bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lack of intergenerational reproductive conflict, rather than lack of inclusive fitness benefits, explains absence of post-reproductive lifespan in long-finned pilot whales
Authors: McCormack Jack L , Arbuckle Kevin , Fullard Karen , Amos William , Nichols Hazel J 
Published: August 2023

Abstract
Life-history theory suggests that individuals should reproduce until death, yet females of a small number of mammals live for a significant period after ceasing reproduction, a phenomenon known as post-reproductive lifespan. It is thought that the evolution of this trait is facilitated by increasing local relatedness throughout a female’s lifetime. This allows older females to gain inclusive fitness through helping their offspring (known as a mother effect) and/or grandoffspring (known as a grandmother effect), rather than gaining direct fitness through reproducing. However, older females may only benefit from stopping reproducing when their direct offspring compete with those of their daughters. Here, we investigate whether a lack of post-reproductive lifespan in long-finned pilot whales (Globicephala melas) results from minimal benefits incurred from the presence of older females, or from a lack of costs resulting from mother–daughter co-reproduction. Using microsatellite data, we conducted parentage analysis on individuals from 25 pods and find that younger females were more likely to have offspring if their mother was present in their pod, indicating that mothers may assist inexperienced daughters to reproduce. However, we found no evidence of reproductive conflict between co-reproducing mothers and daughters, indicating that females may be able to reproduce into old age while simultaneously aiding their daughters in reproduction. This highlights the importance of reproductive conflict in the evolution of a post-reproductive lifespan and demonstrates that mother and grandmother effects alone do not result in the evolution of a post-reproductive lifespan.
DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors
Authors: Muntoni Anna Paola , Pagnani Andrea 
Published: August 2023

Abstract

Summary
DCAlign is a new alignment method able to cope with the conservation and the co-evolution signals that characterize the columns of multiple sequence alignments of homologous sequences. However, the pre-processing steps required to align a candidate sequence are computationally demanding. We show in v1.0 how to dramatically reduce the overall computing time by including an empirical prior over an informative set of variables mirroring the presence of insertions and deletions.

Availability and implementation
DCAlign v1.0 is implemented in Julia and it is fully available at https://github.com/infernet-h2020/DCAlign.
Complications after open and laparoscopic right-sided colectomy with central lymphadenectomy for colon cancer: randomized controlled trial
Authors: Lygre Kristin B , Eide Geir E , Forsmo Havard M , Dicko Aly , Storli Kristian E , Pfeffer Frank 
Published: August 2023

Abstract

Background
A central lymphadenectomy in right-sided colon cancer involves dissection along the superior mesenteric axis, but the extent is debated due to a lack of consensus and the fear of major complications. This randomized controlled trial compared the rate of postoperative morbidity in patients undergoing laparoscopic versus open right-sided colectomy with central lymphadenectomy.

Methods
This open, prospective, randomized controlled trial compared patients operated on with open and laparoscopic right-sided colectomy (cStages I–III) with a central lymphadenectomy at two Norwegian institutions between October 2016 and December 2021. Dissections were conducted along the superior mesenteric vein in the laparoscopic group, and along the left anterior border of the superior mesenteric artery in the open group, both according to complete mesocolic excision principles. Surgery was standardized and performed by three experienced surgeons for each study group. The primary outcome of interest was to measure postoperative 30-day complications (Clavien–Dindo ≥ grade II).

Results
Of 273 eligible patients, 135 were randomized and 128 analysed (63 operated on with open and 65 using laparoscopic procedures). Postoperative complications occurred in 42.8 per cent of the patients treated with open and 38.4 per cent of the patients treated using laparoscopic surgery, P = 0.372. The incidence of Clavien–Dindo grade IIIb complications was 7.9 per cent in the open versus 4.6 per cent in the laparoscopic group, P = 0.341. There were no grade IV or V complications, and no re-operations due to anastomotic leakages. There was no significant difference in the mean(s.e.m.) number of removed lymph nodes (open versus laparoscopic respectively: 31.9(1.8) versus 29.3(1.3); P = 0.235).

Conclusion
There was no significant difference in complications between the two groups. Standardized oncologic right-sided colectomy with central lymphadenectomy along the mesenterial root was performed safely, both open and laparoscopic, with incidence of major complications ranging between 4.6 and 7.9 per cent and no re-operations for anastomotic leakage. Radicality in terms of lymphadenectomy was comparable between the two groups.
Registration number: NCT03776591 (http://www.clinicaltrials.gov).
Antibiotics on Demand: Advances in Asynchronous Telemedicine Call for Increased Antibiotic Surveillance
Authors: O’Toole Rebecca , Martinez Kathryn A , Rothberg Michael B , Diiorio Gillian , Stenehjem Edward A , Ward Kristina E , LaPlante Kerry L 
Published: August 2023

