bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP)
Authors: Schiltz Colin , Rappoport Dmitrij , Mandelshtam Vladimir A. 
Published: May 2023

The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided.
Diet of the finescale triggerfish, Balistes polylepis (Steindachner), in the Gulf of California
Authors: Acosta-Pachón Tatiana A. , López-Vivas Juan Manuel , Mazariegos-Villarreal Alejandra , León-Cisneros Karla , Medina-López Marco A. , Barjau González Emelio , Serviere-Zaragoza Elisa 
Published: May 2023

Context Establishing the roles that different species play within ecosystems is key to understanding how ecosystems function and determining the feeding relationships among species. Aims This study analysed the stomach contents of finescale triggerfish, Balistes polylepis, at two sites in the southern Gulf of California, in order to describe its diet. Methods The prey-specific index of relative importance (%PSIRIi) was determined, diet width was calculated with Levins’ index and the Costello method, and the trophic position was estimated using the R package dietr. Key results B. polylepis is an omnivorous species with a preference for animal material (TL = 3.1) that feeds on a wide range of prey. It is categorised as a generalist predator (Levins’ index, Bi = 0.99). The most important items in the diet were the colonial ascidian Lissoclinum fragile (%PSIRIi = 13.52) at Las Ánimas, and the Xanthidae family (%PSIRIi = 13.24) at San Juan de la Costa. Implications B. polylepis plays an important role. Because it can exploit a broad variety of resources, it participates in trophic interactions with several other species. It is essential to determine the trophic habits of this species in other areas of its distribution.
Supporting complex care in general practice via an eConsultant model of care: the Australian specialist perspective
Authors: Petre Joel , Donald Maria , Jackson Claire 
Published: May 2023

Background Accessing timely specialist physician advice and guidance is of critical importance to both Australian GP specialists (GPs) and their patients. The traditional method of referral, triage and subsequent face-to-face (FTF) consultation is facing challenges from an ever increasing volume of referrals and the needs of underserved populations. In response to such issues, electronic consults (eConsults) have been successfully used internationally to provide GPs with a means of asynchronously accessing specialist physician advice and guidance within 72 h. Few studies have addressed the potential impact of eConsults from the view of the non-GP specialist receiving the request, and none specifically related to specialist adult medicine physicians. The aim of this study was to determine the perceptions of current Royal Australasian College of Physicians (RACP) adult medicine Fellows towards establishing an eConsult model of care within their own clinical practice. Methods Semi-structured interviews were conducted with 14 RACP adult medicine Fellows between December 2019 and February 2020. Purposive and snowball sampling strategies were used to recruit physicians of differing ages and gender from diverse specialties and healthcare settings. The data were subjected to a descriptive thematic analysis. Results We describe five key themes of relevance to study participants: (1) improved access to non-GP specialist care; (2) the business model in relation to remuneration and time; (3) enhanced GP–Physician relationships; (4) impact on physician work–life balance; and (5) the need for a structured model of care. There was broad consensus that a significant number of outpatient referrals to adult medicine physicians would be more appropriately addressed in primary care with support via an asynchronous eConsult arrangement. RACP Fellows agreed this could improve access to timely specialist advice, place downward pressure on outpatient FTF clinic waiting times and reduce unnecessary patient travel. Conclusion These findings identify the drivers and barriers to the establishment of an Australian eConsultant model of care from the adult medicine physician’s perspective.
Improving HIV pre-exposure prophylaxis (PrEP) uptake and initiation: process evaluation and recommendation development from a national PrEP program†
Authors: Estcourt Claudia S. , MacDonald Jennifer , Saunders John , Nandwani Rak , Young Ingrid , Frankis Jamie , Clutterbuck Dan , Steedman Nicola , McDaid Lisa , Dalrymple Jenny , Flowers Paul 
Published: May 2023

