bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research
Authors: von Reumont Bjoern M , Anderluh Gregor , Antunes Agostinho , Ayvazyan Naira , Beis Dimitris , Caliskan Figen , Crnković Ana , Damm Maik , Dutertre Sebastien , Ellgaard Lars , Gajski Goran , German Hannah , Halassy Beata , Hempel Benjamin-Florian , Hucho Tim , Igci Nasit , Ikonomopoulou Maria P , Karbat Izhar , Klapa Maria I , Koludarov Ivan , Kool Jeroen , Lüddecke Tim , Ben Mansour Riadh , Vittoria Modica Maria , Moran Yehu , Nalbantsoy Ayse , Ibáñez María Eugenia Pachón , Panagiotopoulos Alexios , Reuveny Eitan , Céspedes Javier Sánchez , Sombke Andy , Surm Joachim M , Undheim Eivind A B , Verdes Aida , Zancolli Giulia 
Published: October 2024

Abstract
Venoms have evolved &gt;100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants
Authors: Tang Zhongjie , Zhang Weixing , Shi Peiyu , Li Sijun , Li Xinhui , Li Yueming , Xu Yicong , Shu Yaqing , Hu Zheng , Xu Jin 
Published: October 2024

Abstract
Multiplexing across donors has emerged as a popular strategy to increase throughput, reduce costs, overcome technical batch effects, and improve doublet detection in single-cell genomic studies. To eliminate additional experimental steps, endogenous nuclear genome variants are used for demultiplexing pooled single-cell RNA sequencing (scRNA-seq) data by several computational tools. However, these tools have limitations when applied to single-cell sequencing methods that do not cover nuclear genomic regions well, such as single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq). Here, we demonstrate that mitochondrial germline variants are an alternative, robust, and computationally efficient endogenous barcode for sample demultiplexing. We propose MitoSort, a tool that uses mitochondrial germline variants to assign cells to their donor origins and identify cross-genotype doublets in single-cell genomic datasets. We evaluate its performance by using in silico pooled mitochondrial scATAC-seq (mtscATAC-seq) libraries and experimentally multiplexed data with cell hashtags. MitoSort achieves high accuracy and efficiency in genotype clustering and doublet detection for mtscATAC-seq data, addressing the limitations of current computational techniques tailored for scRNA-seq data. Moreover, MitoSort exhibits versatility, and can be applied to various single-cell sequencing approaches beyond mtscATAC-seq provided that the mitochondrial variants are reliably detected. Furthermore, we demonstrate the application of MitoSort in a case study where B cells from eight donors were pooled and assayed by single-cell multi-omics sequencing. Altogether, our results demonstrate the accuracy and efficiency of MitoSort, which enables reliable sample demultiplexing in various single-cell genomic applications. MitoSort is available at https://github.com/tangzhj/MitoSort.
Effect of dietary calcium and vitamin D supplements on plasma bone turnover biomarkers, bone mineralization, bone strength, and lameness score in gilts
Authors: Bruun Thomas S , Jensen Søren K , Larsen Torben , Nielsen Mai Britt F , Roger Laurent , Feyera Takele 
Published: October 2024

Abstract
This study investigated the impact of calcium (Ca) and vitamin D supplements on bone metabolism, bone measurement, lameness, and selection rate in gilts fed 5 dietary treatments. Two Ca levels (6.85/6.42 [adequate; ACa] or 8.99/8.56 [high; HCa] g/kg) were combined with either 856 IU/kg vitamin D3 (Danish feeding standards; adequate; AD3) or 50 μg/kg 25-hydroxyvitamin D3 (high; HHyD) to create ACaAD3, HCaAD3, ACaHHyD, and HCaHHyD diets. The values 6.85/6.42 and 8.99/8.56 g/kg correspond to adequate and high Ca supply for gilts weighing 32 to 100 and 100 to 180 kg body weight (BW), respectively. The fifth diet was a combination of HCa and 2,000 IU/kg vitamin D3 (high; HD3) to create HCaHD3. Two hundred gilts were phase fed the dietary treatments from 32 to 100 and 100 to 180 kg BW until they were slaughtered, either at 100 or 180 kg BW. The gilts were weighed fortnightly, and plasma and urine samples were collected at 100 and 180 kg BW. At slaughter, the 2nd and 3rd metacarpal bones were collected for bone parameters measurements. Lameness and selection rate were assessed within the last 7 d at 100 and 180 kg BW. Dietary treatments did not affect gilts’ growth performance and plasma concentration of Ca, but the urinary concentration of Ca was greater in HCa-supplemented gilts at both 100 (P = 0.003) and 180 (P = 0.05) kg BW. Plasma concentration of vitamin D3 (P &lt; 0.001) and 25-hydroxyvitamin D3 (P &lt; 0.001) showed dose-dependent responses at both 100 and 180 kg BW. Bone-specific alkaline phosphatase was greater (P = 0.02) in the plasma sample collected at 180 kg BW in gilts fed the HCaHD3 diet and tended to be greater in gilts fed the ACaAD3 diet (P = 0.06). The bone ash content (P = 0.02) was greater in gilts fed the HCaAD3 diet and slaughtered at 100 kg BW compared with gilts fed the ACaAD3 and ACaHHyD diets. However, bone weight, length, thickness, dry matter, and mineral content did not differ among the dietary treatments at both 100 and 180 kg BW (P &gt; 0.05). Neither lameness nor selection rate was affected by the dietary treatments. The average daily gain of gilts weighing 32 to 100 and 100 to 180 kg BW showed a positive correlation with bone strength (r = 0.37; P &lt; 0.001) and bone ash content (r = 0.24; P = 0.02), respectively. In conclusion, higher Ca and vitamin D3 supplementation slightly increased bone ash content but had no effect on the lameness or selection rate of the gilts compared to those fed according to the Danish nutrient standards.
The essential oil blend Agolin Ruminant L reduces methane production in vitro and in vivo when included in the drinking water of cattle
Authors: Batley Ryan J , Romanzini Eliéder P , da Silva Kawane D , de Souza William L , Quigley Simon P , Harper Karen J , Trotter Mark G , Bernardes Priscila A , Naiker Mani , Costa Diogo F A 
Published: October 2024

