bluuebunny/crossref_metadata_2025 huggingface dataset:
Superior performance enabled by supramolecular interactions in metal−organic cathode: the power of weak bonds
Authors: Li An-Che , Chang Cheng-Han , Ivanov Alexander S. , Lo Yi-An , Popovs Ilja , Chen Jeng-Lung , Chuang Yu-Chun , Chang Yu-Chung , Chen Bo-Hao , Lee Jui-Chin , Chen Teng-Hao , Kaveevivitchai Watchareeya
Published: April 2022

Supramolecular interactions have been found to be essential for exceptional electrochemical performance of a close-packed metal–organic-based cathode, considered one of the best ever reported.
Mineralization of calcium phosphate on two-dimensional polymer films with controllable density of carboxyl groups
Authors: Zhang Xinyu , Wu Lingli , Feng Guangyuan , Lei Shengbin
Published: April 2022

Two-dimensional polymers provide a valuable platform to study the effect of functional group density on the mineralization of calcium phosphate.
Cloud‐edge collaboration based peer to peer services redirection strategy for passive optical network
Authors: Tang Yongli , You Junru , Qin Panke , Fu Yanyan , Wang Wenke
Published: April 2022

With the increasing number of fibre access users, P2P file sharing download traffic has gradually become one of the enormous bandwidth consumptions for the access network. Localizing traffic could save bandwidth and reduce latency, but it caused optical line terminal (OLT) overload problems. A cloud‐edge collaboration technology (IRS‐CECT) based P2P redirection strategy is proposed for this problem. OLT assumes the role of the cloud computing centre in the strategy. Optical network unit (ONU) serves as an edge computing node to share traffic load for the cloud computing centre. ONU intercepts the upstream query packets for OLT. This strategy can reduce the problem of OLT overload caused by increasing users. Simulation results indicate that the IRS‐CECT strategy can reduce the delay by nearly half and reduce the traffic load on the cloud computing centre OLT.
A generalized piecewise linear time‐variable droop frequency controller with adaptive parameters for de‐loaded wind turbine generators
Authors: Xu You‐Ning , Huang Yu‐Chen , Chen Yi‐Wei , Chuang Cheng‐Han , Hsu Yuan‐Yih
Published: April 2022

This paper proposes a generalized piecewise linear time‐variable droop frequency controller with a ramp‐up period for a de‐loaded wind turbine generator. The authors present an analytical model using a simplified system frequency response (SFR) to explain the need for a ramp‐up period under the conditions of variable wind speed. In order to achieve the highest frequency nadir under different operating conditions, the durations and peak value of the time‐variable droop function must be adapted in real time. This adaptation is achieved using an artificial neural network (ANN) based on current system variables such as wind speed, penetration, pitch angle, wind speed change, and outage capacity. Dynamic frequency responses for a power system subject to generator outages and wind speed changes are simulated using MATLAB/Simulink to demonstrate the effectiveness of the proposed droop controller. These results show that the frequency nadir can be improved by the proposed algorithm through adaption of the durations and peak value.
Distributed radar fusion and recurrent networks for classification of continuous human activities
Authors: Guendel Ronny G. , Fioranelli Francesco , Yarovoy Alexander
Published: April 2022

Continuous Human Activity Recognition (HAR) in arbitrary directions is investigated in this paper using a network of five spatially distributed pulsed Ultra‐Wideband radars. While activities performed continuously and in unconstrained trajectories provide a more realistic and natural scenario for HAR, the network of radar sensors is proposed to address the issue of unfavourable or occluded perspectives when using only a single sensor. Different techniques to combine the relevant information from the multiple radars in the network are investigated, focussing on signal level fusion directly applied on Range‐Time maps, and the selection of radar nodes based on location and velocity of the target derived from multilateration processing and tracking. Recurrent Neural Networks with and without bidirectionality are used to classify the activities based on the micro‐Doppler (μD) spectrograms obtained for sensor fusion techniques. To assess classification performances, novel evaluation metrics accounting for the continuous nature of the sequence of activities and inherent imbalances in the dataset are proposed and compared with existing metrics. It is shown that the conventional accuracy metric may not capture all the important aspects for continuous HAR, and the proposed metrics can be considered for a more comprehensive evaluation.
Energy-adaptive Riemannian optimization on the Stiefel manifold
Authors: Altmann Robert , Peterseim Daniel , Stykel Tatjana
Published: April 2022

This paper addresses the numerical solution of nonlinear eigenvector problems such as the Gross–Pitaevskii and Kohn–Sham equation arising in computational physics and chemistry. These problems characterize critical points of energy minimization problems on the infinite-dimensional Stiefel manifold. To efficiently compute minimizers, we propose a novel Riemannian gradient descent method induced by an energy-adaptive metric. Quantified convergence of the methods is established under suitable assumptions on the underlying problem. A non-monotone line search and the inexact evaluation of Riemannian gradients substantially improve the overall efficiency of the method. Numerical experiments illustrate the performance of the method and demonstrates its competitiveness with well-established schemes.
A multiple timescale network model of intracellular calcium concentrations in coupled neurons: Insights from ROM simulations
Authors: Bandera A. , Fernández-García S. , Gómez-Mármol M. , Vidal A.
Published: April 2022