Abstract
The rapid growth of telehealth services has brought about direct-to-consumer telemedicine platforms, enabling patients to request antibiotics online without a virtual or face-to-face consultation. While telemedicine aims to enhance accessibility, this trend raises significant concerns regarding appropriate antimicrobial use and patient safety. In this viewpoint, we share our first-hand experience with 2 direct-to-consumer platforms, where we intentionally sought inappropriate antibiotic prescriptions for nonspecific symptoms strongly indicative of a viral upper respiratory infection. Despite the lack of clear necessity, requested antibiotic prescriptions were readily transmitted to our local pharmacy following a simple monetary transaction. The effortless acquisition of patient-selected antibiotics online, devoid of personal interactions or consultations, underscores the urgent imperative for intensified antimicrobial stewardship initiatives led by state and national public health organizations in telehealth settings. By augmenting oversight and regulation, we can ensure the responsible and judicious use of antibiotics, safeguard patient well-being, and preserve the efficacy of these vital medications.
Extracorporeal Membrane Oxygenation–Dependent Fulminant Melioidosis From Caspase 4 Mutation Reversed by Interferon Gamma Therapy
Authors: Amali Aseervatham Anusha , Ravikumar Sharada , Chew Wei Leong , Tan Zhaohong , Sam Qi Hui , Chen Kaiwen W , Boucher Dave , MacLaren Graeme , Chai Louis Yi Ann 
Published: August 2023

Abstract
We describe bedside-to-bench immunological and genetic elucidation of defective pyroptosis attributable to novel caspase 4 defect mediating pathogen-triggered inflammatory programmed cell death, in the setting of severe pneumonia and abscess-forming melioidosis in an overtly healthy host failing to clear Burkholderia pseudomallei infection, and how targeted adjunctive biological therapy led to a successful outcome.
Clinical Outcomes and Management of NAAT-Positive/Toxin-Negative Clostridioides difficile Infection: A Systematic Review and Meta-Analysis
Authors: Prosty Connor , Hanula Ryan , Katergi Khaled , Longtin Yves , McDonald Emily G , Lee Todd C 
Published: August 2023

Abstract

Background
Standalone nucleic acid amplification tests (NAATs) are frequently used to diagnose Clostridioides difficile infections (CDI), although they may be unable to distinguish colonization from disease. A 2-stage algorithm pairing NAATs with toxin immunoassays (Toxin) may improve specificity. We evaluated clinical outcomes of patients who were NAAT+/Toxin+ versus NAAT+/Toxin− and treated versus untreated NAAT+/Toxin− cases through systematic review and meta-analysis.

Methods
We searched EMBASE and MEDLINE from inception to April 1, 2023 for articles comparing CDI outcomes among symptomatic patients tested by NAAT and Toxin tests. The risk differences (RD) of all-cause mortality and CDI recurrence were computed by random effects meta-analysis between patients who were NAAT+/Toxin+ and NAAT+/Toxin−, as well as between patients who were NAAT+/Toxin− and treated or untreated.

Results
Twenty-six observational studies comprising 12 737 patients were included. The 30-day all-cause mortality was not significantly different between those who were NAAT+/Toxin+ (8.4%) and NAAT+/Toxin− (6.7%) (RD = 0.41%, 95% confidence interval [CI] = −.67, 1.49). Recurrence at 60 days was significantly higher among patients who were NAAT+/Toxin+ (19.8%) versus NAAT+/Toxin− (11.0%) (RD = 7.65%, 95% CI = 4.60, 10.71). Among treated compared to untreated NAAT+/Toxin- cases, the all-cause 30-day mortalities were 5.0% and 12.7%, respectively (RD = −7.45%, 95% CI = −12.29, −2.60), but 60-day recurrence was not significantly different (11.6% vs 7.0%, respectively; RD = 5.25%, 95% CI −1.71, 12.22).

Conclusions
Treatment of patients who were NAAT+/Toxin− was associated with reduced all-cause mortality but not recurrence. Although subject to the inherent limitations of observational studies, these results suggest that some patients who are NAAT+/Toxin− may benefit from treatment.
A Hybrid Solution For The Cold Start Problem In Recommendation
Authors: Jafri Syed Irteza Hussain , Ghazali Rozaida , Javid Irfan , Mazwin Mohmad Hassim Yana , Hayat Khan Mubashir 
Published: August 2023