Background HIV pre-exposure prophylaxis (PrEP) is key to HIV transmission elimination but implementation is challenging and under-researched. We undertook a process evaluation of the first 2 years of a national PrEP program to explore barriers and facilitators to implementation and to develop recommendations to improve implementation, focusing on PrEP uptake and initiation. Methods Stage 1 involved semi-structured telephone interviews and focus groups (September 2018–July 2019) with geographically and demographically diverse patients seeking/using/declining/stopping PrEP (n = 39), sexual healthcare professionals (n = 54), community-based organisation service users (n = 9) and staff (n = 15) across Scotland. We used deductive thematic analysis, to derive and then map key barriers and facilitators to priority areas that experts agreed would enhance uptake and initiation. In Stage 2, we used analytic tools from implementation science to systematically generate evidence-based, theoretically-informed recommendations to enhance uptake and initiation of PrEP. Results Barriers and facilitators were multi-levelled and interdependent. Barriers included the rapid pace of implementation without additional resource, and a lack of familiarity with PrEP prescribing. Facilitators included opportunities for acquisition of practice-based knowledge and normalisation of initiation activities. We refined our 68 ‘long-list’ recommendations to 41 using expert input and the APEASE (Acceptability, Practicability, Effectiveness, Affordability, Side-effects, and Equity) criteria. Examples include: provision of PrEP in diverse settings to reach all in need; co-produced, culturally sensitive training resources for healthcare professionals, with focused content on non-daily dosing; meaningful collaborative working across all stakeholders. Conclusions These evidence-based, theory informed recommendations provide a robust framework for optimising PrEP uptake and initiation in diverse settings to ensure PrEP reaches all who may benefit.
SMARCB1 regulates the hypoxic stress response in sickle cell trait
Authors: Soeung Melinda , Perelli Luigi , Chen Ziheng , Dondossola Eleonora , Ho I-Lin , Carbone Federica , Zhang Li , Khan Hania , Le Courtney N. , Zhu Cihui , Peoples Michael D. , Feng Ningping , Jiang Shan , Zacharias Niki Millward , Minelli Rosalba , Shapiro Daniel D. , Deem Angela K. , Gao Sisi , Cheng Emily H. , Lucchetti Donatella , Walker Cheryl L. , Carugo Alessandro , Giuliani Virginia , Heffernan Timothy P. , Viale Andrea , Tannir Nizar M. , Draetta Giulio F. , Msaouel Pavlos , Genovese Giannicola 
Published: May 2023

Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor suppressor
SMARCB1
. Because renal ischemia induced by red blood cell sickling exacerbates chronic renal medullary hypoxia in vivo, we investigated whether the loss of SMARCB1 confers a survival advantage under the setting of SCT. Hypoxic stress, which naturally occurs within the renal medulla, is elevated under the setting of SCT. Our findings showed that hypoxia-induced SMARCB1 degradation protected renal cells from hypoxic stress. SMARCB1 wild-type renal tumors exhibited lower levels of SMARCB1 and more aggressive growth in mice harboring the SCT mutation in human hemoglobin A (HbA) than in control mice harboring wild-type human HbA. Consistent with established clinical observations, SMARCB1-null renal tumors were refractory to hypoxia-inducing therapeutic inhibition of angiogenesis. Further, reconstitution of SMARCB1 restored renal tumor sensitivity to hypoxic stress in vitro and in vivo. Together, our results demonstrate a physiological role for SMARCB1 degradation in response to hypoxic stress, connect the renal medullary hypoxia induced by SCT with an increased risk of SMARCB1-negative RMC, and shed light into the mechanisms mediating the resistance of SMARCB1-null renal tumors against angiogenesis inhibition therapies.
Cargo-selective and adaptive delivery of nucleic acid therapeutics by bola-amphiphilic dendrimers
Authors: Chen Jiaxuan , Zhu Dandan , Lian Baoping , Shi Kangjie , Chen Peng , Li Ying , Lin Wenyi , Ding Ling , Long Qiulin , Wang Yang , Laurini Erik , Lan Wenjun , Li Yun , Tintaru Aura , Ju Caoyun , Zhang Can , Pricl Sabrina , Iovanna Juan , Liu Xiaoxuan , Peng Ling 
Published: May 2023

Nucleic acid therapeutics are becoming an important drug modality, offering the unique opportunity to address “undruggable” targets, respond rapidly to evolving pathogens, and treat diseases at the gene level for precision medicine. However, nucleic acid therapeutics have poor bioavailability and are chemolabile and enzymolabile, imposing the need for delivery vectors. Dendrimers, by virtue of their well-defined structure and cooperative multivalence, represent precision delivery systems. We synthesized and studied bola-amphiphilic dendrimers for cargo-selective and on-demand delivery of DNA and small interfering RNA (siRNA), both important nucleic acid therapeutics. Remarkably, superior performances were achieved for siRNA delivery with the second-generation dendrimer, yet for DNA delivery with the third generation. We systematically studied these dendrimers with regard to cargo binding, cellular uptake, endosomal release, and in vivo delivery. Differences in size both of the dendrimers and their nucleic acid cargos impacted the cooperative multivalent interactions for cargo binding and release, leading to cargo-adaptive and selective delivery. Moreover, both dendrimers harnessed the advantages of lipid and polymer vectors, while offering nanotechnology-based tumor targeting and redox-responsive cargo release. Notably, they allowed tumor- and cancer cell-specific delivery of siRNA and DNA therapeutics for effective treatment in different cancer models, including aggressive and metastatic malignancies, outperforming the currently available vectors. This study provides avenues to engineer tailor-made vectors for nucleic acid delivery and precision medicine.
Design of rigid protein–protein interaction inhibitors enables targeting of undruggable Mcl-1
Authors: Hargreaves David , Carbajo Rodrigo J. , Bodnarchuk Michael S. , Embrey Kevin , Rawlins Philip B. , Packer Martin , Degorce Sébastien L. , Hird Alexander W. , Johannes Jeffrey W. , Chiarparin Elisabetta , Schade Markus 
Published: May 2023