In Fernández-García and Vidal [Physica D 401 (2020) 132129], the authors have analyzed the synchronization features between two identical 3D slow-fast oscillators, symmetrically coupled, and built as an extension of the FitzHugh—Nagumo dynamics generating Mixed-Mode Oscillations. The third variable in each oscillator aims at representing the time-varying intracellular calcium concentration in neurons. The global model is therefore six-dimensional with two fast variables and four slow variables with strong symmetry properties. In the present article, we consider an extension of this model in two different directions. First, we consider heterogeneity among cells and analyze the coupling of two oscillators with different values for one parameter which tunes the intrinsic frequency of the output. We therefore identify new patterns of antiphasic synchronization, with non trivial signatures and that exhibit a Devil’s Staircase phenomenon in signature transitions when varying the coupling gain parameter value. Second, we introduce a network of N cells divided into two clusters: the coupling between neurons in each cluster is excitatory, while the coupling between the two clusters is inhibitory. Such system aims at modelling the interactions between neurons tending to synchronization in each of two subpopulations that inhibit each other, like ipsi- and contra-lateral motoneurons assemblies. To perform the numerical simulations in this case when N is large, as an initial step towards the network analysis, we consider Reduced Order Models in order to save computational costs. We present the numerical reduction results in a network of 100 cells. For the sake of validation of the numerical reduction method, we both compare the outputs and CPU times obtained with the original and the reduced models in different cases of network coupling structures.
Patientenverfügungen und palliative ärztliche
Versorgung in Pflegeheimen – Studie zu Alltag und Relevanz
außerhalb regulärer Praxiszeiten
Authors: Witthauer Beate , Kolominsky-Rabas Peter
Published: April 2022

Hintergrund In Pflegeheimen nimmt der Anteil der Bewohner*innen
zu, die eine Patientenverfügung verfasst haben. Es gibt keine
Untersuchungen, inwieweit diese Patientenverfügungen im Rahmen des
ärztlichen Bereitschaftsdienstes oder des Notarztdienstes
Berücksichtigung finden. Auch fehlen Aussagen zu Unterschieden
hinsichtlich der Einstellungen der Dienstärzt*innen
verschiedener Fachrichtungen zu therapeutischen Optionen in palliativen
Situationen.

Methoden Im Rahmen von Untersuchungen der ärztlichen Versorgung
von Pflegeheimpatient*innen außerhalb regulärer
Praxiszeiten wurde das Vorhandensein von Patientenverfügungen und deren
Berücksichtigung durch die Dienstärzt*innen (DÄ)
oder Notärzt*innen (NÄ) erfragt (n=101).
Zusätzlich wurden Einstellungen und Meinungen der DÄ
(n=60) und einer Kontrollgruppe von Palliativärzt*innen
(PÄ) (n=19) hinsichtlich palliativmedizinischer Erfahrung, der
Erfragung von Vorausverfügungen und der Vorgehensweise bei einem
fiktiven palliativen Fall erfasst.

Ergebnisse Von 82 Bewohner*innen hatten 71% eine
schriftliche Vorausverfügung. Bei 101 Arztkontakten im Pflegeheim wurde
in 54% der Fälle von DÄ oder NÄ nach
Vorausverfügungen gefragt. In 92% wurde die erfragte
Verfügung befolgt. Signifikante Unterschiede zwischen DÄ und
NÄ ergaben sich nicht. Bei einem fiktiven palliativen Fall
würden 92% der DÄ und 95% der PÄ nach
einer Vorausverfügung fragen. Allgemeinärzt*innen,
Internist*innen und PÄ setzen häufiger schnellwirkende
Opioide und Anxiolytika in palliativen Fällen ein, rufen seltener den NA
und weisen seltener stationär ein. Damit unterscheiden sie sich von
anderen Fachrichtungen.

Schlussfolgerungen DÄ oder NÄ erfragen
Vorausverfügungen in den Pflegeheimen nur in 54% aller
Arzt-Patienten-Kontakte. Zum einen erscheint eine weitere Sensibilisierung der
Ärzteschaft bezüglich der Nachfrage nach
Patientenverfügungen bei unbekannten Patient*innen sinnvoll. Zum
anderen sollte der Patientenwille in Kurzform als Aktenvermerk in der
Pflegedokumentation schnell ersichtlich sein. Vorausschauende
Therapieabsprachen, das frühzeitige Hinzuziehen palliativ erfahrener
Ärzt*innen (AAPV, SAPV), aber auch eine verstärkte
palliativmedizinische Fortbildung aller Ärzt*innen
könnten die Betreuung der Pflegeheimbewohner*innen
verbessern.
Four-Year Efficacy and Safety of iTrack Ab-interno Canaloplasty as a Standalone Procedure and Combined with Cataract Surgery in Open-Angle Glaucoma
Authors: Koerber Norbert , Ondrejka Simon
Published: April 2022

Purpose To evaluate the long-term effectiveness of ab-interno canaloplasty (ABiC), performed with the iTrack microcatheter (Nova Eye Medical, Fremont, CA, USA), in reducing
intraocular pressure (IOP) as well as the number of required glaucoma medications in patients with open-angle glaucoma (OAG).

Methods In this retrospective single-center consecutive case series, 27 eyes of 21 patients (mean age 77.3 ± 5.8 years) were treated with ABiC performed as a standalone procedure or
combined with cataract surgery. Patients with uncontrolled IOP OAG or controlled IOP (≤ 18 mmHg) OAG with intolerance to medications or lack of compliance were included. Patients were
followed for up to 4 years following the procedure. The iTrack microcatheter was used to perform a 360-degree circumferential intubation and viscodilation of Schlemmʼs canal. Primary
efficacy endpoints included IOP and the number of glaucoma medications at 12, 24, 36, and 48 months after surgery.

