of the facet trace region in 4H-SiC substrate on the glide and propagation behaviors of basal plane dislocations in 4H-SiC homoepitaxial layers
Authors: Izawa Takuto , Okano Hirono , Morita Shintaro , Ohtani Noboru
Published: September 2021

The influence of the facet trace region in the 4H-SiC substrate on the glide and propagation behaviors of basal plane dislocations (BPDs) in a 4H-SiC homoepitaxial layer was investigated using x-ray topography, high-resolution x-ray diffraction, and micro-Raman scattering spectroscopy. The facet trace region in the substrate, which has a higher nitrogen doping concentration than the other regions in the substrate, is of great interest since it could influence the glide and propagation behaviors of BPDs during 4H-SiC homoepitaxial growth through enhanced nitrogen doping concentration in the region. It was found that the epitaxial layer grown on the facet trace region in the substrate significantly suppressed glide motion of BPDs and exhibited a reduced conversion probability of BPDs to threading edge dislocations during the homoepitaxial growth process. Based on these results, the mechanisms that the epilayer grown on a substrate region with a slightly higher nitrogen concentration showed significantly different glide and propagation behaviors of BPDs are discussed.
A numerical study on water entry of cylindrical projectiles
Authors: Chang Yanni , Tong Albert Y.
Published: September 2021

A series of numerical experiments carried out on the water entry of circular cylinders are presented in this study. A cylinder was entering into the water with a prescribed inclined angle and velocity. The interface between water and air is tracked by the piecewise linear interface calculation schemes in conjunction with the volume of fluid method. Overset meshes, which have been widely used for problems with relative motions, are applied to handle the moving cylinder. The numerical model is built on the framework of OpenFOAM, which is an open-source C++ toolbox. The results of the numerical model, such as the transient positions and inclined angles of the moving circular cylinder, have been validated with experimental data in the literature. The fluid physics of the oblique water entry problem has been examined. The formation and development of the air entrapment have been explored. Parametric studies on the hydrodynamics of the water entry problem have been performed. It has been revealed that the head geometry, entry impact velocity, entry inclined angle, liquid density, and object density are of considerable significance for the penetration depth and inclination of the diving cylinder. Surface wetness, which affects the detachment of the air channel, has also been studied.
Nonuniform heating of a substrate in evaporative lithography
Authors: Al-Muzaiqer Mohammed A. , Kolegov Konstantin S. , Ivanova Natalia A. , Fliagin Viktor M.
Published: September 2021

This work is devoted to a method to generate particle cluster assemblies and connected to evaporative lithography. Experiments are carried out using nonuniform evaporation of an isopropanol film containing polystyrene microspheres in a cylindrical cell. The local inhomogeneity of the vapor flux density is achieved by exploiting the temperature gradient. A copper rod is mounted in the central part of the bottom of the cell for further heating. The thermocapillary flow resulting from the surface tension gradient, due in turn to the temperature drop, transfers the particles that were originally at rest at the bottom of the cell. The effect of the initial thickness of the liquid layer on the height and base area of the cluster formed in the central region of the cell is studied. The velocity is measured using particle image velocimetry. A model describing the initial stage of the process is developed. The equations of heat transfer and thermal conductivity are used to define the temperature distribution in the liquid and in the cell. The fluid flow is simulated using the lubrication approximation. The particle distribution is modeled using the convection–diffusion equation. The evaporation flux density is calculated using the Hertz–Knudsen equation. The dependence of the liquid viscosity on the particle concentration is described by Mooney's formula. Numerical results show that the liquid film gradually becomes thinner in the central region, as the surface tension decreases with the increasing temperature. The liquid flow is directed to the heater near the substrate, and it transfers the particles to the center of the cell. The volume fraction of the particles increases over time in this region. The heat flow from the heater affects the geometry of the cluster for two reasons: First, the Marangoni flow velocity depends on the temperature gradient, and second, the decrease in film thickness near the heater depends on the temperature. The results of the simulation are in general agreement with the experimental data.
Exact Beltramian solutions for hemispherically bounded cyclonic flowfields
Authors: Williams Langston L. , Majdalani Joseph
Published: September 2021