Abstract
Two experiments were conducted to determine the potential for the essential oil blend Agolin Ruminant L (Agolin) to reduce enteric methane (CH4) emissions from beef cattle when delivered via drinking water. Experiment 1 evaluated aqueous solutions of Agolin (50 mg/L) and a nonprotein nitrogen and mineral solution (uPRO ORANGE [uPRO]; 1.7 mL/L) individually and in combination, where Agolin was added to concentrated uPRO at 3%, 4.5%, and 6% Agolin (w/w) prior to dilution with water at 1.7 mL/L, for a total of 5 treatments. These were incubated for 48 h with a medium-quality Rhodes grass (Chloris gayana) hay substrate, with gas production, CH4 concentration in gas, and digestibility measured in vitro. In experiment 2, Droughtmaster steers (n = 24) were fed a basal diet of Rhodes grass hay and were allocated to 1 of 3 water treatments (n = 8 per treatment) supplemented with either uPRO (2.27 mL uPRO/L water), or 1 of 2 inclusion rates of Agolin in combination with uPRO (2.27 mL uPRO and 6 µL Agolin/L water or 2.27 mL uPRO and 24 µL Agolin/L water) with enteric CH4 emissions, feed and water intake, and live-weight gain (LWG) measured over 56 d. In experiment 1, the inclusion of Agolin in uPRO at 6% (w/w) resulted in a reduction in CH4 production (15.8%; P = 0.003) and the proportion of CH4 in the gas produced (24.5%; P &lt; 0.001). In experiment 2, steers consuming the lower quantity of Agolin via drinking water had a 16.4% (P = 0.0027) reduction in CH4 production over the experiment, declining from 140 g/d during week 1 to 117 g/d in week 8. This inclusion rate of Agolin in the drinking water also resulted in a 25 g (17.6%) CH4/d decrease in emissions by steers compared to control steers (P = 0.0205). However, no significant differences in CH4 yield (g CH4/kg dry matter intake), or CH4 intensity (g CH4/kg LWG) by steers were observed between treatments. These results demonstrated that Agolin reduces CH4 emissions when mixed in an aqueous solution under in vitro and in vivo conditions, providing a potential method to reduce enteric CH4 emissions from cattle in extensive production systems.
Mitochondria–giant lipid droplet proximity and autophagy suppression in nitrogen-depleted oleaginous yeast Lipomyces starkeyi cells
Authors: Duan Lan , Togou Akinobu , Ohta Keisuke , Okamoto Koji 
Published: October 2024

Abstract
Balancing energy production and storage is a fundamental process critical for cellular homeostasis in most eukaryotes that relies on the intimate interplay between mitochondria and lipid droplets (LDs). In the oleaginous yeast Lipomyces starkeyi under nitrogen starvation, LD forms a single giant spherical structure that is easily visible under a light microscope. Currently, how mitochondria behave in L. starkeyi cells undergoing giant LD formation remains unknown. Here we show that mitochondria transition from fragments to elongated tubules and sheet-like structures that are in close proximity to a giant LD in nitrogen-depleted L. starkeyi cells. Under the same conditions, mitochondrial degradation and autophagy are strongly suppressed, suggesting that these catabolic events are not required for giant LD formation. Conversely, carbon-depleted cells suppress mitochondrial elongation and LD expansion, whereas they promote mitochondrial degradation and autophagy. We propose a potential link of mitochondrial proximity and autophagic suppression to giant LD formation.
Modes of Securitization and Desecuritization of Transnational Kinship Ties: Overseas Chinese in Southeast Asia amidst Rising Chinese Power
Authors: Han Enze 
Published: October 2024