Results In all eyes, mean IOP and number of glaucoma medications were significantly reduced from 19.8 ± 5.2 mmHg and 1.9 ± 1.00 at baseline to 14.6 ± 3 mmHg and 0.9 ± 0.8,
respectively, at the 48-month follow-up (p < 0.001). IOP was stable from 12 months to 48 months (p > 0.005). After 48 months, 39% of the eyes required zero medications compared to 3.7%
at baseline, and 72.2% of eyes required only one medication or less. Of all eyes, 77.8% recorded an IOP ≤ 17 mmHg. No serious complications were recorded.

Conclusion iTrack ABiC performed as a standalone procedure or in combination with cataract surgery significantly reduced IOP and number of medications in patients with OAG up to 4
years after the procedure.
Severe Retinopathy of Prematurity in Big Babies
Authors: Bekmez Sinan , Eris Dilem
Published: April 2022

Background Evaluation of babies with gestational age (GA) over 32 weeks and with a birth weight (BW) over 1500 g, who underwent treatment for retinopathy of prematurity (ROP).

Materials and Methods The data of babies with ROP between June 2015 – 2020 were analyzed retrospectively and cross-sectionally. All infants treated for ROP were evaluated. Big babies
who were older than 32 weeks GA with a BW higher than 1500 g were determined. Other treated premature infants formed the control group.

Results We retrospectively scanned 6581 patients who underwent ROP examination. Of these babies, 109 were treated for ROP. Thirteen babies (12%) who were treated for ROP were born
over 32 weeks of GA and above the weight of 1500 g. One big infant was excluded because of missing file data. Eleven of these infants had type 1 ROP and 1 had aggressive posterior ROP. The
mean GA and BW of big babies was 33.58 ± 0.88 weeks and 1860.83 ± 257.73 g, respectively. The mean GA and BW of the control group was 27.85 ± 2.02 weeks and 1068.28 ± 313.78 g, respectively.
Both the big babies and the control group received oxygen treatment for 15.25 ± 11.44 and 19.17 ± 12.11 days (p = 0.29), respectively. Sepsis was seen in one big infant but 18 infants were
observed to have sepsis in the control group. Similarly, one big infant had necrotizing enterocolitis (NEC), while in the control group, 12 infants had NEC.

Conclusions Total oxygen intake days, NEC, and sepsis rates were found to be relatively lower in big babies with severe ROP. This could suggest that other factors may have a greater
effect on the development of severe ROP in big babies.
Änderungen bei der Verordnung oraler Antikoagulation in
Hausarztpraxen nach Einführung der direkten oralen
Antikoagulanzien
Authors: Bleckwenn Markus , Schumacher Nadine , Puth Marie-Therese , Just Johannes Maximilian , Weckbecker Klaus
Published: April 2022

Ziel der Studie Seit 2011 erweitern die nicht-Vitamin-K-abhängigen
oralen Antikoa-gulanzien (NOAK) das Spektrum der Antikoagulation.
Zunächst war die Zulassung der NOAK auf die Prophylaxe von
postoperativen Thrombosen beschränkt, im Verlauf wurde das Spektrum auf
die Therapie von Thrombosen und Embolien sowie zur Antikoagulation bei
nicht-valvulärem Vorhofflimmern erweitert. In dieser Studie sollte
untersucht werden, wie sich die Zulassung der NOAK auf das Verordnungsverhalten
der Hausärzte in den ersten Jahren der Zulassung ausgewirkt hat.

Methodik In einer retrospektiven Längsschnittuntersuchung wurden
die Verordnungen von Antikoagulanzien zwischen 2012 und 2017 in 3 Hausarztpraxen
im Raum Bonn analysiert. Dabei wurden alle Patienten in die Studie
eingeschlossen, bei denen mindestens eine Verordnung eines NOAK oder eines
Vitamin-K-Antagonisten (VKA) in diesem Untersuchungszeitraum im
Verwaltungssystem der Praxen dokumentiert war.

Ergebnisse Insgesamt wurden Akten von n=579 Patienten ausgewertet
(47% weib-lich; Alter im Mittel 75 Jahre). Davon nahmen 47% ein
VKA und 40% ein NOAK (59% Rivaroxaban, 29% Apixaban,
9% Dabigatran und 3% Edoxaban) ein. Im Unter-suchungszeitraum
nahm der Anteil von VKA-Verordnungen von 45% auf 14% ab und der
Anteil der NOAK von 28% auf 87% zu. Bei 12% der
Patienten kam es zu einem Wechsel der Antikoagulation. Dabei war der Wechsel von
einem VKA auf ein NOAK (70%) am häufigsten.

Schlussfolgerung Nach der Marktzulassung nahm der Anteil an NOAK bei den
Erstverordnungen kontinuierlich zu. Dieser Trend ist auch in anderen
europäischen Studien erkennbar. Die VKA werden vor allem Patienten mit
einer stabilen oralen Antikoagulation verordnet. Ein Wechsel der Antikoagulation
wird, wie in den Leitlinien empfohlen, vor allem bei Problemen unter der
Therapie durchgeführt. Sollte der Trend bei der Verordnung von
Antikoagulantien anhalten, werden mittelfristig VKA nur bei langjährig
stabil eingestellten Patienten und bei Patienten mit künstlichen
Herzklappen verordnet werden.
A Pediatric COVID-19 Study: Retinal Nerve Fiber Layer, Ganglion Cell Layer, and Alterations in Choroidal Thickness in Swept-Source OCT Measurements
Authors: Akpolat Cetin , Cetinkaya Tugba , Kurt Muhammed M.
Published: April 2022

Purpose To investigate early covid measurements of central macular thickness (CMT), retinal nerve fiber layer (RNFL), ganglion cell layer (GCL) thickness, and choroidal thickness
(ChT) in children recovered from coronavirus disease 2019 (COVID-19).

