bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
Authors: Qiu Yuchi , Wei Guo-Wei 
Published: August 2023

AbstractProtein engineering is an emerging field in biotechnology that has the potential to revolutionize various areas, such as antibody design, drug discovery, food security, ecology, and more. However, the mutational space involved is too vast to be handled through experimental means alone. Leveraging accumulative protein databases, machine learning (ML) models, particularly those based on natural language processing (NLP), have considerably expedited protein engineering. Moreover, advances in topological data analysis (TDA) and artificial intelligence-based protein structure prediction, such as AlphaFold2, have made more powerful structure-based ML-assisted protein engineering strategies possible. This review aims to offer a comprehensive, systematic, and indispensable set of methodological components, including TDA and NLP, for protein engineering and to facilitate their future development.
Truly Listening to Accounts of Mental Health Act Assessments: Reflections on my Practice
Authors: Blakley Louise 
Published: August 2023

Abstract
This article draws upon the experience of the author whilst undertaking a qualitative research study exploring service user experiences of being assessed for detention to a mental health hospital. Doing research as a social work practitioner is a growing area and a common motivation is to improve practice. This article brings a different way of reporting research, which is embedded in the reflective tradition of social work. It explores practitioner research and insider/outsider perspectives. Through reflection, the author examines in depth two participants’ narratives, how this impacted her as a mental health social worker and the changes in her practice. These assessments are complex pieces of social work with involuntary service users in a pressured setting and are a challenging area for practitioners to improve service user experiences.
Tree pruning improves tree form but not understory plant production in mixed stands of Sitka spruce and western hemlock, USA
Authors: Nelson Kellen N , Barnard Jeffrey C , Massingham Preston M , Crotteau Justin S 
Published: August 2023

Abstract
Precommercial thinning and tree pruning are frequently used together to improve timber quality and wildlife habitat in even-aged Sitka spruce (Picea sitchensis) and western hemlock (Tsuga heterophylla) stands. Thinning enhances crop tree growth and understory plant production; however, the benefits and drawbacks of tree pruning have received less attention. Tree pruning was investigated in two long-term experiments on the Tongass National Forest, Alaska, USA. Experiment 1 tracked four uniformly thinned sites for ~30 years that received 2.4, 3.6, and 5.2 m lift, and no pruning treatments. Experiment 2 tracked 11 sites for 16 years that received thinning/no pruning, thinning plus pruning (25% of trees), thinning plus pruning (50% of trees), and no thinning/no pruning treatments. We investigated (i) how pruning lift height affects tree form and understory production and (ii) how pruning density affects canopy closure and understory production. In Experiment 1, pruning reduced butt log taper and did not adversely affect diameter or height in either species. Pruning lift was visible in height-to-live crown measurements. Crown recession occurred first in low lift treatments and later in all treatments until crown form was similar after 28–31 years. Epicormic branching rates in Sitka spruce peaked 6–9 years after treatment before falling sharply. Deer forage declined through time and did not differ between lift treatments. In Experiment 2, canopy closure was lower shortly after thinning and pruning, but did not differ from the control after 16 years. Epicormic branching rates were greater shortly after thinning and pruning but did not differ from the control after 16 years. Deer forage declined with canopy closure and thinned and pruned treatments exhibited greater forage than the control. We conclude that pruning can improve log quality for timber applications but does not enhance understory plant biomass and deer forage over thinning treatment alone.
Optimizing Motor Learning in Older Adults
Authors: Khalaji Zahra , Nezakat Alhosseini Maryam , Safavi Hamami Shila , Iwatsuki Takehiro , Wulf Gabriele 
Published: August 2023

Abstract

Objectives
According to the Optimizing Performance Through Intrinsic Motivation and Attention for Learning (OPTIMAL) theory of Wulf and Lewthwaite, enhanced expectancies (EE), autonomy support (AS), and an external focus (EF) of attention facilitate motor performance and learning. The present study examined whether consecutive implementation of EE, AS, and EF during practice would enhance the learning of a square-stepping task in older adults.

Methods
Participants were randomly assigned to optimized and control groups. After the pretest, 1 of the 3 factors was implemented during each of the three 12-trial practice blocks, in a counterbalanced order, in the optimized group: positive feedback (EE), choice of mat color (AS), and instructions to focus on the squares (EF). Control group participants practiced without any of these factors.

