bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of divergence time and comparative plastid genomics of Orchis species (Orchidaceae)
Authors: Calevo Jacopo , Viruel Juan , Adamo Martino , Bersweden Leif , Gargiulo Roberta , Cowan Robyn S , Fay Michael F 
Published: August 2024

Abstract
Low-coverage sequencing in plants allows whole plastomes to be obtained that can be used to investigate phylogenetic relationships among groups. The genus Orchis (c. 20 species), is usually divided into Orchis subgenera Orchis and Masculae. These subgenera are composed of three (Anthropophorae, Italicae, and Orchis) and four (Masculae, Provinciales, Pusillae, and Robustocalcare) sections, respectively. In this study, we used genome-skimming data to assemble the plastid genomes of 11 species (15 accessions) of Orchis, representing six out of the seven sections, from which we constructed a dated phylogenetic tree. Results suggest that the divergence between the subgenera occurred c. 10.53 Mya, whereas the main separation of the sections is dated between 6.53 and 3.48 Mya. Furthermore, we found 206 (in O. anthropophora) to 230 (in O. provincialis) microsatellite regions in the assembled plastomes, which could be used to design specific primers for further population genetics and phylogenetic studies and, ultimately, inform conservation efforts. The plastome data here presented represent a new contribution to the molecular systematics of the genus, and they can be used to further explore infrageneric and infrascpecific molecular variation in Orchis.
Cognitive outcomes following unilateral magnetic resonance–guided focused ultrasound thalamotomy for essential tremor: findings from two cohorts
Authors: Petersen Julie , McGough Josh , Gopinath Georgia , Scantlebury Nadia , Tripathi Richa , Brandmeir Cheryl , Boshmaf Silina Z , Brandmeir Nicholas J , Sewell Isabella J , Konrad Peter E , Abrahao Agessandro , Murray Ann , Lam Benjamin , Ranjan Manish , Hamani Clement , Frey Jessica , Rohringer Camryn , McSweeney Melissa , Mahoney James J , Schwartz Michael L , Rezai Ali , Lipsman Nir , Scarisbrick David M , Rabin Jennifer S 
Published: August 2024

Abstract
Magnetic resonance–guided, focused ultrasound thalamotomy is a neurosurgical treatment for refractory essential tremor. This study examined cognitive outcomes following unilateral magnetic resonance–guided, focused ultrasound thalamotomy, targeting the ventral intermediate nucleus of the thalamus for essential tremor. The research was conducted at two sites: Sunnybrook Research Institute in Toronto, Canada, and West Virginia University School of Medicine Rockefeller Neuroscience Institute in West Virginia, USA. The study focused on cognitive changes at both the group and individual levels. Patients with refractory essential tremor completed cognitive testing before and after magnetic resonance–guided, focused ultrasound thalamotomy at both sites. The cognitive testing assessed domains of attention, processing speed, working memory, executive function, language and learning/memory. Postoperative changes in cognition were examined using paired t-tests and Wilcoxon signed-rank tests, as appropriate. Reliable change indices were calculated to assess clinically significant changes at the individual level. A total of 33 patients from Toronto and 22 patients from West Virginia were included. Following magnetic resonance–guided, focused ultrasound thalamotomy, there was a significant reduction in tremor severity in both cohorts. At the group level, there were no significant declines in postoperative cognitive performance in either cohort. The reliable change analyses revealed some variability at the individual level, with most patients maintaining stable performance or showing improvement. Taken together, the results from these two independent cohorts demonstrate that unilateral magnetic resonance–guided, focused ultrasound thalamotomy significantly reduces tremor severity without negatively impacting cognition at both the group and individual levels, highlighting the cognitive safety of magnetic resonance–guided focused ultrasound thalamotomy for essential tremor.
Effective incorporation of Ti atom into TS-1 zeolite assisted with oxalic acid additive
Authors: Techasarintr Piyapatch , Yin Liu , Wang Yong , Xiao Peipei , Bekhti Samya , Kondo Junko N , Yokoi Toshiyuki 
Published: August 2024