Abstract
Recommender systems are becoming more and more significant in today’s digital world and in the modern economy. They make a substantial contribution to company operations by offering tailored advice and decreasing overwhelm. Collaborative filtering, being popular in the domain of recommendation, is used to offer recommendations to attract the target audience based on the feedback of people with comparable interests. This method has some limitations, such as a cold-start issue, which makes the system less effective in anticipating unknown objects. We provide a hybrid deep-learning-based strategy centered on a method to enrich user and item profiles to address the cold-start issue in the recommendation process using a collaborative filtering approach. We employ pretrained deep learning models to produce rich user and item feature vectors that aid in the creation of useful suggestions and handling of user and item cold-start issues. The creation of more precise and tailored similarity matrices is made possible by adding metadata to the extracted features of the user and item. The results of the experiment demonstrate that in terms of precision and rate coverage, the proposed method performs better than the baseline techniques.
Provider–patient experiences and HIV care utilization among people living with HIV who inject drugs in St. Petersburg, Russia
Authors: Raj Anita , Gnatienko Natalia , Cheng Debbie M , Blokhina Elena , Dey Arnab K , Wagman Jennifer A , Toussova Olga , Truong Ve , Rateau Lindsey , Lunze Karsten , Krupitsky Evgeny , Samet Jeffrey H 
Published: August 2023

Abstract
Providers’ disrespect and abuse of patients is a recognized but understudied issue affecting quality of care and likely affecting healthcare utilization. Little research has examined this issue among people living with HIV (PWH) who inject drugs, despite high stigmatization of this population. No research has examined this issue in the context of Russia. This study assesses patients’ reports of disrespect and abuse from providers as a barrier to healthcare and examines the association between these reports and HIV care outcomes.We conducted a cross-sectional analysis of the associations between disrespect/abuse from health providers as a barrier to care and the following HIV care outcomes: (i) anti-retroviral treatment (ART) uptake ever, (ii) past 6-month visit to HIV provider, and (iii) CD4 count. Participants (N = 221) were people living with HIV who injected drugs and were not on ART at enrollment.Two in five participants (42%) reported a history disrespect/abuse from a healthcare provider that they cited as a barrier to care. Those reporting this concern had lower odds of ever use of ART (adjusted odds ratio 0.46 [95% CI 0.22, 0.95]); we found no significant associations for the other HIV outcomes. We additionally found higher representation of women among those reporting prevalence of disrespect/abuse from provider as a barrier to care compared to those not reporting this barrier (58.1% versus 27.3%).Almost half of this sample of PWH who inject drugs report disrespect/abuse from a provider as a barrier to healthcare, and this is associated with lower odds of receipt of ART but not with other HIV outcomes studied. There is need for improved focus on quality of respectful and dignified care from providers for PWH who inject drugs, and such focus may improve ART uptake in Russia.
Contact semilattices
Authors: Lipparini Paolo 
Published: August 2023

Abstract
We devise exact conditions under which a join semilattice with a weak contact relation can be semilattice embedded into a Boolean algebra with an overlap contact relation, equivalently, into a distributive lattice with additive contact relation. A similar characterization is proved with respect to Boolean algebras and distributive lattices with weak contact, not necessarily additive, nor overlap.
Optimizing the strain engineering process for industrial-scale production of bio-based molecules
Authors: Abbate Eric , Andrion Jennifer , Apel Amanda , Biggs Matthew , Chaves Julie , Cheung Kristi , Ciesla Anthony , Clark-ElSayed Alia , Clay Michael , Contridas Riarose , Fox Richard , Hein Glenn , Held Dan , Horwitz Andrew , Jenkins Stefan , Kalbarczyk Karolina , Krishnamurthy Nandini , Mirsiaghi Mona , Noon Katherine , Rowe Mike , Shepherd Tyson , Tarasava Katia , Tarasow Theodore M , Thacker Drew , Villa Gladys , Yerramsetty Krishna 
Published: August 2023

Abstract
Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design–Build–Test–Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.
Production of S-methyl-methionine using engineered Saccharomyces cerevisiae sake K6
Authors: Lee Jun-Min , Park Min-Ho , Park Bu-Soo , Oh Min-Kyu 
Published: August 2023

Abstract

S-methyl-methionine (SMM), also known as vitamin U, is an important food supplement produced by various plants. In this study, we attempted to produce it in an engineered microorganism, Saccharomyces cerevisiae, by introducing an MMT gene encoding a methionine S-methyltransferase from Arabidopsis thaliana. The S. cerevisiae sake K6 strain, which is a Generally Recognized as Safe (GRAS) strain, was chosen as the host because it produces a significant amount of S-adenosylmethionine (SAM), a precursor of SMM. To increase SMM production in the host, MHT1 and SAM4 genes encoding homocysteine S-methyltransferase were knocked out to prevent SMM degradation. Additionally, MMP1, which encodes S-methyl-methionine permease, was deleted to prevent SMM from being imported into the cell. Finally, ACS2 gene encoding acetyl-CoA synthase was overexpressed, and MLS1 gene encoding malate synthase was deleted to increase SAM availability. Using the engineered strain, 1.92 g/L of SMM was produced by fed-batch fermentation.

