bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomics and Pervasive Genome-Wide Phylogenetic Discordance Among Fin Whales (Balaenoptera physalus)
Authors: Furni Fabricio , Secchi Eduardo R , Speller Camilla , DenDanto Daniel , Ramp Christian , Larsen Finn , Mizroch Sally , Robbins Jooke , Sears Richard , Urbán R Jorge , Bérubé Martine , Palsbøll Per J 
Published: August 2024

Abstract
Phylogenomics has the power to uncover complex phylogenetic scenarios across the genome. In most cases, no single topology is reflected across the entire genome as the phylogenetic signal differs among genomic regions due to processes, such as introgression and incomplete lineage sorting. Baleen whales are among the largest vertebrates on Earth with a high dispersal potential in a relatively unrestricted habitat, the oceans. The fin whale (Balaenoptera physalus) is one of the most enigmatic baleen whale species, currently divided into four subspecies. It has been a matter of debate whether phylogeographic patterns explain taxonomic variation in fin whales. Here we present a chromosome-level whole genome analysis of the phylogenetic relationships among fin whales from multiple ocean basins. First, we estimated concatenated and consensus phylogenies for both the mitochondrial and nuclear genomes. The consensus phylogenies based upon the autosomal genome uncovered monophyletic clades associated with each ocean basin, aligning with the current understanding of subspecies division. Nevertheless, discordances were detected in the phylogenies based on the Y chromosome, mitochondrial genome, autosomal genome and X chromosome. Furthermore, we detected signs of introgression and pervasive phylogenetic discordance across the autosomal genome. This complex phylogenetic scenario could be explained by a puzzle of introgressive events, not yet documented in fin whales. Similarly, incomplete lineage sorting and low phylogenetic signal could lead to such phylogenetic discordances. Our study reinforces the pitfalls of relying on concatenated or single locus phylogenies to determine taxonomic relationships below the species level by illustrating the underlying nuances that some phylogenetic approaches may fail to capture. We emphasize the significance of accurate taxonomic delineation in fin whales by exploring crucial information revealed through genome-wide assessments.
Mistletoe-induced carbon, water and nutrient imbalances are imprinted on tree rings
Authors: González de Andrés Ester , Gazol Antonio , Querejeta José Ignacio , Colangelo Michele , Camarero J Julio 
Published: August 2024

Abstract
Mistletoes are xylem-tapping hemiparasites that rely on their hosts for water and nutrient uptake. Thus, they impair tree performance in the face of environmental stress via altering the carbon and water relations and nutritional status of trees. To improve our understanding of physiological responses to mistletoe and ongoing climate change, we investigated radial growth, stable carbon and oxygen isotopic signals, and elemental composition of tree rings in silver fir (Abies alba Mill.) and Scots pine (Pinus sylvestris L.) forests infested with Viscum album L. We compared temporal series (1990–2020) of basal area increment (BAI), intrinsic water-use efficiency (iWUE), oxygen isotope composition (δ18O), nutrient concentrations and stoichiometric ratios between non-infested (NI) and severely infested (SI) fir and pine trees from populations located close to the xeric distribution limit of the species in north-eastern Spain. The SI trees showed historically higher growth, but the BAI trend was negative for more than three decades before 2020 and their growth rates became significantly lower than those of NI trees by the mid-2010s. Mistletoe infestation was related to an enhanced sensitivity of radial growth to vapour pressure deficit (atmospheric drought). The SI trees showed less pronounced iWUE increases (fir) and lower iWUE values (pine) than NI trees. The lower tree-ring δ18O values of SI trees may be the result of several superimposed effects operating simultaneously, including leaf-level evaporative enrichment, source water isotopic signals, and anatomical and phenological differences. We observed a deterioration of potassium (K) nutrition in tree-ring wood of both species in SI trees, along with accumulation of manganese (Mn). We suggest that such nutritional patterns are driven by the indirect effect of mistletoe-induced drought stress, particularly in pine. The combined analyses of different physiological indicators imprinted on tree rings provided evidence of the progressive onset of carbon, water and nutrient imbalances in mistletoe-infested conifers inhabiting seasonally dry regions.
Biogeography and phylogeny of the scavenging amphipod genus Valettietta (Amphipoda: Alicelloidea), with descriptions of two new species from the abyssal Pacific Ocean
Authors: Stewart Eva C D , Bribiesca-Contreras Guadalupe , Weston Johanna N J , Glover Adrian G , Horton Tammy 
Published: August 2024