Abstract
The effect of introducing oxalic acid into the mother gel of TS-1 zeolite on the crystallization behavior and physiochemical properties was investigated. The addition of oxalic acid with a buffering action significantly accelerated the crystallization process of TS-1 while simultaneously inhibiting the formation of anatase. The resultant TS-1 zeolites displayed enhanced performance in catalyzing the epoxidation of 1-hexene with H2O2 as an oxidant.
Association of baseline and changes in health-related quality of life with mortality following myocardial infarction: multicentre longitudinal linked cohort study
Authors: Dondo Tatendashe B , Munyombwe Theresa , Hurdus Ben , Aktaa Suleman , Hall Marlous , Soloveva Anzhela , Nadarajah Ramesh , Haris Mohammad , West Robert M , Hall Alistair S , Gale Chris P 
Published: August 2024

Abstract

Background
Health-related quality of life (HRQoL) for patients following myocardial infarction (MI) is frequently impaired. We investigated the association of baseline and changes in HRQoL with mortality following MI.

Methods and results
Nationwide longitudinal study of 9474 patients admitted to 77 hospitals in England as part of the Evaluation of the Methods and Management of Acute Coronary Events study. Self-reported HRQoL was collected using EuroQol EQ-5D-3L during hospitalization and at 1, 6, and 12 months following discharge. The data was analysed using flexible parametric and multilevel survival models. Of 9474 individuals with MI, 2360 (25%) were women and 2135 (22.5%) died during the 9-year follow-up period. HRQoL improved over 12 months (baseline mean, mean increase: EQ-5D 0.76, 0.003 per month; EQ-VAS 69.0, 0.5 per month). At baseline, better HRQoL was inversely associated with mortality [Hazard ratio (HR) 0.55, 95% CI 0.47–0.63], and problems with self-care (HR 1.73, 1.56–1.92), mobility (1.65, 1.50–1.81), usual activities (1.34, 1.23–1.47), and pain/discomfort (1.34, 1.22–1.46) were associated with increased mortality. Deterioration in mobility, pain/discomfort, usual activities, and self-care over 12 months were associated with increased mortality (HR 1.43, 95% CI 1.31–1.58; 1.21, 1.11–1.32; 1.20, 1.10–1.32; 1.44, 1.30–1.59, respectively).

Conclusion
After MI, poor HRQoL at baseline, its dimensions, and deterioration over time are associated with an increased risk of mortality. Measuring HRQoL in routine clinical practice after MI could identify at-risk groups for interventions to improve prognosis.
Sex-related differences in severe native valvular heart disease: the ESC-EORP Valvular Heart Disease II survey
Authors: Mascherbauer Julia , Kammerlander Andreas , Nitsche Christian , Bax Jeroen , Delgado Victoria , Evangelista Arturo , Laroche Cecile , Maggioni Aldo Pietro , Magne Julien , Vahanian Alec , Iung Bernard 
Published: August 2024

Abstract

Background and Aims
To assess sex differences in disease characteristics and treatment of patients with severe native valvular heart disease (VHD) included in the VHD II EURObservational Research Programme.

Methods
A total of 5219 patients were enrolled in 208 European and North African centres and followed for 6 months [41.2% aortic stenosis (AS), 5.3% aortic regurgitation (AR), 4.5% mitral stenosis (MS), 21.3% mitral regurgitation (MR), 2.7% isolated right-sided VHD, 24.9% multiple left-sided VHD]. Indications for intervention were considered concordant if corresponding to class I recommendations specified in the 2012 ESC or 2014 AHA/ACC VHD guidelines.

Results
Overall, women were older, more symptomatic, and presented with a higher EuroSCORE II. Bicuspid aortic valve and AR were more prevalent among men while mitral disease, concomitant tricuspid regurgitation (TR), and AS above age 65 were more prevalent among women. On multivariable regression analysis, concordance with recommended treatment was significantly poorer in women with MS and primary MR (both P &lt; .001). Age, patient refusal, and decline of symptoms after conservative treatment were reported significantly more often as reasons to withhold the intervention in females. Concomitant tricuspid intervention was performed at a similar rate in both sexes although prevalence of significant TR was significantly higher in women. In-hospital and 6-month survival did not differ between sexes.