This study focuses on the development of two analytical models that describe the wall-bounded cyclonic flowfield in a hemispherical domain. The closed-form solutions that we pursue are motivated by the need to characterize the swirling bidirectional motion engendered in an upper stage thrust chamber, namely, the VR35K-A VORTEX® engine, conceived and developed by Sierra Nevada Corporation. Our analysis proceeds from the Bragg–Hawthorne formulation, which is quite effective in the treatment of steady, inviscid, and axisymmetric flows. In this work, we show that two rotational solutions may be derived for particular specifications of the stagnation head and tangential angular momentum expressions that appear in the Bragg–Hawthorne equation. Then, with the parental streamfunctions in hand, other properties of interest are deduced and these include the main velocity and pressure variations, vorticities, crossflow velocities, extensional and shearing strain rates, virtual energy dissipation rates, and both axial and polar mantle distributions; the latter consist of pairs of rotating, non-translating interfacial layers, separating the so-called inner and outer bidirectional and bipolar regions, respectively. More specifically, two Beltramian solutions are identified with mantles that appear at 50% and 61.06% of the chamber radius, respectively. By matching the outlet radius of the chamber to the mantle location in the equatorial plane, the outflow is permitted to exit the chamber seamlessly. In both models, the axial and radial velocities vary linearly with the injection speed and a characteristic inflow parameter consisting of a geometric ratio of the inlet area and the chamber radius squared.
High-reliability, high-melting, lead-free, mixed solder paste System—BiAgXⓇ
Authors: Zhang HongWen , Lee Ning-Cheng
Published: September 2021

BiAgX®, a mixed solder powder paste composed of a primary high-melting solder powder and an additive low-melting solder powder, exhibited a melting temperature above 260 °C and was comparable to, or even better than, the reliability of high-lead solders. The additive solder is designed to react preferentially with various surface metallizations and form a controllable intermetallic layer. Inside the joints, sub-micron AgSn particles are dispersed surrounding Bi colonies, which constrain the dislocation movement, thus enhancing strength, ductility, and associated joint reliability.
Computed tomography turns 50
Authors: Boone John M. , McCollough Cynthia H.
Published: September 2021

Modern high-performance CT scanners are unparalleled among three-dimensional imaging systems in data acquisition speed and spatial resolution.
Strain hardening in molecular crystal cyclotetramethylene-tetranitramine (β-HMX): a theoretical evaluation
Authors: Khan Mohammad , Picu Catalin R
Published: September 2021

The molecular crystal cyclotetramethylene-tetranitramine (β-HMX) is a broadly used energetic material. Its plastic deformation is important when describing the detonation behavior. This work aims to clarify the importance of strain hardening for the plastic deformation of this crystal. To this end, we use a line tension model to evaluate the strength of junctions formed by dislocations moving in different slip systems. We evaluate analytically the contribution to the flow stress of repulsive interactions between dislocations. Further, we test using atomistic models and confirm the conjecture that neutral core–core interactions of crossing dislocations do not contribute to the flow stress. This information is used to define the hardening matrix which can be further used in continuum crystal plasticity models. We conclude that strain hardening is weak at all realistic dislocation densities, and leads to a modest increase of the flow stress above the critical resolved shear stress corresponding to the vanishing dislocation density limit. A procedure is provided which allows extrapolating these results from ambient conditions to pressures and temperatures relevant for shock loading.
Hybridization three subbands at Dirac point in special designed strained HgTe thin films with structural inversion asymmetry
Authors: Marchewka M , Ruszała M , Krzemiński P
Published: September 2021

We study specially designed strained thin HgTe layers with structural inversion asymmetry (SIA) which allow us to distinguish the topological surface states (TSS) typical for a two dimensional (2D) quantum well system in a subband state. To obtain such a dispersion relation on the basis of the eight-band kp model, the theoretical investigation calculations of thin (below 25 nm wide) HgTe strained films with SIA are investigated. The numerical band-gap engineering and dispersion relation allow us to obtain a new class of materials that are characterized by a Dirac-like dispersion and hybridization of the three different charges describing two TSS and one quantum well subband at Γ-point (zero gap). This opens up many possibilities from the applications point of view. An external electric field removed this degeneration and opened a band gap between Γ6,