Abstract
Valettietta Lincoln & Thurston, 1983 (Amphipoda: Alicelloidea) is an infrequently sampled genus of scavenging amphipod, with a known bathymetric range from 17–5467 m encompassing a variety of habitats from anchialine caves to abyssal plains. Molecular systematics studies have uncovered cryptic speciation in specimens collected from the abyssal Pacific, highlighting uncertainty in the description of Valettietta anacantha (Birstein & Vinogradov, 1963). Here, we apply an integrative taxonomic approach and describe two new species, Valettietta trottarum sp. nov. and Valettietta synchlys sp. nov., collected at abyssal depths in the Clarion-Clipperton Zone, Pacific Ocean. Both species can be distinguished by characters of the gnathopods, uropod 3, and the inner plate of the maxilliped. Further, molecular phylogenetic analyses of two mitochondrial (16S rDNA and COI) and two nuclear (Histone 3 and 28S rRNA) regions found both new species to form well-supported clades and allowed us to re-identify previously published records based on genetic species delimitation. The biogeography of Valettietta is discussed in light of these re-evaluated records, and a new taxonomic key to the genus is provided. These new taxa highlight the strength of applying an integrated taxonomic approach to uncover biodiversity, which is critical in regions being explored for potential industrial purposes.
Microbiome and metabolome analyses indicate variations in the gut microbiota that disrupt regulation of appetite
Authors: Qi Renli , Zhang Bin , Qiu Xiaoyu , Liu Xin , Bao Shili , Wang Jing , Wang Qi , Yang Yong , Yang Haili , Liu Zuohua 
Published: August 2024

AbstractThe mechanism connecting gut microbiota to appetite regulation is not yet fully understood. This study identifies specific microbial community and metabolites that may influence appetite regulation. In the initial phase of the study, mice were administered a broad‐spectrum antibiotic cocktail (ABX) for 10 days. The treatment significantly reduced gut microbes and disrupted the metabolism of arginine and tryptophan. Consequently, ABX‐treated mice demonstrated a notable reduction in feed consumption. The hypothalamic expression levels of CART and POMC, two key anorexigenic factors, were significantly increased, while orexigenic factors, such as NPY and AGRP, were decreased. Notably, the levels of appetite‐suppressing hormone cholecystokinin in the blood were significantly elevated. In the second phase, control mice were maintained, while the ABX‐treated mice received saline, probiotics, and short‐chain fatty acids (SCFAs) for an additional 10 days to restore their gut microbiota. The microbiota reconstructed by probiotic and SCFA treatments were quite similar, while microbiota of the naturally recovering mice demonstrated greater resemblance to that of the control mice. Notably, the abundance of Akkermansia and Bacteroides genera significantly increased in the reconstructed microbiota. Moreover, microbiota reconstruction corrected the disrupted arginine and tryptophan metabolism and the abnormal peripheral hormone levels caused by ABX treatment. Among the groups, SCFA‐treated mice had the highest feed intake and NPY expression. Our findings indicate that gut microbes, especially Akkermansia, regulate arginine and tryptophan metabolism, thereby influencing appetite through the microbe‐gut‐brain axis.
Medical management of endometriosis
Authors: Alonso Anais , Gunther Kate , Maheux-Lacroix Sarah , Abbott Jason 
Published: August 2024

Purpose of review
While laparoscopic surgery plays a key role in the management of endometriosis, symptoms commonly recur, and repeat surgery comes with increased risk. Medical management, including hormonal and nonhormonal treatment, is vital in managing painful symptoms. This review summarizes recent evidence regarding various medical management options available to treat pelvic pain associated with endometriosis.

Recent findings
Efficacy of dienogest vs. combined oral contraceptive on pain associated with endometriosis: randomized clinical trial.
Once daily oral relugolix combination therapy vs. placebo in patients with endometriosis-associated pain: two replicate phase 3, randomised, double-blind, studies (SPIRIT 1 and 2).
A randomized, double-blind, placebo-controlled pilot study of the comparative effects of dienogest and the combined oral contraceptive pill in women with endometriosis.
Two-year efficacy and safety of relugolix combination therapy in women with endometriosis-associated pain: SPIRIT open-label extension study.