Conclusions
(i) Valvular heart disease subtype varied between sexes; (ii) concordance with recommended intervention for MS and primary MR was significantly lower for women; and (iii) survival of men and women was similar at 6 months.
Automated measurement of teleseismic P-, SH- and SV-wave arrival times using autoregressive prediction and the instantaneous phase of multicomponent waveforms
Authors: Stampa J , Eckel F , Keers H , Lebedev S , Meier T ,   AlpArray and SWATH-D Working Groups
Published: August 2024

SUMMARY
A new automated algorithm for picking the arrival times of the global P-, SH- and SV-wave phases from multi-component seismic waveform data is presented. This picker is based on a sequential approach using autoregressive prediction of the filtered waveform in a sliding time window, the Akaike Information Criterion and the Hilbert transform of the original waveform. The quality of the individual picks is computed by combining signal-to-noise ratios and higher order statistics into a single measure. Synthetic tests are used to find values for high and low quality thresholds. The algorithm is applied to a global data set of waveforms from teleseismic events with magnitude 6 or higher that occurred between 1990 and 2019. This resulted in approximately 4 million P-phase arrival times as well as approximately 3 million SH- and SV-phase arrival times each. These automatic picks are compared to approximately $830\, 000$ manual P-picks as well as approximately $70\, 000$ manual S-picks from the ISC-EHB catalogue. An upper bound for the picking errors of the automatic picks is estimated by using high quality picks of neighbouring stations. This upper bound is found to be 0.55 s for the P-picks and 4.3 s for the S-picks. If only high quality picks are considered, this represents 50 per cent of the P-picks and 25 per cent of the S-picks, then these errors decrease to 0.35 s for the P-picks and 1.5 s for the S-picks, respectively. As a by-product of the picking, the dominant periods of the arriving signals are determined as well.
Model-based inference of a dual role for HOPS in regulating guard cell vacuole fusion
Authors: Hodgens Charles , Flaherty D T , Pullen Anne-Marie , Khan Imran , English Nolan J , Gillan Lydia , Rojas-Pierce Marcela , Akpa Belinda S 
Published: August 2024

Abstract
Guard cell movements depend, in part, on the remodelling of vacuoles from a highly fragmented state to a fused morphology during stomata opening. Indeed, full opening of plant stomata requires vacuole fusion to occur. Fusion of vacuole membranes is a highly conserved process in eukaryotes, with key roles played by two multi-subunit complexes: HOPS (homotypic fusion and vacuolar protein sorting) and SNARE (soluble NSF attachment protein receptor). HOPS is a vacuole tethering factor that is thought to chaperone SNAREs from apposing vacuole membranes into a fusion-competent complex capable of rearranging membranes. In plants, recruitment of HOPS subunits to the tonoplast has been shown to require the presence of the phosphoinositide phosphatidylinositol 3-phosphate. However, chemically depleting this lipid induces vacuole fusion. To resolve this counter-intuitive observation regarding the role of HOPS in regulating plant vacuole morphology, we defined a quantitative model of vacuole fusion dynamics and used it to generate testable predictions about HOPS-SNARE interactions. We derived our model by using simulation-based inference to integrate prior knowledge about molecular interactions with limited, qualitative observations of emergent vacuole phenotypes. By constraining the model parameters to yield the emergent outcomes observed for stoma opening—as induced by two distinct chemical treatments—we predicted a dual role for HOPS and identified a stalled form of the SNARE complex that differs from phenomena reported in yeast. We predict that HOPS has contradictory actions at different points in the fusion signalling pathway, promoting the formation of SNARE complexes, but limiting their activity.
Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea
Authors: Thomy Julie , Sanchez Frederic , Prioux Camille , Yau Sheree , Xu Yangbing , Mak Julian , Sun Ruixian , Piganeau Gwenael , Yung Charmaine C M 
Published: August 2024