Methods This cross-sectional study was carried out 4 weeks after completed COVID-19 treatment. The diagnosis of the Alpha variant COVID-19 was made by the polymerase chain reaction
test after prediagnosis with clinical, laboratory, and radiological findings. A total of 46 children were included in the study. Pediatric patients who received COVID-19 treatment comprised
the COVID-19 group (24 children), and healthy children were enrolled in the control group (22 children). Only the right eyes of the participants were enrolled in the study. All pediatric
patients in the COVID-19 group required hospitalization without the need for intubation. Swept-source optical coherence tomography (SS-OCT) was used to measure CMT, RNFL, and GCL thickness,
and ChT measurements.

Results The COVID-19 and control groups had similar mean values of visual acuity, intraocular pressure, spherical equivalent, axial length, and CMT (p > 0.05 for all). RNFL
thickening, GCL, and choroidal thinning were observed in all SS-OCT measurements of COVID-19 children. However, RNFL thickening was significant only in the global and nasal peripapillary
quadrants. GCL thinning was significant in the nasal/inferior sector (p < 0.002 for all). Some significant correlations were observed between the mean levels of inflammatory markers and
OCT measurements (p < 0.002).

Conclusion This study may be among the first reports of SS-OCT examination of COVID-19 children. OCT measurements showed changes in retinal and ChT in the COVID-19 children as in
adult patients.
Macrophage Depletion Attenuates Acute Renal Damage after Exhaustive
Exercise in Mice
Authors: Mizokami Tsubasa , Shimada Michiko , Suzuki Katsuhiko
Published: April 2022

Exhaustive exercise is known to induce acute renal damage. However, the precise
mechanisms remain unclear. We investigated the effects of macrophage depletion
on exhaustive exercise-induced acute renal damage. Male
C57BL/6 J mice were divided into four groups: sedentary with
control liposome (n=8), sedentary with clodronate liposome
(n=8), exhaustive exercise with control liposome (n=8), and
exhaustive exercise with clodronate liposome (n=8). Mice were treated
with clodronate liposomes or control liposomes intraperitoneally for
48 h before undergoing exhaustive exercise. Renal function and renal
histology were tested at 24 h. The expression levels of kidney injury
molecule (KIM)-1 and inflammatory cytokines in kidney tissues were measured by
quantitative RT-PCR, and KIM-1 concentration was semi-quantified by
immunostaining. As a result, exhaustive exercise increased macrophage
infiltration into the kidney. However, clodronate reduced it. Although
exhaustive exercise resulted in an increase in KIM-1 mRNA expression levels and
concentration, injection of clodronate liposome reduced it. In addition, TUNEL
positive apoptotic cells were increased after exercise, but significantly
reduced by clodronate. Clodronate liposome treatment also decreased the mRNA
expression levels of inflammatory cytokines (TNF-α, IL-1β, and
IL-6) in the kidney after exhaustive exercise. These results suggest that
macrophages play a critical role in increasing renal damage by regulating
inflammation.
Effect of Two Different Temperature Settings on Patient Comfort Level during Respiratory Therapy by High-Flow Nasal Cannula
Authors: Kumari Mamta , Taneja Rashmi , Grover Niharika , Soni Megha
Published: April 2022

Background Hypoxemic respiratory failure may require high flow O2 therapy (>15 L/m), which can be delivered using a high-flow nasal cannula (HFNC) device. There are three variables: FiO2, flow, and temperature that can be controlled while using HFNC. This study was planned to assess the degree of comfort level of patients at two different temperature settings.

Methods A prospective interventional cross-over study was performed on 40 hypoxemic respiratory failure patients, who were on HFNC. Primary outcome was to assess patient comfort during HFNC therapy at two different temperatures (31 and 37°C), at the flow of 60 L/m for 30 minutes at each temperature setting, leaving FiO2 unchanged. After 30 minutes of each temperature setting, the comfort level was assessed using 11 score visual numerical scale (ranging from 0 to 10) together with other vital parameters.

Result Patients were found to be more comfortable at temperature settings of 31°C than at 37°C (p-value < 0.05%). Also, an increase in blood pressure was observed at 37°C after completion of 30 minutes, which was statistically significant but not clinically significant.