Summary
All symptomatic women with suspected endometriosis who are not desiring immediate fertility can be offered suppressive treatment to control symptoms and slow the progression of disease. First-line treatments include the combined oral contraceptive pill and progestogens. Second-line treatments include gonadotropin-releasing hormone agonists and antagonists but current guidelines recommend that these should be reserved for people whose symptoms fail to be controlled by first-line agents. The use of complementary and alternative medicines is also increasing in both volume and number of agents used.
The Utility of Preoperative Phenylephrine Testing in Müller Muscle Conjunctival Resection Surgery for Involutional Ptosis
Authors: Saffari Persiana S. , Dallalzadeh Liane O. , Kikkawa Don O. , Korn Bobby S. , Ramesh Sathyadeepak , Shinder Roman , Rootman Daniel B. 
Published: August 2024

Purpose:
Phenylephrine testing prior to Müller muscle conjunctival resection has traditionally been used to predict postoperative outcomes. The purpose of this study is to determine if preoperative phenylephrine testing impacts postoperative changes in eyelid position.

Methods:
In this multicenter cross-sectional cohort study, 270 eyelids of participants with involutional ptosis and levator function >12 mm who underwent Müller muscle conjunctival resection were divided into 2 comparison groups. Participants who had preoperative phenylephrine testing served as the control group and those who did not were the study group. The primary outcome measure was postoperative marginal reflex distance from the upper eyelid margin (marginal reflex distance 1 [MRD1]) at the latest follow-up visit. Secondary outcomes included change in MRD1, reoperation rate, and predictive capacity of preoperative phenylephrine testing.

Results:
Of the 270 eyelids that underwent Müller muscle conjunctival resection, 116 eyelids served as controls and 154 were in the study group. Mean age of participants was 62.6 years. Levator function, resection length, preoperative MRD1, change in MRD1, and latest postoperative MRD1 measures when compared in the control and study groups demonstrated no significance (p > 0.05) via 2-tailed t-test. Postoperative MRD1 was correctly predicted within 1 mm for 60.2% of eyelids that underwent preoperative phenylephrine testing.

Conclusions:
Preoperative phenylephrine testing does not significantly predict postoperative eyelid elevation following Müller muscle conjunctival resection. Surgeons may thereby reassess the utility of preoperative phenylephrine testing given the lack of influence on surgical outcomes.
Long-term Outcome of Conjunctival Transposition Flaps for Contracted Sockets
Authors: Vahdani Kaveh , Rose Geoffrey E. 
Published: August 2024

Purpose:To assess the efficacy, and reintervention rate, of a conjunctival transposition technique in the treatment of contracted fornices in anophthalmic sockets.Methods:Retrospective case-note review of patients with contracted anophthalmic sockets who received a novel conjunctival mucosal transposition flap for augmentation of socket lining. Contracted anophthalmic sockets were categorized as grade 1 (minimal contraction), grade 2 (inferior and/or superior fornix), grade 3 (advanced scarring of the entire upper and lower fornices), and grade 4 (severe palpebral phimosis, recurrent cases, and irradiated sockets).Results:Of 32 patients (56% male), 53% had mild-to-moderate contracted anophthalmic sockets (grades 1 or 2). The transposition flap was combined with secondary ball implantation (3 cases), ball exchange (1 case), primary orbital floor (1 case), or revisional floor (3 cases) implantation. By an average follow up of 9.2 years, 16% (5 cases with grade 3 or 4) required additional relining, with another patient declining further surgery; this yielding an overall anatomic success of 81% (100% in grades 1 and 2; 60% in grades 3 and 4). At the last follow up, 91% of patients had adequate socket lining and 94% reported a comfortable socket with stable prostheses.Conclusions:Having results similar to free grafting but without remote donor-site morbidity, this novel transposition flap satisfactorily addresses mild-to-moderate fornix contracture, and most patients achieve stable and comfortable prosthetic wear. Some patients with severe contracted anophthalmic sockets required further autologous grafting: this generally arose because the transposition flap included tissue from above the socket’s horizontal raphé (with later contracture of the upper fornix).
Peripheral nerve injury results in a biased loss of sensory neuron subpopulations
Authors: Cooper Andrew H. , Barry Allison M. , Chrysostomidou Paschalina , Lolignier Romane , Wang Jinyi , Redondo Canales Magdalena , Titterton Heather F. , Bennett David L. , Weir Greg A. 
Published: August 2024