Γ

8

l
h

(lh—light hole) and

Γ

8

h
h

(hh—heavy hole) subbands characteristic for TSS and the subband characteristic for the 2D quantum well state, respectively. The width of the band gap as a function of the external electric field is also considered. Due to consideration being given to the possible applications, analysis of the dispersion relation and Landau levels (LL) energy shape with SIA is also investigated. The possibility of tuning a band gap is promising from the point of view of, for example, THz detectors and emitters. What is very important, the proposed structures allow the avoidance of the coexistence of TSS with bulk states, as very often occurs in so-called 3D strained HgTe-like materials. Analysis of the wave function as a function of the width of the investigated structure as well as the external electric field is also presented. Due to the strong correlation between both states (2D and TSS), and their very well known properties, we expect that such HgTe films can be used as optical active layers in the THz region.
Designing arbitrary single-axis rotations robust against perpendicular time-dependent noise
Authors: Li Bikun , Calderon-Vargas Fernando A. , Zeng Junkai , Barnes Edwin
Published: September 2021

Low-frequency time-dependent noise is one of the main obstacles on the road toward a fully scalable quantum computer. The majority of solid-state qubit platforms, from superconducting circuits to spins in semiconductors, are greatly affected by 1/f noise. Among the different control techniques used to counteract noise effects on the system, dynamical decoupling sequences are one of the most effective. However, most dynamical decoupling sequences require unbounded and instantaneous pulses, which are unphysical and can only implement identity operations. Among methods that do restrict to bounded control fields, there remains a need for protocols that implement arbitrary gates with lab-ready control fields. In this work, we introduce a protocol to design bounded and continuous control fields that implement arbitrary single-axis rotations while shielding the system from low-frequency time-dependent noise perpendicular to the control axis. We show the versatility of our method by presenting a set of non-negative-only control pulses that are immediately applicable to quantum systems with constrained control, such as singlet-triplet spin qubits. Finally, we demonstrate the robustness of our control pulses against classical 1/f noise and noise modeled with a random quantum bath, showing that our pulses can even outperform ideal dynamical decoupling sequences.
Realizing Majorana fermion modes in the Kitaev model*
Authors: Yang Lu , Zhang Jia-Xing , Liang Shuang , Chen Wei , Wang Qiang-Hua
Published: September 2021

We study the possibility to realize a Majorana zero mode that is robust and may be easily manipulated for braiding in quantum computing in the ground state of the Kitaev model in this work. To achieve this we first apply a uniform [111] magnetic field to the gapless Kitaev model and turn the Kitaev model to an effective p + ip topological superconductor of spinons. We then study possible vortex binding in such system to a topologically trivial spot in the ground state. We consider two cases in the system: one is a vacancy and the other is a fully polarized spin. We show that in both cases, the system binds a vortex with the defect and a robust Majorana zero mode in the ground state at a weak uniform [111] magnetic field. The distribution and asymptotic behavior of these Majorana zero modes are studied. The Majorana zero modes in both cases decay exponentially in space, and are robust against local perturbations and other Majorana zero modes far away, which makes them promising candidates for braiding in topological quantum computing.
Hydrological modelling of Air Bengkulu river watershed in Indonesia using SUH and HEC-HMS models
Authors: Gunawan G
Published: September 2021