Conclusion Starting HFNC therapy at lower temperature gives better patient acceptance and reduces chances of failure due to discomfort.
Fully reversible magnetoelectric voltage controlled THz polarization rotation in magnetostrictive spintronic emitters on PMN-PT
Authors: Lezier G. , Koleják P. , Lampin J.-F. , Postava K. , Vanwolleghem M. , Tiercelin N.
Published: April 2022

THz polarization control upon generation is a crucially missing functionality. THz spintronic emitters based on the inverse spin Hall effect (ISHE) allow for this by the strict implicit orthogonality between their magnetization state and the emitted polarization. This control was until now only demonstrated using cumbersome external magnetic field biasing to impose a polarization direction. We present here an efficient voltage control of the polarization state of terahertz spintronic emitters. Using a ferromagnetic spin pumping multilayer exhibiting simultaneously strong uniaxial magnetic anisotropy and magnetostriction in a crossed configuration, an emitter is achieved where, in principle, the stable magnetization direction can be fully and reversibly controlled over a 90° angle span only by an electric voltage. To achieve this, an engineered rare-earth based ferromagnetic multilayer is deposited on a piezoelectric (1−x)[Pb(Mg0.33Nb0.66)O3]−x[PbTiO3] (PMN-PT) substrate. We demonstrate experimentally a reversible 70° THz polarization rotation by sweeping the substrate voltage over 400 V. This demonstration allows for a fully THz polarization controlled ISHE spintronic terahertz emitter not needing any control of the magnetic bias.
Computation of flexoelectric coefficients of a MoS2 monolayer with a model of self-consistently distributed effective charges and dipoles
Authors: Yang Yida , Hirsinger Laurent , Devel Michel
Published: April 2022

Flexoelectricity is an electromechanical coupling phenomenon that can generate noticeable electric polarization in dielectric materials for nanoscale strain gradients. It is gaining increasing attention because of its potential applications and the fact that experimental results were initially an order of magnitude higher than initial theoretical predictions. This stimulated intense experimental and theoretical research to investigate flexoelectric coefficients in dielectric materials such as two-dimensional materials. In this study, we concentrate on the calculation of the flexoelectric coefficients of 2D-MoS2 due to a model using self-consistently determined charges and dipoles on the atoms. More specifically, we study the importance of two contributions that were neglected/omitted in previous papers using this model, namely, the charge term in the total polarization and the conservation of electric charge through a Lagrange multiplier. Our calculations demonstrate that the results for flexoelectric coefficients computed with this improved definition of polarization agree better with experimental measurements, provided that consistent definitions for signs are used. Additionally, we show how two physical contributions with opposite signs compete to give net values of flexoelectric coefficients that can be either positive or negative depending on their relative importance and give net values for the case of MoS2.
Describing the photo-isomerization of a retinal chromophore model with coupled and quantum trajectories
Authors: Talotta Francesco , Lauvergnat David , Agostini Federica
Published: April 2022

The exact factorization of the electron–nuclear wavefunction is applied to the study of photo-isomerization of a retinal chromophore model. We describe such an ultrafast nonadiabatic process by analyzing the time-dependent potentials of the theory and by mimicking nuclear dynamics with quantum and coupled trajectories. The time-dependent vector and scalar potentials are the signature of the exact factorization, as they guide nuclear dynamics by encoding the complete electronic dynamics and including excited-state effects. Analysis of the potentials is, thus, essential—when possible—to predict the time-dependent behavior of the system of interest. In this work, we employ the exact time-dependent potentials, available for the numerically exactly solvable model used here, to propagate quantum nuclear trajectories representing the isomerization reaction of the retinal chromophore. The quantum trajectories are the best possible trajectory-based description of the reaction when using the exact-factorization formalism and, thus, allow us to assess the performance of the coupled-trajectory, fully approximate schemes derived from the exact-factorization equations.
Effects of local order parameter dependent transport coefficient in diblock copolymers under applied electric fields
Authors: Zhang Shuaifang , Kumar Rajeev
Published: April 2022

We present an approach for constructing thermodynamically consistent time-dependent models relevant to thin films of diblock copolymers in applied electric fields. The approach is based on the principles of linear irreversible thermodynamics, and, in this work, it is applied to study the effects of electric fields on thin films of incompressible diblock copolymers. Enforcement of local incompressibility constraint at all times leads to a local order parameter dependent transport coefficient in the model for the diblock copolymers. The dependence of the transport coefficient on the local order parameter is used to relate it with the diffusion constant of Rouse chains and leads to sensitivity of the model to initial conditions. In addition, transient behavior is found to be affected when compared with an ad hoc model assuming a constant transport coefficient. Numerical results such as electric field induced alignment of lamellae domains due to the field are found to be in qualitative agreement with experiments. This approach opens up a systematic way of developing kinetic models for simulating effects of electrolytes added to thin films containing diblock copolymers in the presence of applied electric fields.
Cooperative molecular structure in polaritonic and dark states
Authors: Cederbaum Lorenz S.
Published: April 2022

An ensemble of identical, intrinsically non-interacting molecules exposed to quantum light is discussed. Their interaction with the quantum light induces interactions between the molecules. The resulting hybrid light–matter states exhibit a complex structure even if only a single vibrational coordinate per molecule is considered. Since all molecules are identical, it is appealing to start from the uniform situation where all molecules possess the same value of this vibrational coordinate. Then, polaritons and dark states follow like in atoms but are functions of this coordinate, and this vibrational degree of freedom makes the physics different from that of atoms. However, despite all molecules being identical, each molecule does have its own vibrational coordinate. It is thus a vital issue to understand the meaning of the uniform situation and how to depart from it and enable one to realistically investigate the ensemble. A rigorous and physically relevant meaning of the polariton energy curves in the uniform situation has been found. It is proven that any point on a polariton energy curve is a (local) minimum or maximum for departing from the uniform situation. It is shown how to explicitly compute the energetic impact of departing from the uniform situation using solely properties of a single free molecule in the absence of the quantum light. The structure of the dark states and their behavior upon departing from the uniform situation are analyzed as well. Useful techniques not used in this topical domain are introduced, and general results on, for example, minimum energy path and symmetry breaking and restoration are obtained. It is shown how to transfer the findings to include several or even many nuclear degrees of freedom per molecule and thus to address the problem of quantum light interacting with many complex molecules. It is demonstrated that the interplay of several vibrational degrees of freedom in a single molecule of the ensemble is expected to lead to additional and, in part, qualitatively different physics. General consequences are discussed.
Preprint Highlight: Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration
Authors: De Lora Jacqueline
Published: April 2022