Abstract
There is a rich literature describing the loss of dorsal root ganglion (DRG) neurons following peripheral axotomy, but the vulnerability of discrete subpopulations has not yet been characterised. Furthermore, the extent or even presence of neuron loss following injury has recently been challenged. In this study, we have used a range of transgenic recombinase driver mouse lines to genetically label molecularly defined subpopulations of DRG neurons and track their survival following traumatic nerve injury. We find that spared nerve injury leads to a marked loss of cells containing DRG volume and a concomitant loss of small-diameter DRG neurons. Neuron loss occurs unequally across subpopulations and is particularly prevalent in nonpeptidergic nociceptors, marked by expression of Mrgprd. We show that this subpopulation is almost entirely lost following spared nerve injury and severely depleted (by roughly 50%) following sciatic nerve crush. Finally, we used an in vitro model of DRG neuron survival to demonstrate that nonpeptidergic nociceptor loss is likely dependent on the absence of neurotrophic support. Together, these results profile the extent to which DRG neuron subpopulations can survive axotomy, with implications for our understanding of nerve injury–induced plasticity and pain.
Long-term outcomes in critically ill patients with acute respiratory failure
Authors: Ippolito Mariachiara , Galvano Alberto Nicolò , Cortegiani Andrea 
Published: August 2024

Purpose of review
This review aims to explore the latest evidence on long-term outcomes in patients admitted to the ICU because of acute respiratory failure (ARF).

Recent findings
As the survival rate of critically ill patients with acute respiratory failure improves, long-term mortality and disability still influence the quality of life of survivors and their caregivers. Patients admitted to the ICU because of ARF are at risk of developing the postintensive care syndrome, which presents with physical, cognitive and mental symptoms, all of which may impair their quality of life. Caregivers seem to be affected as well, which may lead to intergenerational trauma. The need for more care, including prone positioning, invasive support (e.g. mechanical ventilation, ECMO) and deep sedation are probably adjunctive risk factors for poor long-term outcomes.

Summary
There is not much data on the long-term outcomes of patients who have survived ARF. More follow-up studies should be conducted, especially in centers providing higher levels of costly care (e.g. ECMO). Randomized controlled trials on interventions for ARF should include patient-centered long-term outcomes in addition to mortality rates. The high mortality rates associated with ARF mandate collaboration among multiple centers to achieve an adequate sample size for studying the long-term outcomes of survivors.
Evaluating 64Cu-DOTA-rituximab as a PET agent in patients with B-cell lymphoma: a head-to-head comparison with 18F-fluorodeoxyglucose PET/computed tomography
Authors: Lee Inki , Byun Byung Hyun , Kim Byung Il , Choi Chang Woon , Kang Hye Jin , Kang Chi Soo , Woo Sang-Keun , Lee Kyo Chul , Kang Joo Hyun , Lim Ilhan 
Published: August 2024

Background
This study aimed to evaluate the biodistribution of 64Cu-DOTA-rituximab and its diagnostic feasibility for lymphoma using CD20-targeted 64Cu-DOTA-rituximab PET/computed tomography (PET/CT).

Methods
A prospective study involving six patients diagnosed with lymphoma was conducted between January 2022 and January 2023. These patients underwent 18F-fluorodeoxyglucose (18F-FDG) and 64Cu-DOTA-rituximab PET/CT scans. 64Cu-DOTA-rituximab PET/CT images were acquired at 1, 24, and 48 h after administering 64Cu-DOTA-rituximab to assess the biodistribution and dosimetry over time. The observed lymph nodes were categorized into specific regions, including cervical and supraclavicular, axillary and infraclavicular, mediastinal, hilar, abdominal paraaortic and retroperitoneal, iliac, mesenteric, and inguinal regions, to compare the diagnostic ability of 18F-FDG and 64Cu-DOTA-rituximab PET/CT in detecting lymphoma lesions. Furthermore, the tumor-to-background ratio was calculated and compared with the maximum standardized uptake (SUVmax) of the tumors and the mean standardized uptake (SUVmean) of normal organs. Internal radiation dosimetry was determined using the OLINDA/EXM software.

Results

64Cu-DOTA-rituximab uptake in lymph nodes associated with lymphoma progressively increased from 1 to 48 h after injection. In contrast, 64Cu-DOTA-rituximab uptake in normal organs, such as blood, lung, kidney, bladder, muscle, bone, and brain, decreased over time, whereas it increased in the liver and spleen. When it comes to the comparison between 64Cu-DOTA-rituximab and 18F-FDG, the SUVmax of tumors was higher on 64Cu-DOTA-rituximab PET/CT (18.1 ± 8.3) than on 18F-FDG PET/CT (5.2 ± 1.5). Additionally, the tumor-to-background ratio, measured using the SUVmean of normal muscles, was higher on 64Cu-DOTA-rituximab PET/CT (55.7 ± 31.0) than on 18F-FDG PET/CT (8.6 ± 2.8). No adverse events related to 64Cu-DOTA-rituximab injection were reported.