Abstract
Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host–virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus–host interactions in marine environments.
Real-world treatment costs of first-line treatment for metastatic colorectal cancer: a survey of the JCOG colorectal cancer study group
Authors: Takashima Atsuo , Ishiguro Megumi , Sasaki Keita , Machida Ryunosuke , Nagashima Fumio , Imaizumi Jun , Hamaguchi Tetsuya , Yamamoto Yoshiyuki , Masuishi Toshiki , Asayama Masako , Ueno Hideki , Shinozaki Katsunori , Kudo Toshihiro , Machida Nozomu , Matsuoka Hiroshi , Ishida Hideyuki , Yamaguchi Toshifumi , Nogami Hitoshi , Yamada Takeshi , Takegawa Naoki , Kito Yosuke , Tonoike Yuko , Sawada Ryoichi , Tsukamoto Shunsuke , Kanemitsu Yukihide ,   Colorectal Cancer Study Group (CCSG) of the Japan Clinical Oncology Group (JCOG)
Published: August 2024

Abstract

Background
Although treatment outcomes for metastatic colorectal cancer (mCRC) have dramatically improved over the past few decades, drug costs have also significantly increased. This study aimed to investigate which first-line treatment regimens for mCRC are actually used (frequency) in Japanese practice and at what cost.

Methods
We collected data on patients with mCRC who received first-line treatment at 37 institutions of the Japan Clinical Oncology Group Colorectal Cancer Study Group from July 2021 to June 2022, and calculated the cost of regimens. The cost per month of each regimen was estimated based on standard usage, assuming a patient with a weight of 70 kg and a body surface area of 1.8 m2. We categorized the regimens into very high-cost (≥1 000 000 Japanese yen [JPY]/month), high-cost (≥500 000 JPY/month), and others (&lt;500 000 JPY/month).

Results
The study included 1880 participants, 24% of whom were ≥ 75 years. Molecular targeted containing regimens were received by 78% of the patients. The most frequently used regimen was the doublet regimen (fluoropyrimidine with either oxaliplatin or irinotecan) plus bevacizumab (43%), followed by doublet plus cetuximab or panitumumab (21%). The cost of molecular targeted drugs-containing regimens (ranging from 85 406 to 843 602 JPY/month) is much higher than that of only cytotoxic drug regimens (ranging from 17 672 to 51 004 JPY/month). About 16% received high-cost treatments that included panitumumab-containing regimens and pembrolizumab (17% of patients aged ≤74 years and 11% of patients aged ≥75 years).

Conclusion
About 16% of mCRC patients received first-line treatment with regimens costing &gt;500 000JPY/month, and molecular targeted drugs being the main drivers of cost.
Ceftazidime-Avibactam Treatment for Carbapenemase-Producing Enterobacterales in a South African Children’s Hospital
Authors: Tootla Hafsah Deepa , Van Niekerk Saamiya , Gumede Thandolwethu , Nuttall James , Salie Shamiel , Eley Brian 
Published: August 2024

Abstract
This study describes ceftazidime-avibactam use in 17 young children from a resource-constrained country, where intra-abdominal infection was common. All-cause mortality was 53%. Earlier initiation, dose optimization, recording infusion times, and reviewing the need for additional antibiotics were identified as easy-to-implement-antimicrobial-stewardship interventions.
Stigma and Barriers to Care, Online Mental Health Tools, and Suicidality in California’s Veterans
Authors: Hill Lydia , Inagaki Tristen K , Schmied Emily A , Vaughn Allison A 
Published: August 2024

ABSTRACT

Introduction
Veterans have a higher national suicide rate than non-veterans (31.6 versus 18.0 per 100,000). Psychotherapy and other treatments are effective at reducing suicidality, yet stigma and barriers to care reduce willingness to seek help. For veterans who do seek help, they are often undertreated leaving them still in need of help. Online mental health tools (OMHTs) provide another option for obtaining help; however, there is limited research regarding the relationship between stigma and barriers to care, OMHT use, and suicidality. We hypothesized that stigma and barriers are related to higher likelihood of OMHT use and OMHT use is related to lower likelihood of suicidality.