Results
Results indicated that the optimized group had faster movement times than the control group during the practice phase and on 24-hr retention and transfer tests.

Discussion
The key variables in the OPTIMAL theory can be applied sequentially in order to facilitate motor performance and learning in older adults.
The Impact of Cannabis Use on Clinical Outcomes in Inflammatory Bowel Disease: A Population-based Longitudinal Cohort Study
Authors: Glickman Danny , Dalessio Shannon , Raup-Konsavage Wesley M , Vrana Kent E , Coates Matthew D 
Published: August 2023

Abstract

Background
Cannabis use is common in inflammatory bowel disease (IBD). Recent studies demonstrated that use of cannabis may relieve symptoms; however, it is still unclear how safe cannabis and its derivatives are for IBD patients. We performed this study to evaluate the impact of cannabis use on several key clinical outcomes in IBD.

Methods
We performed a retrospective study using the TriNetX Diamond Network. Cannabis use and noncannabis use subcohorts were identified for 3 patient groups: (1) IBD, (2) Crohn’s disease (CD), and (3) ulcerative colitis (UC). Baseline differences between subcohorts for each group were controlled by propensity score matching. In each group, we compared relative incidence of emergency department (ED) visits, hospitalization, corticosteroid use, opioid use, IBD-related surgery, and death between cannabis users and noncannabis users.

Results
Inflammatory bowel disease cannabis users demonstrated an increased risk for corticosteroid use (risk ratios [R],1.095; 95% CI, 1.021-1.174; P = .011), ED visits (RR, 2.143; 95% CI, 2.034-2.257; P &lt; .001), hospitalizations (RR, 1.925; 95% CI, 1.783-2.079; P &lt; .001) and opioid use (RR, 1.35; 95% CI, 1.14-1.6); P &lt; .001), but not an increased risk of IBD-related surgery or death. The CD and UC groups exhibited similar outcomes, except only CD demonstrated an increased risk for corticosteroid and opioid use.

Conclusions
Cannabis use in IBD patients is associated with several poor clinical outcomes, including increased risk of corticosteroid and opioid use, ED visits and hospitalization, though not IBD-related surgery or death. It is not clear what drives these risks or whether they are directly related to IBD-associated disease activity or other factors. Further prospective studies are warranted to more carefully investigate these relationships.
Clinical pharmacists’ perspective of medication adherence support in Ethiopian hospital settings: a qualitative study
Authors: Tegegn Henok G , Wark Stuart , Tursan d’Espaignet Edouard , Spark M Joy 
Published: August 2023

Abstract

Background
Hospital pharmacists can assist patients with medication adherence in a hospital setting. No studies have explored the views of hospital pharmacists on medication adherence.

Objectives
The study aimed to explore Ethiopian clinical pharmacists’ understanding of and experience with medication adherence, and identify strategies for medication adherence support.

Methods
Semi-structured interviews were conducted via ZOOM/Skype. Hospital pharmacists were recruited through a professional network and snowball sampling. All interviews were audio recorded, transcribed verbatim, translated into English and analysed using thematic analysis techniques. The data coding followed a hybrid deductive and inductive approach.

Key findings
Fourteen Ethiopian clinical pharmacists participated in the study. Analysis yielded five main themes including: medication adherence definition and measurement; pharmacists’ perceived roles; enablers of medication adherence; barriers to medication adherence; and ways forward. Participants indicated that accurately assessing medication adherence was complicated because of an absence of cost-effective and validated tools. Pharmacist education, clinical pharmacy services, physical structure, sources of medication information, and government initiatives to reduce financial burdens were the facilitators identified. Eight barriers were identified, and these were broadly classified as factors intrinsic or extrinsic to the patient.