The purpose of this research is to develop a synthetic unit hydrograph model to determine the most suitable model for predicting peak discharge in the Air Bengkulu Watershed. Rainfall data were obtained from the Bengkulu Province Meteorology, Climatology, Geophysics Agency, from 2000 to 2019 year. The Synthetic Unit Hydrograph (SUH) method used to estimate the discharge in the Air Bengkulu River Watershed is the synthetic unit hydrograph, namely Snyder, ITB-1 and ITB-2, in addition to that also used HEC-HMS software. The estimation results of peak discharge and peak time for each type of hydrograph in the Air Bengkulu watershed are: Peak Discharge of Snyder 1,302.76 m3 / s with Peak Time 6,596 hours, Peak Discharge of ITB-1 2,395.50 m3 / s with Peak Time of 4,705 hours, Peak Discharge of ITB-2 2,165.857 m3 / s with Peak Time of 6,341 hours. It can be concluded that the synthetic unit hydrograph has been able to estimate the peak discharge based on the time sequence of a rain event, so there is a relationship between peak time and peak discharge. The peak and peak times obtained from the output of each method are different, so more in-depth research is needed if this model is to be used as a basis for decision making.
Distributed robust adaptive output-feedback synchronization
Authors: Rosa M R , Susanto E
Published: September 2021

This paper addresses the output synchronization of heterogeneous uncertain linear systems in the presence of input disturbance. The synchronization problem is solved by introducing the distributed model reference adaptive control. The distinguishing features of the proposed approach are the capability to synchronize the entire network output by using only the control input and the output of neighbouring systems. It also provides synchronization in the presence of bounded control input disturbance. The control input disturbance is handled by extending the proposed method with the sigma-modification. By using the distributed matching condition assumptions, the coupling gains between the agents can be updated adaptively. The distributed robust adaptive controller is first analysed by using the distributed Lyapunov function. Its effectiveness is validated in the simulation of the cart inverted pendulum systems stabilization problem.
High altitude long endurance of unmanned aerial vehicle (UAV) ITB solar panel conceptual design
Authors: Moelyadi M A , Sulthoni M A , Zulkarnain M F , Akbar M F , Assakandari B K
Published: September 2021

One of the factors for the long endurance of high altitude long endurance (HALE) of an unmanned aerial vehicle (UAV) that belong to Institut Teknologi Bandung, Indonesia or called as HALE UAV ITB is the design of battery and solar panel. This paper discusses the method to calculate battery and solar panel requirements for HALE UAV ITB to fly for more than 24 hours at 20.000 feet. Several designs, configuration, and type of solar panels are analysed to fulfil HALE UAV ITB requirements. The variable compared is solar panel area, weight, and types. As a result, the use of Monocrystalline Silicone solar cell was found to be much more efficient than Polycrystalline Silicon, CIGS Thin Film, and Amorphous Silicon Thin Film with power generated per area of 224 Watt/m2 and power per weight of 436 Watt/kg. The minimum area required for a Monocrystalline Silicone type solar cell to generate power is 5.94 m2 with a total cell weight of 5.31 kg.
Sensitivity study and structural optimization of an aircraft wing in the maximum-stress and flutter constraints
Authors: Kusni M , Widiramdhani M , Hadi B K
Published: September 2021

Optimization process is very important to be done since the preliminary design step, not only for the static load aspect but also dynamic load as well. In the past, aeroelastic behavior aspect is often neglected in this stage and consequently becomes a problem at the later stage of design. This paper contains multi-constraints design sensitivity and optimization which include both maximum stress constraint and damping flutter constraint. Sensitivity study was performed to assist optimization process and makes the process more efficient. Wing structure was modeled as skins, ribs, spar-webs, and spar-caps. Optimization process was done by changing thickness of each component and beam dimension. The methodology used in this paper is a gradient-based optimization developed by MSC Nastran. The final cycle of this optimization has successfully reduced structural weight up to 33% without violating static and flutter constraint.
Numerical simulation on the permeability of non-crimp Carbon fiber epoxy using out-of-autoclave manufacturing method
Authors: Levino A , Hadi B K , Kuswoyo A
Published: September 2021