Conclusion
The results of this study demonstrate the feasibility of using 64Cu-DOTA-rituximab PET/CT to evaluate the CD20 expression. The increased 64Cu-DOTA-rituximab uptake in lymph nodes associated with tumors, higher SUVmax, and tumor-to-muscle ratios observed with 64Cu-DOTA-rituximab PET/CT compared with 18F-FDG PET/CT, highlight the diagnostic potential of this imaging modality.
Brief Report:Availability of and Interest in Gender-Affirming Care, PrEP, and HIV Prevention Services in a Global Sample of Transmasculine Persons
Authors: Paine Emily Allen , Appenroth Max , Scheim Ayden , Goldrich Madison , Giguere Rebecca , Sandfort Theodorus 
Published: August 2024

Background:
We assessed access to pre-exposure prophylaxis (PrEP) and interest in integration of PrEP with gender-affirmative care in a global sample of transmasculine persons.

Methods:
Transmasculine persons (N = 590) aged 18 years and above from 57 countries completed a brief online survey from April to July 2022 about sexual behavior, knowledge, and interest in PrEP, current access to PrEP and gender-affirmative care, and preferred context for accessing PrEP. Descriptive analyses were stratified by country income group.

Results:
Most participants (54.4%) lived near a health center offering care to trans people. Overall, 1.9% of respondents reported ever receiving a positive HIV test result. Among those who had not (n = 579), more than a third reported engaging in receptive sex in the past year (35.2%) or anticipated doing so in the next year (41.5%), 86.9% had never received information about HIV prevention specific to transmasculine people, and 76.3% had heard of PrEP. Among those who had heard of PrEP (n = 440), only 18.9% had discussed or been offered it by a provider, and only 3.6% were currently taking it—yet 67.9% who had heard of it but were not using it would “definitely” (28.5%) or “maybe” (39.4%) be interested in taking it were it available for free. Out of these participants, the majority (60.5%) preferred the idea of accessing PrEP from the same clinic where they received gender-affirming care.

Conclusions:
Interventions are needed to improve PrEP access for transmasculine people globally. Clinics already providing gender-affirming care to trans people are acceptable clinical contexts to integrate such interventions.
Feasibility of Epicardial Adipose Tissue Quantification Using Non–electrocardiogram-Gated Chest Computed Tomography Images
Authors: Mikami Tomio , Yokomachi Kazushi , Mizuno Kenji , Kobayashi Masayuki 
Published: August 2024

Objective
Epicardial adipose tissue (EAT) is an important imaging indicator of cardiovascular risk. EAT volume is usually measured using electrocardiogram (ECG) gating. However, there are concerns regarding the influence of motion artifacts when measuring EAT volume on non‐ECG-gated plain chest computed tomography (CT) images. Few studies have evaluated the EAT volume using non-ECG gating. This study aimed to validate the accuracy of EAT quantification using non‐ECG-gated chest CT imaging.

Methods
We included 100 patients (64 males, 36 females) who underwent simultaneous coronary artery calcification score imaging (ECG gated) and plain chest CT imaging (non‐ECG gated). Images taken using non-ECG gating were reconstructed using the same field of view and slice thickness as those obtained with ECG gating. The EAT capacity of each image was measured and compared. An AZE Virtual Place (Canon) was used for the measurements. The Mann-Whitney U test and intraclass correlation coefficient were used for statistical analyses. P values <0.05 were considered statistically significant. Concordance was evaluated using Bland-Altman analysis.

Results
The mean EAT volume measured by ECG-gated imaging was 156.5 ± 66.9 mL and 155.4 ± 67.9 mL by non‐ECG-gated imaging, with no significant difference between the two groups (P = 0.86). Furthermore, the EAT volumes measured using ECG-gated and non‐ECG-gated imaging showed a strong correlation (r = 0.95, P < 0.05). Bland-Altman analysis revealed that the mean error of the EAT volume (non‐ECG-gated imaging ‐ ECG-gated imaging) was −1.02 ± 2.95 mL (95% confidence interval, −6.49 to 4.76).

Conclusions
The EAT volume obtained using non‐ECG-gated imaging was equivalent to that obtained using ECG-gated imaging.