Conclusions
Medication adherence support could face barriers intrinsic or extrinsic to patients. Strategies were proposed to overcome the identified barriers and to harness existing facilitators. These strategies included the need for validated local language medication adherence tools, instituting regular adherence measurement and prioritizing patients for available interventions. Patient’s preferred dosage form should be considered along with medication complexity and medication knowledge when supporting medication adherence.
Modified peritoneal flap hernioplasty and abdominoplasty in large incisional hernia after cesarean section with midline vertical incision: a case report
Authors: Elfiah Ulfa , Saputra Antonius Dwi 
Published: August 2023

Abstract
An incisional hernia (IH) is a common complication after a cesarean section (CS). Large IH mesh repair is problematic when initial fascial closure cannot be accomplished. We report the case of a large IH for 20 months after a CS with a midline vertical incision that was treated with a combination of modified peritoneal flap hernioplasty and abdominoplasty. There was a large fascia defect (15 × 21 cm) and adhesions of the omentum and the ileum to the anterior abdominal wall. CS with midline vertical incision, history of surgical site infections and obesity are risk factors that increase IH. In conclusion, this combination successfully repairs a large IH, reduces obesity, prevents recurrence and complications after hernia repair, improves the abdominal shape and patient quality of life. Abdominoplasty is also performed to create new umbilical and vascular preservation.
The Pristine dwarf galaxy survey–V. The edges of the dwarf galaxy Hercules
Authors: Longeard Nicolas , Jablonka Pascale , Battaglia Giuseppina , Malhan Khyati , Martin Nicolas , Sánchez-Janssen Rubén , Sestito Federico , Starkenburg Else , Venn Kim A 
Published: August 2023

ABSTRACT
We present a new spectroscopic study of 175 stars in the vicinity of the dwarf galaxy Hercules (d ∼ 132 kpc) with data from the Anglo-Australian Telescope and its AAOmega spectrograph together with the Two Degree Field multi-object system to solve the conundrum that whether Hercules is tidally disrupting. We combine broad-band photometry, proper motions from Gaia, and our Pristine narrow-band and metallicity-sensitive photometry to efficiently weed out the Milky Way contamination. Such cleaning is particularly critical in this kinematic regime, as both the transverse and heliocentric velocities of Milky Way populations overlap with Hercules. Thanks to this method, three new member stars are identified, including one at almost 10rh of the satellite. All three have velocities and metallicities consistent with that of the main body. Combining this new data set with the entire literature cleaned out from contamination shows that Hercules does not exhibit a velocity gradient (d〈v〉/dχ $= 0.1^{+0.4}_{-0.2}$ km s−1 arcmin−1, 1.6 km s−1 arcmin−1 as a 3σ upper limit) and, as such, does not show evidence to undergo tidal disruption.
Photoevaporation versus enrichment in the cradle of the Sun
Authors: Patel Miti , Polius Cheyenne K M , Ridsdill-Smith Matthew , Lichtenberg Tim , Parker Richard J 
Published: August 2023

ABSTRACT
The presence of short-lived radioisotopes (SLRs) 26Al and 60Fe in the Solar system places constraints on the initial conditions of our planetary system. Most theories posit that the origin of 26Al and 60Fe is in the interiors of massive stars, and they are either delivered directly to the protosolar disc from the winds and supernovae of the massive stars, or indirectly via a sequential star formation event. However, massive stars that produce SLRs also emit photoionizing far and extreme ultraviolet radiation, which can destroy the gas component of protoplanetary discs, possibly precluding the formation of gas giant planets like Jupiter and Saturn. Here, we perfom N-body simulations of star-forming regions and determine whether discs that are enriched in SLRs can retain enough gas to form Jovian planets. We find that discs are enriched and survive the photoionizing radiation only when the dust radius of the disc is fixed and not allowed to move inwards due to the photoevaporation, or outwards due to viscous spreading. Even in this optimal scenario, not enough discs survive until the supernovae of the massive stars and so have zero or very little enrichment in 60Fe. We therefore suggest that the delivery of SLRs to the Solar system may not come from the winds and supernovae of massive stars.
On constraining cosmology and the halo mass function with weak gravitational lensing
Authors: Gu Shiming , Dor Marc-Antoine , van Waerbeke Ludovic , Asgari Marika , Mead Alexander , Tröster Tilman , Yan Ziang 
Published: August 2023