Composites made using Resin Transfer Molding (RTM) processes have attractive properties to the aerospace and automotive industries because they can produce complex composite parts with good surface finishing. However, it still has a problem filling a large part with high fiber content at low injection pressure. Therefore, during the experiment, resin flow has to be the primary concern. This work presents a resin flow simulation of two types of mold where it will visualize the manufacturing process without actually doing it. Numerical simulation for the RTM manufacturing process is attempted by using Fluent-Ansys. It allows us to simulate the resin flow through the porous medium and obtain the total mold filling time and volumetric flow rate. It will lead to an explanation of the strength of the composite produced. Several assumptions and techniques are used to simplify the problem. Some variables, such as porosity and pressure injection, will be varied to see the effect of those variables on the RTM manufacturing process. According to the simulation result, porosity and pressure injection affect the RTM manufacturing process, especially for resin filling time and volumetric flow rate. The increase of porosity will increase the flow time, while pressure injection will decrease the flow. It happens due to how easy the resin flows through the porous medium, and the total area needs to be filled by the resin. This work is validated by comparing the obtained results with analytic solutions for a specific mold of Darcy’s law.
Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass
Authors: Hollizeck S , Wong S Q , Solomon B , Chandrananda D , Dawson S-J
Published: September 2021

This work describes two novel workflows for variant calling that extend the widely used algorithms of Strelka2 and FreeBayes to call somatic mutations from multiple related tumour samples and one matched normal sample. We show that these workflows offer higher precision and recall than their single tumour-normal pair equivalents in both simulated and clinical sequencing data.

Availability and implementation

Source code freely available at the following link: https://atlassian.petermac.org.au/bitbucket/projects/DAW/repos/multisamplevariantcalling and executable through Janis (https://github.com/PMCC-BioinformaticsCore/janis) under the GPLv3 licence.

Supplementary information

Supplementary data are available at Bioinformatics online.
Healthcare Personnel (HCP) Attitudes About Coronavirus Disease 2019 (COVID-19) Vaccination After Emergency Use Authorization
Authors: Shaw Jana , Hanley Samantha , Stewart Telisa , Salmon Daniel A , Ortiz Christine , Trief Paula M , Asiago Reddy Elizabeth , Morley Christopher P , Thomas Stephen J , Anderson Kathryn B
Published: September 2021

Background

We previously reported on coronavirus disease 2019 (COVID-19) vaccination intent among healthcare personnel (HCP) before emergency use authorization. We found widespread hesitancy and a substantial proportion of HCP did not intend to vaccinate.

Methods

We conducted a cross-sectional survey of HCP, including clinical and nonclinical staff, researchers, and trainees between 21 February and 19 March 2021. The survey evaluated vaccine attitudes, beliefs, intent, and acceptance.

Results

Overall, 3981 (87.7%) of respondents had already received a COVID-19 vaccine or planned to get vaccinated. There were significant differences in vaccine acceptance by gender, age, race, and hospital role. Males (93.7%) were more likely than females (89.8%) to report vaccine acceptance (P < .001). Mean age was higher among those reporting vaccine acceptance (P < .001). Physicians and scientists showed the highest acceptance rate (97.3%), whereas staff in ancillary services showed the lowest acceptance rate (79.9%). Unvaccinated respondents were more likely to be females, to have refused vaccines in the past due to reasons other than illness or allergy, to care for COVID-19 patients, or to rely on themselves when making vaccination decision. Vaccine acceptance was more than twice previous intent among Black respondents, an increase from 30.8% to 73.8%, and across all hospital roles with all > 80% vaccine acceptance.

Conclusions

The majority of HCP were vaccinated, much higher than reporting intent before vaccine was available. However, many HCP—particularly ancillary services—are still hesitant. Feasible and effective interventions to address the hesitant, including individually-tailored education strategies are needed, or vaccine can be mandated.
Home Infusions for Inflammatory Bowel Disease Are Safe: US Experience and Patient Perspectives
Authors: Kochar Bharati , Jiang Yue , Chen Wenli , Bu Yuting , Barnes Edward L , Long Millie D
Published: September 2021

Background

Home infusions (HIs) for biologic medications are an option for inflammatory bowel disease (IBD) patients in the United States. We aimed to describe the population receiving HIs and report patient experience with HIs.