The individual contributions of E- and N-cadherin junctions in collective cell migration, especially in the context of cells transitioning between epithelial and mesenchymal states during cancer progression, are controversial. This study aims to clarify the respective roles of these two cell adherens junction proteins using a combination of imaging of collectively migrating cells and a computational model of spreading behavior. The data, obtained by confinement and release of cells micropatterned on a surface, are used to develop a new model that reveals the mechanical contributions of E- and N-cadherin on cell migration. The study demonstrates and validates that disrupting E- and N-cadherin cellular contacts leads to a reduction in spreading efficiency of the cell collective, a result of interest to the field of metastatic cancer research.
Preprint Highlight: FLAgellum Member 8 modulates extravascular trypanosome distribution in the mammalian host
Authors: Dean Samuel
Published: April 2022

Trypanosomes are extracellular protozoan parasites that cause human and animal disease. Trypanosomes predominantly inhabit the blood, skin, and adipose tissue and are transmitted by the biting tsetse fly. Little is known of how tissue tropism is regulated or its importance for transmission and pathogenicity. This study investigates FLAM8, a trypanosome flagellar membrane protein of unknown function. The authors show that FLAM8 knockout mutants have normal parasitemia and can differentiate to the transmissible lifecycle stages. However, FLAM8 is required for the parasite to disseminate to the extravascular compartment of the skin, potentially a key point for transmission to new hosts. FLAM8 may therefore be an important player in parasite transmission. This study is of interest to parasitologists studying host–parasite interaction and to cell biologists studying cellular sensing.
Preprint Highlight: Growth temperature is the principal driver of chromatinization in archaea
Authors: Dey Gautam
Published: April 2022

Almost all organisms express proteins that coat and organize DNA (nucleoid-associated proteins or NAPs). NAPs (such as histones in eukaryotes) play many roles, from scaffolding and protecting the DNA to regulating transcription, replication and epigenetic signaling, making it difficult to reconstruct their evolutionary histories and original functions. Here comparative genomics with protein abundance measurements across a range of archaea reveal a wide spectrum of NAP levels strongly correlated with growth temperature. Surprisingly, a family within the large taxonomic grouping of the Diaforarchaea appear to encode no NAPs at all. This work suggests that DNA-binding activities evolved primarily as a way to cope with heat stress, with implications for the evolution of chromatin in other archaea and a thermophilic origin for the first eukaryotes.
Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations
Authors: Zhang Ruibo , Ghosh Souparno , Pal Ranadip
Published: April 2022

Predicting protein properties from amino acid sequences is an important problem in biology and pharmacology. Protein–protein interactions among SARS-CoV-2 spike protein, human receptors and antibodies are key determinants of the potency of this virus and its ability to evade the human immune response. As a rapidly evolving virus, SARS-CoV-2 has already developed into many variants with considerable variation in virulence among these variants. Utilizing the proteomic data of SARS-CoV-2 to predict its viral characteristics will, therefore, greatly aid in disease control and prevention. In this paper, we review and compare recent successful prediction methods based on long short-term memory (LSTM), transformer, convolutional neural network (CNN) and a similarity-based topological regression (TR) model and offer recommendations about appropriate predictive methodology depending on the similarity between training and test datasets. We compare the effectiveness of these models in predicting the binding affinity and expression of SARS-CoV-2 spike protein sequences. We also explore how effective these predictive methods are when trained on laboratory-created data and are tasked with predicting the binding affinity of the in-the-wild SARS-CoV-2 spike protein sequences obtained from the GISAID datasets. We observe that TR is a better method when the sample size is small and test protein sequences are sufficiently similar to the training sequence. However, when the training sample size is sufficiently large and prediction requires extrapolation, LSTM embedding and CNN-based predictive model show superior performance.
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis
Authors: Gaynor Sheila M , Westerman Kenneth E , Ackovic Lea L , Li Xihao , Li Zilin , Manning Alisa K , Philippakis Anthony , Lin Xihong
Published: April 2022

We developed the variant-Set Test for Association using Annotation infoRmation (STAAR) workflow description language (WDL) workflow to facilitate the analysis of rare variants in whole genome sequencing association studies. The open-access STAAR workflow written in the WDL allows a user to perform rare variant testing for both gene-centric and genetic region approaches, enabling genome-wide, candidate and conditional analyses. It incorporates functional annotations into the workflow as introduced in the STAAR method in order to boost the rare variant analysis power. This tool was specifically developed and optimized to be implemented on cloud-based platforms such as BioData Catalyst Powered by Terra. It provides easy-to-use functionality for rare variant analysis that can be incorporated into an exhaustive whole genome sequencing analysis pipeline.

Availability and implementation

The workflow is freely available from https://dockstore.org/workflows/github.com/sheilagaynor/STAAR_workflow.