ABSTRACT
The discrepancy between the weak lensing (WL) and the Planck measurements of S8 has been a subject of several studies. Assuming that residual systematics are not the cause, these studies tend to show that a strong suppression of the amplitude of the mass power spectrum P(k) in the late Universe at high k could resolve it. The WL signal at the small scale is sensitive to various effects not related to lensing, such as baryonic effects and intrinsic alignment. These effects are still poorly understood therefore the accuracy of P(k) depends on the modelling precision of these effects. A common approach for calculating P(k) relies on a halo model. Among the various components necessary for the construction of P(k) in the halo model framework, the halo mass function (HMF) is an important one. Traditionally, the HMF has been assumed to follow a fixed model, motivated by dark matter-only numerical simulations. Recent literature shows that baryonic physics, among several other factors, could affect the HMF. In this study, we investigate the impact of allowing the HMF to vary. This provides a way of testing the validity of the halo model-HMF calibration using data. In the context of the aforementioned S8 discrepancy, we find that the Planck cosmology is not compatible with the vanilla HMF for both the DES-y3 and the KiDS-1000 data. Moreover, when the cosmology and the HMF parameters are allowed to vary, the Planck cosmology is no longer in tension. The modified HMF predicts a matter power spectrum with a $\sim 25~{{\ \rm per\ cent}}$ power loss at k ∼ 1 h Mpc−1, in agreement with the recent studies that try to mitigate the S8 tension with modifications in P(k). We show that stage IV surveys will be able to measure the HMF parameters with a few per cent accuracy.
The extended ‘stellar halo’ of the Ursa Minor dwarf galaxy
Authors: Sestito Federico , Zaremba Daria , Venn Kim A , D’Aoust Lina , Hayes Christian , Jensen Jaclyn , Navarro Julio F , Jablonka Pascale , Fernández-Alvar Emma , Glover Jennifer , McConnachie Alan W , Chené André-Nicolas 
Published: August 2023

ABSTRACT
Stellar candidates in the Ursa Minor (UMi) dwarf galaxy have been found using a new Bayesian algorithm applied to Gaia EDR3 data. Five of these targets are located in the extreme outskirts of UMi, from ∼5 to 12 elliptical half-light radii (rh), where rh(UMi) = 17.32 ± 0.11 arcmin, and have been observed with the high-resolution Gemini Remote Access to CFHT ESPaDOnS Spectrograph at the Gemini North telescope. Precise radial velocities (σRV &lt; 2 km s−1) and metallicities ($\sigma _{\rm {{\rm [Fe/H]}}}\ \lt\ 0.2$ dex) confirm their memberships of UMi. Detailed analysis of the brightest and outermost star (Target 1, at ∼12rh), yields precision chemical abundances for the α (Mg, Ca, and Ti), odd-Z (Na, K, and Sc), Fe-peak (Fe, Ni, and Cr), and neutron-capture (Ba) elements. With data from the literature and APOGEE data release 17, we find the chemical patterns in UMi are consistent with an outside-in star-formation history that includes yields from core-collapse supernovae, asymptotic giant branch stars, and Type Ia supernovae. Evidence for a knee in the [α/Fe] ratios near [Fe/H] ∼ −2.1 indicates a low star-formation efficiency similar to that in other dwarf galaxies. Detailed analysis of the surface number density profile shows evidence that UMi’s outskirts have been populated by tidal effects, likely as a result of completing multiple orbits around the Galaxy.
Role of the Killer Immunoglobulin-like Receptor and Human Leukocyte Antigen I Complex Polymorphisms in Kaposi Sarcoma–Associated Herpesvirus Infection
Authors: Zhang Xin , Li Yi , Han Xinyu , Xu Yiyun , Wang Haili , Wang Tianye , Zhang Tiejun 
Published: August 2023