The structure-based design of small-molecule inhibitors targeting protein–protein interactions (PPIs) remains a huge challenge as the drug must bind typically wide and shallow protein sites. A PPI target of high interest for hematological cancer therapy is myeloid cell leukemia 1 (Mcl-1), a prosurvival guardian protein from the Bcl-2 family. Despite being previously considered undruggable, seven small-molecule Mcl-1 inhibitors have recently entered clinical trials. Here, we report the crystal structure of the clinical-stage inhibitor AMG-176 bound to Mcl-1 and analyze its interaction along with clinical inhibitors AZD5991 and S64315. Our X-ray data reveal high plasticity of Mcl-1 and a remarkable ligand-induced pocket deepening. Nuclear Magnetic Resonance (NMR)-based free ligand conformer analysis demonstrates that such unprecedented induced fit is uniquely achieved by designing highly rigid inhibitors, preorganized in their bioactive conformation. By elucidating key chemistry design principles, this work provides a roadmap for targeting the largely untapped PPI class more successfully.
Sequential absorption of two photons creates a bistable form of RubyACR responsible for its strong desensitization
Authors: Sineshchekov Oleg A. , Govorunova Elena G. , Li Hai , Wang Yumei , Spudich John L. 
Published: May 2023

Channelrhodopsins with red-shifted absorption, rare in nature, are highly desired for optogenetics because light of longer wavelengths more deeply penetrates biological tissue. RubyACRs (Anion ChannelRhodopsins), a group of four closely related anion-conducting channelrhodopsins from thraustochytrid protists, are the most red-shifted channelrhodopsins known with absorption maxima up to 610 nm. Their photocurrents are large, as is typical of blue- and green-absorbing ACRs, but they rapidly decrease during continuous illumination (desensitization) and extremely slowly recover in the dark. Here, we show that long-lasting desensitization of RubyACRs results from photochemistry not observed in any previously studied channelrhodopsins. Absorption of a second photon by a photocycle intermediate with maximal absorption at 640 nm (P
640
) renders RubyACR bistable (i.e., very slowly interconvertible between two spectrally distinct forms). The photocycle of this bistable form involves long-lived nonconducting states (L
long
and M
long
), formation of which is the reason for long-lasting desensitization of RubyACR photocurrents. Both L
long
and M
long
are photoactive and convert to the initial unphotolyzed state upon blue or ultraviolet (UV) illumination, respectively. We show that desensitization of RubyACRs can be reduced or even eliminated by using ns laser flashes, trains of short light pulses instead of continuous illumination to avoid formation of L
long
and M
long
, or by application of pulses of blue light between pulses of red light to photoconvert L
long
to the initial unphotolyzed state.
Impacts of Individual and Pair Housing on Calves
Authors: Mahendran Sophie 
Published: May 2023

Abstract
Calf rearing is a large financial cost to farms, with particular importance for dairy heifer replacements where the forward investment does not receive any pay-back for 3 to 4 years. Ensuring the critical pre-weaning phase is carried out optimally and understanding the impact that housing has on this time are important. Historically, individual calf housing has been used to reduce disease transmission between calves, but there is limited evidence that pair housing has any detrimental impact on this. Instead, research over the past decade has served to highlight the range of benefits that pair housing can provide. Pair-housed calves start to eat concentrates at an earlier age and in greater amounts, although this does not always translate to increased growth rates during the pre-weaning period. Pair housing allows calves to start forming social relationships, which can have a calming effect in stressful situations and can improve behaviour when heifers enter the milking herd. Additionally, calves housed with others have increased play behaviours, which is a positive indicator of well-being. This growing body of evidence suggests that pair housing of calves results in overall better health and welfare compared to individual housing; therefore, practitioners should help encourage farmers to move towards this housing type.

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Real-time control applications of JET heterodyne radiometer electron temperature profiles using ICRH
Authors: Cappelli M. , Cardinali A. , Zerbini M. , Pucella G. , Giovannozzi E. , JET contributors  
Published: May 2023