Materials and Methods
The California Health Interview Survey is a population-based state health survey that collects data over a 2-year cycle via web and phone interviews. The sample was 4,435 veterans (91% male, 75% White, and average age 67 years old). The study was institutional review board exempt because data storage and analyses were done at the Data Access Center at University of California—Los Angeles.

Results
Logistic regressions showed endorsing stigma and barriers indicated a higher likelihood of using OMHTs. Additionally, use of OMHTs was unexpectedly associated with greater suicidality.

Conclusions
Findings reinforce the need for research aimed at identifying ways to reduce stigma and barriers toward seeking help. Online mental health tools are a viable option for individuals experiencing stigma and barriers and for individuals who previously experienced suicidality.
A review of lobomycosis and lobomycosis-like skin disease in cetaceans worldwide, with new data from the Gulf of Guayaquil, Ecuador
Authors: Van Bressem Marie-Françoise , Félix Fernando , Van Waerebeek Koen 
Published: August 2024

Abstract
Lobomycosis, also called paracoccidioidomycosis ceti, is a chronic mycotic cutaneous disease affecting odontocetes. Lobomycosis-like disease (LLD) has a clinical presentation consistent with lobomycosis but lacks a histological and molecular diagnosis. We review the literature on lobomycosis aetiology, clinical signs and pathogenesis, species affected and geographic distribution and examine the factors influencing the presence, transmission and prevalence of the disease, to better understand its ecology. In addition, we provide unpublished information on LLD in two common bottlenose dolphin (Tursiops truncatus) communities inhabiting the Gulf of Guayaquil, Ecuador. Lobomycosis and LLD occur in Delphinidae from the Atlantic, Pacific, and Indian Oceans between 33°N and 35°S. Primary risk factors include habitat, sex, age, sociality, and pollution. In dolphins from the Americas and Japan, lobomycosis is caused by Paracoccidioides ceti, family Ajellomycetaceae. The disease is characterized by cutaneous granulomatous lesions that may occur anywhere on the body, grow to large size, and may ulcerate. Histologically, the lesions consist of acanthosis and histiocytic granulomas between the skin and subcutaneous tissues, with inflammatory changes that extend deep into the dermis. Multiple yeast cells with a double refringent layer stained positive using Gomori-Grocott methenamine silver in the dermis of a T. truncatus from Ecuador diagnosed with LLD since 2011, a first record for the Southeast Pacific. Injuries may enable the entry of P. ceti into the dermis while skin contact likely favours transmission, putting males at higher risk than females. Lobomycosis and LLD may have a negative impact on small communities already threatened by anthropogenic factors.
Within-subject comparison of near-death and psychedelic experiences: acute and enduring effects
Authors: Martial Charlotte , Carhart-Harris Robin , Timmermann Christopher 
Published: August 2024

Abstract
Mystical-like states of consciousness may arise through means such as psychedelic substances, but may also occur unexpectedly during near-death experiences (NDEs). So far, research studies comparing experiences induced by serotonergic psychedelics and NDEs, along with their enduring effects, have employed between-subject designs, limiting direct comparisons. We present results from an online survey exploring the phenomenology, attribution of reality, psychological insights, and enduring effects of NDEs and psychedelic experiences (PEs) in individuals who have experienced both at some point during their lifetime. We used frequentist and Bayesian analyses to determine significant differences and overlaps (evidence for null hypotheses) between the two. Thirty-one adults reported having experienced both an NDE (i.e. NDE-C scale total score ≥27/80) and a PE (intake of lysergic acid diethylamide, psilocybin/mushrooms, ayahuasca, N,N-dimethyltryptamine, or mescaline). Results revealed areas of overlap between both experiences for phenomenology, attribution of reality, psychological insights, and enduring effects. A finer-grained analysis of the phenomenology revealed a significant overlap in mystical-like effects, while low-level phenomena (sensory effects) were significantly different, with NDEs displaying higher scores of disembodiment and PEs higher scores of visual imagery. This suggests psychedelics as a useful model for studying mystical-like effects induced by NDEs, while highlighting distinctions in sensory experiences.