Methods

We conducted a retrospective cohort study in the Quintiles-IMSLegacy PharMetrics Adjudicated Claims Database from 2010 to 2016 to describe the population receiving infliximab (IFX) and vedolizumab (VDZ) HIs and determine predictors for an urgent/emergent visit post-HIs. We then administered a cross-sectional survey to IBD Partners Internet-based cohort participants to assess knowledge and experience with infusions.

Results

We identified claims for 11 892 conventional IFX patients, 1573 home IFX patients, 438 conventional VDZ patients, and 138 home VDZ patients. There were no differences in demographics or median charges with IFX home and conventional infusions. Home VDZ infusions had a greater median charge than conventional VDZ infusion. Less than 4% of patients had an urgent/emergent visit post-HIs. Charlson comorbidity index > 0 (odds ratio [OR]: 1.95; 95% confidence interval [CI], 1.01-3.77) and Medicaid (OR: 3.01; 95% CI, 1.53-5.94) conferred significantly higher odds of urgent/emergent visit post-HIs. In IBD Partners, 644 IBD patients responded; 56 received HIs. The majority chose HIs to save time and preferred HIs to conventional infusions. Only 2 patients reported an urgent/emergent visit for HI-related problems.

Conclusions

HI appears to be safe in IBD patients receiving IFX and VDZ. However, patients with fewer resources and more comorbidities are at increased risk for an urgent/emergent visit post-HIs. The overall patient experience with HI is positive. Expansion of HIs may result in decreased therapy-related logistic burden for carefully selected patients.
A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria
Authors: Takenaka Shinkuro , Kawashima Takeshi , Arita Masanori
Published: September 2021

In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.
Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni
Authors: Stitz Maria , Chaparro Cristian , Lu Zhigang , Olzog V Janett , Weinberg Christina E , Blom Jochen , Goesmann Alexander , Grunau Christoph , Grevelding Christoph G
Published: September 2021

A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.
The Privilege of a Good Death: An Intersectional Perspective on Dying a Good Death in America
Authors: Corpora Miranda
Published: September 2021

All individuals deserve an equitable opportunity to achieve a good death. Unfortunately, access to end-of-life care and services is largely unequal on the basis of race, gender, class, and other social identities. We need to understand how individuals with multiple marginalized identities face different access in attaining a good death and use this knowledge to bring equity to end-of-life care. The conceptual framework for this argument derives from intersectionality theory and the existing disparities in end-of-life care. This argument sheds light on the relationship between intersectionality and a good death, demonstrated by a case vignette, and suggests that the more marginalized social identities one has, the more difficult their access to a good death. Because it is particularly important to both recognize and actively combat these inequities, I offer 3 practical strategies for end-of-life researchers and practitioners. For the sake of our increasingly diverse population, advancements in end-of-life care must be made to facilitate a good death for all.
Essential Cases: Land Law
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. Essential Cases provides you with succinct summaries of some of the landmark and most influential cases in land law. Each summary begins with a review of the main case facts and decisions. The summary is then concluded with expert commentary on the case from the author, Aruna Nair, including her assessment of the wider questions raised by the decision.
Walsh v Lonsdale (1882) 21 Ch D 9, Court of Appeal
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Walsh v Lonsdale (1882) 21 Ch D 9, Court of Appeal. The document also includes supporting commentary from author Aruna Nair.
Bruton v London & Quadrant Housing Trust [1999] 1 AC 406, House of Lords
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Bruton v London & Quadrant Housing Trust [1999] 1 AC 406, House of Lords. The document also includes supporting commentary from author Aruna Nair.
Prudential Assurance Co. Ltd v London Residuary Body [1992] 2 AC 386, House of Lords
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Prudential Assurance Co. Ltd v London Residuary Body [1992] 2 AC 386, House of Lords. The document also includes supporting commentary from author Aruna Nair.
Cheltenham & Gloucester plc v Krausz [1997] 1 WLR 1558, Court of Appeal
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Cheltenham & Gloucester plc v Krausz [1997] 1 WLR 1558, Court of Appeal. The document also includes supporting commentary from author Aruna Nair.
Bagum v Hafiz [2015] EWCA Civ 801, Court of Appeal
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Bagum v Hafiz [2015] EWCA Civ 801, Court of Appeal. The document also includes supporting commentary from author Aruna Nair.
Moncrieff v Jamieson [2007] UKHL 42, House of Lords
Authors: Nair Aruna
Published: September 2021