Supplementary information

Supplementary data are available at Bioinformatics online.
Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories
Authors: Waldrop Alexander M , Cheadle John B , Bradford Kira , Preiss Alexander , Chew Robert , Holt Jonathan R , Kebede Yaphet , Braswell Nathan , Watson Matt , Hench Virginia , Crerar Andrew , Ball Chris M , Schreep Carl , Linebaugh P J , Hiles Hannah , Boyles Rebecca , Bizon Chris , Krishnamurthy Ashok , Cox Steve
Published: April 2022

Motivation

As the number of public data resources continues to proliferate, identifying relevant datasets across heterogenous repositories is becoming critical to answering scientific questions. To help researchers navigate this data landscape, we developed Dug: a semantic search tool for biomedical datasets utilizing evidence-based relationships from curated knowledge graphs to find relevant datasets and explain why those results are returned.

Results

Developed through the National Heart, Lung and Blood Institute’s (NHLBI) BioData Catalyst ecosystem, Dug has indexed more than 15 911 study variables from public datasets. On a manually curated search dataset, Dug’s total recall (total relevant results/total results) of 0.79 outperformed default Elasticsearch’s total recall of 0.76. When using synonyms or related concepts as search queries, Dug (0.36) far outperformed Elasticsearch (0.14) in terms of total recall with no significant loss in the precision of its top results.

Availability and implementation

Dug is freely available at https://github.com/helxplatform/dug. An example Dug deployment is also available for use at https://search.biodatacatalyst.renci.org/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Development of the ParaOesophageal hernia SympTom (POST) tool
Authors: Puri Aiysha , Patel Nikhil M , Sounderajah Viknesh , Ferri Lorenzo , Griffiths Ewen A , Low Donald , Maynard Nick , Mueller Carmen , Pera Manuel , van Berge Henegouwen Mark I , Watson David I , Zaninotto Giovanni , Hanna George B , Markar Sheraz R ,   the POST Collaborative, Aye R , Louie B , Baigrie R , Bonavina L , Darling G , Fisichella P M , Jaume-Bottcher S , Lipham J C , Melvin W S , Nason K , Oelschlager B , Puccetti F , Rosati R , Roth J S , Siersma P , Smithers B , Soper N , Thompson S
Published: April 2022

Background

The aim of this study was to develop a symptom severity instrument (ParaOesophageal hernia SympTom (POST) tool) specific to para-oesophageal hernia (POH).

Methods

The POST tool was developed in four stages. The first was establishment of a Steering Committee. In the second stage, items were generated through a systematic review and online scoping survey of international experts. In the third stage, a three-round modified Delphi consensus process was conducted with a group of international experts who were asked to rate the importance of candidate items. An a priori threshold for inclusion was set at 80 per cent. The modified Delphi process culminated in a consensus meeting to develop the first iteration of the tool. In the final stage, two international patient workshops were held to assess the content validity and acceptability of the POST tool.

Results

The systematic review and scoping survey generated 64 symptoms, refined to 20 for inclusion in the modified Delphi consensus process. Twenty-six global experts participated in the Delphi consensus process. Five symptoms reached consensus across two rounds: difficulty getting solid foods down, chest pain after meals, difficulty getting liquids down, shortness of breath only after meals, and an early feeling of fullness after eating. The subsequent patient workshops deemed these five symptoms to be relevant and suggested that reflux should be included; these were taken forward to create the final POST tool.

Conclusion

The POST tool is the first instrument designed to capture POH-specific symptoms. It will allow clinicians to standardize reporting of symptoms of POH and evaluate the response to surgical intervention.
Unravelling the distinct biological functions and potential therapeutic applications of TIMP2 in cancer
Authors: Peeney David , Liu Yueqin , Lazaroff Carolyn , Gurung Sadeechya , Stetler-Stevenson William G
Published: April 2022

Tissue inhibitors of metalloproteinases (TIMPs) are a conserved family of proteins that were originally identified as endogenous inhibitors of matrixin and adamalysin endopeptidase activity. The matrixins and adamalysins are the major mediators of extracellular matrix (ECM) turnover, thus making TIMPs important regulators of ECM structure and composition. Despite their high sequence identity and relative redundancy in inhibitory profiles, each TIMP possesses unique biological characteristics that are independent of their regulation of metalloproteinase activity. As our understanding of TIMP biology has evolved, distinct roles have been assigned to individual TIMPs in cancer progression. In this respect, data regarding TIMP2’s role in cancer have borne conflicting reports of both tumor suppressor and, to a lesser extent, tumor promoter functions. TIMP2 is the most abundant TIMP family member, prevalent in normal and diseased mammalian tissues as a constitutively expressed protein. Despite its apparent stable expression, recent work highlights how TIMP2 is a cell stress-induced gene product and that its biological activity can be dictated by extracellular posttranslational modifications. Hence an understanding of TIMP2 molecular targets, and how its biological functions evolve in the progressing tumor microenvironment may reveal new therapeutic opportunities. In this review, we discuss the continually evolving functions of TIMP proteins, future perspectives in TIMP research, and the therapeutic utility of this family, with a particular focus on TIMP2.
Intraspecific variability in thermal tolerance: a case study with coastal cutthroat trout
Authors: Anlauf-Dunn Kara , Kraskura Krista , Eliason Erika J
Published: April 2022