Abstract
The Real Time ECE data processing has been recently implemented at JET, by using a cross calibration between the Martin-Puplett interferometer (also known as Michelson) measurements and the Heterodyne faster data. The applicability of RT control with ICRH has been discussed in recent works. In particular, in case of a hollow electron temperature profile, central ICRF heating could be applied to restore temperature peaking. In this work a study about the possibility of controlling the electron temperature profile by using ICRH

as an actuator, with inputs from ECE measurements, is described. The ICRH is here used for the optimization of the plasma ramp-down, in order to correct the end of the discharge and avoid the plasma disruption, though a similar approach could also be proposed to improve the plasma performances during the flat top. Preliminary results have been obtained on the physical and logical feasibility of using ICRH in a real-time control loop. A database of good pulses in identifiable conditions has been compiled and validated by covering the main experiments both in the baseline and hybrid scenarios. Such scenarios have been simulated, for a selected numbers of discharges, using the full-wave propagation solver TORIC-SSQLFP, in order to establish the ICRH power deposition profiles to be used to locally restore a peaked electron temperature profile.
Physical design and multi-physics analysis of a 200 MHz continuous wave radio frequency quadrupole accelerator for a proton accelerator facility
Authors: Zhang Z.Y. , Ma W. , Yuan N. , Sun Y.B. , Ge Y.L. , Zou Z.P. , Zhang Z.L. , Zou L.P. , Yang Z. , Lu L. 
Published: May 2023

Abstract
Based on the platform of a proton accelerator facility, a 200 MHz high intensity continuous wave (CW) radio frequency quadrupole (RFQ) accelerator has been designed at the Sino-French Institute of Nuclear Engineering and Technology of Sun Yat-Sen University, China. Employing the conventional four-vane structure, the RFQ can accelerate 20 mA proton beam from 20 keV to 2.5 MeV. In the beam dynamics design, the simulated transmission efficiency reaches 99.5% and the vane length is less than 4 m. In the electromagnetic design, for the long-term stable operation, Pi-mode Stabilizer Loops (PISLs) are utilized to achieve more than 10 MHz mode frequency separation and to decrease the effects of dipole modes. The 48 tuners are optimized to provide a range of ± 2 MHz frequency tuning. Additionally, the undercuts are optimized to ensure a good field flatness along the longitudinal direction. Based on the coolant channel design, the multi-physics analysis is performed to investigate the deformation and stress resulting from the dissipation of RF power within the cavity, as well as determine the temperature tuning coefficients of the coolants within the vane and wall. The entire design and analysis of PAFA-RFQ has been completed, and the scheme of the design can also be applied to the design of other RFQ cavities.
On the noise generation and unsteady performance of combined heaving and pitching foils
Authors: Wagenhoffer Nathan , Moored Keith W , Jaworski Justin W 
Published: May 2023

Abstract
A transient two-dimensional acoustic boundary element solver is coupled to a potential flow boundary element solver via Powell’s acoustic analogy to determine the acoustic emission of isolated hydrofoils performing biologically-inspired motions. The flow-acoustic boundary element framework is validated against experimental and asymptotic solutions for the noise produced by canonical vortex-body interactions. The numerical framework then characterizes the noise production of an oscillating foil, which is a simple representation of a fish caudal fin. A rigid NACA 0012 hydrofoil is subjected to combined heaving and pitching motions for Strouhal numbers (

0.03
<

S
t

<
1

) based on peak-to-peak amplitudes and chord-based reduced frequencies (

0.125
<

f

∗

<
1

) that span the parameter space of many swimming fish species. A dipolar acoustic directivity is found for all motions, frequencies, and amplitudes considered, and the peak noise level increases with both the reduced frequency and the Strouhal number. A combined heaving and pitching motion produces less noise than either a purely pitching or purely heaving foil at a fixed reduced frequency and amplitude of motion. Correlations of the lift and power coefficients with the peak root-mean-square acoustic pressure levels are determined, which could be utilized to develop long-range, quiet swimmers.
Poly(vinyl alcohol)-gelatin crosslinked by silane-functionalized guanidyl-hydroxyurethane oligomer as contact-killing non-leaching antibacterial wound dressings
Authors: Babaahmadi Masoud , Yeganeh Hamid 
Published: May 2023

AbstractThe present work aims to prepare efficient wound dressing with noncytotoxicity, proper mechanical strength, and the ability to preserve a hygienic environment over wounded skin tissue. To fulfill this goal, the synthesis of a novel silane crosslinking agent with antibacterial guanidinium chloride functional group is considered. The resulting reagent was applied to make a series of film-type stable crosslinked networks composed of poly(vinyl alcohol) and gelatin. The potential protection of wounds from external forces was confirmed, as these films had a very good tensile strength (16–31 MPa) and good elongation (54%–101%) under dry conditions. The good dimensional strength of dressings was preserved after hydration with simulated wound exudates. Based on the calculated fluid handling capacity of the prepared dressings (2.43–3.54 g 10−1cm−2d−1), they were suitable for treating wounds with ‘light’ to ‘moderate’ exudate volume. All the prepared dressings showed very good biocompatibility, as determined by the high viability of fibroblast cells directly contacted with dressing (over 80%) or leachates extracted from them (over 90%). In addition, dressings functionalized with guanidinium groups could effectively kill representative gram-positive and gram-negative bacterial strains.