One-Sentence Summary
Introducing a plant-derived MMT gene encoding methionine S-methyltransferase into engineered Saccharomyces cerevisiae sake K6 allowed microbial production of S-methyl-methionine (SMM).
In-office dispensing of oral targeted agents by urology practices in men with advanced prostate cancer
Authors: Hill Dawson , Kaufman Samuel R , Oerline Mary K , Faraj Kassem , Caram Megan E V , Shahinian Vahakn B , Hollenbeck Brent K , Maganty Avinash 
Published: August 2023

Abstract

Background
Management of men with advanced prostate cancer has evolved to include urologists, made possible by oral targeted agents (eg, abiraterone or enzalutamide) that can be dispensed directly to patients in the office. We sought to investigate whether this increasingly common model improves access to these agents, especially for Black men who are historically undertreated.

Methods
We used 20% national Medicare data to perform a retrospective cohort study of men with advanced prostate cancer from 2011 through 2019, managed by urology practices with and without in-office dispensing. Using a difference-in-difference framework, generalized estimating equations were used to measure the effect of in-office dispensing on prescriptions for abiraterone and/or enzalutamide, adjusting for differences between patients, including race.

Results
New prescription fills for oral targeted agents increased after the adoption of in-office dispensing (+4.4%, 95% confidence interval [CI] = 3.4% to 5.4%) relative to that for men managed by practices without dispensing (+2.4%, 95% CI = 1.4% to 3.4%). The increase in the postintervention period (difference-in-difference estimate) was 2% higher (95% CI = 0.6% to 3.4%) for men managed by practices adopting dispensing relative to men managed by practices without dispensing. The effect was strongest for practices adopting dispensing in 2015 (difference-in-difference estimate: +4.2%, 95% CI = 2.3% to 6.2%). The effect of dispensing adoption did not differ by race.

Conclusion
Adoption of in-office dispensing by urology practices increased prescription fills for oral targeted agents in men with advanced prostate cancer. This model of delivery may improve access to this important class of medications.
Flexible marked spatio-temporal point processes with applications to event sequences from association football
Authors: Narayanan Santhosh , Kosmidis Ioannis , Dellaportas Petros 
Published: August 2023

AbstractWe develop a new family of marked point processes by focusing the characteristic properties of marked Hawkes processes exclusively on the space of marks, allowing a separate model specification for the occurrence times. We develop a Bayesian framework for their inference and prediction that can naturally accommodate covariate information to drive cross-excitations, offering broad flexibility for real-world applications. The framework is applied to in-game event sequences from association football, resulting in inferences about previously unquantified characteristics of game dynamics, extraction of event-specific team abilities and predictions for event occurrences, such as goals or fouls in a specified interval of time.
Physical properties of methanol (CH3OH) ice as a function of temperature: density, infrared band strengths, and crystallization
Authors: Carrascosa H , Satorre M Á , Escribano B , Martín-Doménech R , Muñoz Caro G M 
Published: August 2023

ABSTRACT
The presence of methanol among the common ice components in interstellar clouds and protostellar envelopes has been confirmed by the James Webb Space Telescope (McClure et al. 2023). Methanol is often detected in the gas phase towards lines of sight shielded from UV radiation. We measured the volumetric density of methanol ice grown under simulated interstellar conditions and the infrared spectroscopy at different deposition temperatures and during the warm-up. The IR band strengths are provided, and the experimental spectra are compared to those computed with a model. The transition from amorphous to crystalline methanol ice was also explored. Finally, we propose new observations of methanol ice at high resolution to probe the methanol ice structure.
Steady states of the Parker instability
Authors: Tharakkal Devika , Shukurov Anvar , Gent Frederick A , Sarson Graeme R , Snodin Andrew P , Rodrigues Luiz Felippe S 
Published: August 2023

ABSTRACT
We study the linear properties, non-linear saturation, and a steady, strongly non-linear state of the Parker instability in galaxies. We consider magnetic buoyancy and its consequences with and without cosmic rays. Cosmic rays are described using the fluid approximation with anisotropic, non-Fickian diffusion. To avoid unphysical constraints on the instability (such as boundary conditions often used to specify an unstable background state), non-ideal magnetohydrodynamic equations are solved for deviations from a background state representing an unstable magnetohydrostatic equilibrium. We consider isothermal gas and neglect rotation. The linear evolution of the instability is in broad agreement with earlier analytical and numerical models; but we show that most of the simplifying assumptions of the earlier work do not hold, such that they provide only a qualitative rather than quantitative picture. In its non-linear stage the instability has significantly altered the background state from its initial state. Vertical distributions of both magnetic field and cosmic rays are much wider, the gas layer is thinner, and the energy densities of both magnetic field and cosmic rays are much reduced. The spatial structure of the non-linear state differs from that of any linear modes. A transient gas outflow is driven by the weakly non-linear instability as it approaches saturation.