Fish physiological performance is directly regulated by their thermal environment. Intraspecific comparisons are essential to ascertain the vulnerability of fish populations to climate change and to identify which populations may be more susceptible to extirpation and which may be more resilient to continued warming. In this study, we sought to evaluate how thermal performance varies in coastal cutthroat trout (Oncorhynchus clarki clarki) across four distinct watersheds in OR, USA. Specifically, we measured oxygen consumption rates in trout from the four watersheds with variable hydrologic and thermal regimes, comparing three ecologically relevant temperature treatments (ambient, annual maximum and novel warm). Coastal cutthroat trout displayed considerable intraspecific variability in physiological performance and thermal tolerance across the four watersheds. Thermal tolerance matched the historical experience: the coastal watersheds experiencing warmer ambient temperatures had higher critical thermal tolerance compared with the interior, cooler Willamette watersheds. Physiological performance varied across all four watersheds and there was evidence of a trade-off between high aerobic performance and broad thermal tolerance. Given the evidence of climate regime shifts across the globe, the uncertainty in both the rate and extent of warming and species responses in the near and long term, a more nuanced approach to the management and conservation of native fish species must be considered.
Oviposition by a Specialist Herbivore Increases Susceptibility of Canola to Herbivory by a Generalist Herbivore
Authors: Weeraddana Chaminda De Silva , Evenden Maya L
Published: April 2022

Oviposition by specialist herbivores can alter the suitability of the host plant to subsequent infestation by other herbivores. In this study, we tested the effect of previous oviposition on canola, Brassica napus L., by a Brassica specialist, the diamondback moth (DBM), Plutella xylostella (L.) (Lepidoptera: Plutellidae), on subsequent herbivory by the generalist feeder, the bertha armyworm (BAW), Mamestra configurata Walker (Lepidoptera: Noctuidae). The effect of DBM oviposition on subsequent BAW oviposition and larval feeding was tested in no-choice and choice experiments. Oviposition of BAW was not altered by DBM eggs on canola plants, however, BAW had increased larval feeding on plants with DBM eggs. These results suggest that oviposition by a specialist herbivore increased the susceptibility of the host plant to generalist herbivory. In a preliminary experiment, salicylic acid, jasmonic acid, and its conjugates were not altered by DBM oviposition on canola, however, further experimentation is needed to determine if oviposition affects expression of plant defense pathways and other plant traits.
Influence of atrial fibrillation type on outcomes of ablation vs. drug therapy: results from CABANA
Authors: Monahan Kristi H , Bunch T Jared , Mark Daniel B , Poole Jeanne E , Bahnson Tristram D , Al-Khalidi Hussein R , Silverstein Adam P , Daniels Melanie R , Lee Kerry L , Packer Douglas L ,   for the CABANA Investigators
Published: April 2022

Aims

Influence of atrial fibrillation (AF) type on outcomes seen with catheter ablation vs. drug therapy is incompletely understood. This study assesses the impact of AF type on treatment outcomes in the Catheter Ablation vs. Antiarrhythmic Drug Therapy for Atrial Fibrillation Trial (CABANA).

Methods and results

CABANA randomized 2204 patients ≥65 years old or <65 with at least one risk factor for stroke to catheter ablation or drug therapy. Of these, 946 (42.9%) had paroxysmal AF (PAF), 1042 (47.3%) had persistent AF (PersAF), and 215 (9.8%) had long-standing persistent AF (LSPAF) at baseline. The primary endpoint was a composite of death, disabling stroke, serious bleeding, or cardiac arrest. Symptoms were measured with the Mayo AF-Specific Symptom Inventory (MAFSI), and quality of life was measured with the Atrial Fibrillation Effect on Quality of Life (AFEQT). Comparisons are reported by intention to treat. Compared with drug therapy alone, catheter ablation produced a 19% relative risk reduction in the primary endpoint for PAF {adjusted hazard ratio [aHR]: 0.81 [95% confidence interval (CI): 0.50, 1.30]}, and a 17% relative reduction for PersAF (aHR: 0.83, 95% CI: 0.56, 1.22). For LSPAF, the ablation relative effect was a 7% reduction (aHR: 0.93, 95% CI: 0.36, 2.44). Ablation was more effective than drug therapy at reducing first AF recurrence in all AF types: by 51% for PAF (aHR: 0.49, 95% CI: 0.39, 0.62), by 47% for PersAF (aHR: 0.53, 95% CI: 0.43,0.65), and by 36% for LSPAF (aHR 0.64, 95% CI 0.41,1.00). Ablation was associated with greater improvement in symptoms, with the mean difference between groups in the MAFSI frequency score favouring ablation over 5 years of follow-up in all subgroups: PAF had a clinically significant −1.9-point difference (95% CI: −1.2 to −2.6); PersAF a −0.9 difference (95% CI: −0.2 to −1.6); LSPAF a clinically significant difference of −1.6 points (95% CI: −0.1 to −3.1). Ablation was also associated with greater improvement in quality of life in all subgroups, with the AFEQT overall score in PAF patients showing a clinically significant 5.3-point improvement (95% CI: 3.3 to 7.3) over drug therapy alone over 5 years of follow-up, PersAF a 1.7-point difference (95% CI: 0.0 to 3.7), and LSPAF a 3.1-point difference (95% CI: -1.6 to 7.8).

Conclusion

Prognostic treatment effects of catheter ablation compared with drug therapy on the primary and major secondary clinical endpoints did not differ consequentially by AF subtype. With regard to decreases in AF recurrence and improving quality of life, ablation was more effective than drug therapy in all three AF type subgroups.

ClinicalTrials.gov Identifier

NCT00911508