Essential Cases: Land Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Moncrieff v Jamieson [2007] UKHL 42, House of Lords. The document also includes supporting commentary from author Aruna Nair.
Essential Cases: Tort Law
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. Essential Cases provides you with succinct summaries of some of the landmark and most influential cases in tort law. Each summary begins with a review of the main case facts and decision. The summary is then concluded with expert commentary on the case from the author, Craig Purshouse, including his assessment of the wider questions raised by the decision.
Caparo Industries plc v Dickman [1990] 2 AC 605
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Caparo Industries plc v Dickman [1990] 2 AC 605. The document also included supporting commentary from author Craig Purshouse.
Michael v Chief Constable of South Wales Police [2015] UKSC 2
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Michael v Chief Constable of South Wales Police [2015] UKSC 2. The document also included supporting commentary from author Craig Purshouse.
Hedley Byrne & Co. Ltd v Heller & Partners Ltd [1964] AC 465
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Hedley Byrne & Co. Ltd v Heller & Partners Ltd [1964] AC 465. The document also included supporting commentary from author Craig Purshouse.
Smith v Eric S Bush [1990] 1 AC 831
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Smith v Eric S Bush [1990] 1 AC 831. The document also included supporting commentary from author Craig Purshouse.
Bolton v Stone [1951] AC 850
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Bolton v Stone [1951] AC 850. The document also included supporting commentary from author Craig Purshouse.
Dunnage v Randall [2016] QB 639
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Dunnage v Randall [2016] QB 639. The document also included supporting commentary from author Craig Purshouse.
McGhee v National Coal Board [1973] 1 WLR 1
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in McGhee v National Coal Board [1973] 1 WLR 1. The document also included supporting commentary from author Craig Purshouse.
Henderson v Dorset Healthcare University NHS Foundation [2020] UKSC 43
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Henderson v Dorset Healthcare University NHS Foundation Trust [2020] UKSC 43. The document also included supporting commentary from author Craig Purshouse.
Murray v Ministry of Defence [1988] 1 WLR 692
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Murray v Ministry of Defence [1988] 1 WLR 692. The document also included supporting commentary from author Craig Purshouse.
Rylands v Fletcher (1868) LR 3 HL 330
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Rylands v Fletcher (1868) LR 3 HL 330. The document also included supporting commentary from author Craig Purshouse.
Transco plc v Stockport Metropolitan Borough Council [2004] 2 AC 1
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Transco plc v Stockport Metropolitan Borough Council [2004] 2 AC 1. The document also included supporting commentary from author Craig Purshouse.
Lachaux v Independent Print Ltd and others [2019] 3 WLR 18
Authors: Purshouse Craig
Published: September 2021

Essential Cases: Tort Law provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in Lachaux v Independent Print Ltd and others [2019] 3 WLR 18. The document also included supporting commentary from author Craig Purshouse.
Essential Cases: Equity & Trusts
Authors: Whayman Derek
Published: September 2021

Essential Cases: Equity & Trusts provides a bridge between course textbooks and key case judgments. Essential Cases provides you with succinct summaries of some of the landmark and most influential cases in equity and trusts. Each summary begins with a review of the main case facts and decision. The summary is then concluded with expert commentary on the case from the author, Derek Whayman, including his assessment of the wider questions raised by the decision.
McPhail v Doulton, Re Baden’s Deed Trusts (No 1) [1971] AC 424, House of Lords
Authors: Whayman Derek
Published: September 2021

Essential Cases: Equity & Trusts provides a bridge between course textbooks and key case judgments. This case document summarizes the facts and decision in McPhail v Doulton, Re Baden’s Deed Trusts (No 1) [1971] AC 424, House of Lords. The document also includes supporting commentary from author Derek Whayman.