AbstractBackgroundKaposi sarcoma, caused by the pathogen Kaposi sarcoma–associated herpesvirus (KSHV), is the most common neoplasm for patients with AIDS. Susceptibility to KSHV has been associated with several different genetic risk variants. The purpose of this study was to test whether variants of killer cell immunoglobulin-like receptors (KIRs) and their human leukocyte antigen (HLA-I) ligands influence the risk of KSHV infection.MethodsA case-control study was performed in Xinjiang, a KSHV-endemic region of China. We recruited 299 individuals with HIV, including 123 KSHV-seropositive persons and 176 KSHV-seronegative controls. We used logistic regression and the MiDAS package to evaluate the association between KIR/HLA-I polymorphisms and KSHV infection.ResultsHLA-A*31:01, HLA-C*03:04, and HLA-C*12:03 were found to be associated with KSHV infection, with A*31:01 showing a protective effect under 3 different models (dominant: 0.30 [95% confidence interval {CI}, .08–.82], P = .031; additive: 0.30 [95% CI, .09–.80], P = .030; overdominant: 0.31 [95% CI, .09–.88], P = .042). The effect of A*31:01 might cause the variants of amino acid at HLA-A position 56, with individuals carrying an arginine having a lower KSHV infection risk. The increased homozygous KIR2DL3 was associated with a relatively high KSHV viral load (16.30% vs 41.94%, P = .010).ConclusionsThis study provides further insight into the link between HLA-I alleles and KIR genes and KSHV infection, highlighting KSHV-susceptible variants of HLA-I and KSHV replication caused by specific KIR genotype, and revealing a potential role of KIR-mediated natural killer cell activation in anti-KSHV infection.
Assessing the Measurement Properties of the Self-Administered Amyotrophic Lateral Sclerosis Functional Rating Scale–Revised (ALSFRS-R): A Rasch Analysis
Authors: Mehdipour Ava , Teshler Lizabeth , Dal Bello-Haas Vanina , Richardson Julie , Beauchamp Marla , Turnbull John , Chum Marvin , Johnston Wendy , O’Connell Colleen , Luth Westerly , Kuspinar Ayse 
Published: August 2023

AbstractObjectiveThe self-administered version of the Amyotrophic Lateral Sclerosis Functional Rating Scale–Revised (ALSFRS-R) is used to monitor function and disease progression in individuals with amyotrophic lateral sclerosis (ALS). However, the performance of the self-administered ALSFRS-R has not been assessed using Rasch Measurement Theory. Therefore, the purpose of this study was to examine the psychometric properties of the self-administered ALSFRS-R using Rasch analysis.MethodsRasch analysis was performed on self-administered ALSFRS-R data from individuals with ALS across Canada. The following 6 aspects of Rasch analysis were examined using RUMM2030: fit via residuals and chi-square statistics, targeting via person-item threshold maps, dependency via item residual correlations, unidimensionality through principal components analysis of residuals, reliability via person separation index, and stability through differential item functioning analyses for sex, age, and language.ResultsAnalysis was performed on 122 participants (mean age: 52.9 years; 62.8% men). The overall scale demonstrated good fit, reliability, and stability; however, multidimensionality was found. To address this issue, items were divided into 3 subscales (bulbar, motor, and respiratory function), and Rasch analysis was performed for each subscale. The subscales demonstrated good fit, reliability, stability, and unidimensionality. However, there were still issues with item dependency for all subscale and targeting for bulbar and respiratory subscales.ConclusionsThe self-administered ALSFRS-R is reliable, internally valid, and stable across sex, age, and language subgroups; however, it is recommended that the ALSFRS-R be scored by subscale. Future studies can look at revising and/or adding items to tackle misfit, redundancy, and ceiling effects.ImpactSelf-administered measures are simple to administer and inexpensive. The self-administered ALSFRS-R was found to be psychometrically sound and can be used as a tool to monitor disease progression and function in ALS.
The effects of CenteringPregnancy on maternal and infant health outcomes: a moderation analysis
Authors: Park Chul H , Driver Nichola , Richards Robert C , Ward Penny 
Published: August 2023

Abstract

Background
CenteringPregnancy (CP) has been expected to produce beneficial outcomes for women and their infants. However, previous studies paid little attention to testing variations in CP’s effects across women from different demographic groups. This study aimed to test how multiple demographic factors (obesity, race, ethnicity, marital status and socioeconomic status) moderate CP’s effects on health outcomes.

Methods
This study employed a quasi-experimental design. De-identified hospital birth data were collected from 216 CP participants and 1159 non-CP participants. We estimated the average treatment effect of CP on outcome variables as a baseline. Then we estimated the average marginal effect of CP by adding each of the moderating variables in regression adjustment models.

Results
CP produced salutary effects among those who were obese or overweight and unmarried as well as women with lower socioeconomic status. These salutary effects were also strengthened as maternal age increased. However, CP was ineffective for Hispanic/Latinx women.

Conclusions
CP produced more beneficial health outcomes for high-risk women such as obese, unmarried women and those with lower socioeconomic status. These are meaningful findings from a public health perspective.