Abstract
This paper explores under what context the transnational ethnic kinship ties between the overseas Chinese in Southeast Asia and China have not led to their securitization and in what context they have. As the rising great power with exponential economic growth for the past few decades, China has transformed itself from a dirt-poor backwater state to the second largest economy in the world and is also seemingly on the way to reclaim the historical dominant status in East and Southeast Asia. During this process, overseas Chinese in various home states in Southeast Asia have not experienced a uniform securitization of their kinship ties. This paper investigates some of the dynamic patterns about overseas Chinese in Southeast Asia’s relationship between the changing kin state and their home states in the recent past. Focusing on how states in Southeast Asia maintain different types of relations with China in the context of the latter’s rising, this paper contends that the ways in which overseas Chinese communities in the region manage their political space and negotiate their belonging are a function of a combination of international structural changes and domestic political factors. Empirically, this paper compares three states of Southeast Asia—Thailand, Myanmar, and Indonesia—in the different ways of their treatment of the ethnic Chinese, as well as the responding strategies utilized by the ethnic Chinese in navigating their political space and belonging.
The Vaginal Penetration Skills Scale (VPSS): a paradigm shift in genito-pelvic pain/penetration disorder screening, assessment, and stratification
Authors: Maldonado Mariana , Figueira Gabriel Loureiro , Nardi Antonio E , Sardinha Aline 
Published: October 2024

Abstract

Background
Receptive vaginal penetration skills have been implicated in the etiology, explanatory models, and treatment of genito-pelvic pain penetration disorder (GPPPD). However, there are no psychometric skills measures designed to screen, assess, and stratify GPPPD.

Aim
We aimed to develop and psychometrically evaluate a new scale—the Vaginal Penetration Skills Scale (VPSS)—to screen, assess, and stratify GPPPD.

Methods
This study included 148 Brazilian females with GPPPD symptoms (113 lifelong and 35 acquired) and 251 Brazilian females without sexual complaints. We conducted factor analyses considering all participants (n = 399). Then, we conducted latent class analysis within the GPPPD group to identify clusters of individuals with similar VPSS profiles. We assessed convergent validity through intercorrelation with the Brazilian versions of the Female Genital Self-Image Scale (FGSIS) and the 6-item Female Sexual Function Index (FSFI-6).

Outcomes
We developed complete and short-form versions of the VPSS (VPSS-29 and VPSS-SF11, respectively), each with 3 dimensions, to screen, assess, and stratify GPPPD.

Results
Factor analysis yielded a 3-factor VPSS model with the “Nonsexual Genital Self-Exploration,” “Nonsexual Vaginal Penetration Skills,” and “Sexual Vaginal Penetration Skills” dimensions for both VPSS versions. The reliability was excellent for the VPSS-29 (ω = 0.981, α = 0.981) and the VPSS-SF11 (ω = 0.959, α = 0.961). All 3 dimensions could detect significant differences between patients with GPPPD and healthy females. They also differentiated the patients with GPPPD, distinguishing gradient levels. For convergent validity, we found moderate to strong correlations (rho = 0.715–0.745) between the VPSS, FGSIS, and FSFI-6.

Clinical Implications
The VPSS can be applied easily in both clinical and research settings.

Strengths and Limitations
The VPSS provides a concise and thorough evaluation of receptive vaginal penetration skills in both sexual and nonsexual contexts among patients with GPPPD. The sample had limited diversity regarding gender and sexual orientation; therefore, it is important to validate the use of this scale in populations beyond the cisgender heterosexual female population to ensure its applicability in diverse settings.

Conclusion
These results support the reliability and psychometric validity of the VPSS as a self-report measure to screen, assess, and stratify GPPPD symptoms.
Deep Ancestral Introgressions between Ovine Species Shape Sheep Genomes via Argali-Mediated Gene Flow
Authors: Lv Feng-Hua , Wang Dong-Feng , Zhao Si-Yi , Lv Xiao-Yang , Sun Wei , Nielsen Rasmus , Li Meng-Hua 
Published: October 2024

Abstract
Previous studies revealed extensive genetic introgression between Ovis species, which affects genetic adaptation and morphological traits. However, the exact evolutionary scenarios underlying the hybridization between sheep and allopatric wild relatives remain unknown. To address this problem, we here integrate the reference genomes of several ovine and caprine species: domestic sheep, argali, bighorn sheep, snow sheep, and domestic goats. Additionally, we use 856 whole genomes representing 169 domestic sheep populations and their six wild relatives: Asiatic mouflon, urial, argali, snow sheep, thinhorn sheep, and bighorn sheep. We implement a comprehensive set of analyses to test introgression among these species. We infer that the argali lineage originated ∼3.08 to 3.35 Mya and hybridized with the ancestor of Pachyceriforms (e.g. bighorn sheep and snow sheep) at ∼1.56 Mya. Previous studies showed apparent introgression from North American Pachyceriforms into the Bashibai sheep, a Chinese native sheep breed, despite of their wide geographic separation. We show here that, in fact, the apparent introgression from the Pachyceriforms into Bashibai can be explained by the old introgression from Pachyceriforms into argali and subsequent recent introgression from argali into Bashibai. Our results illustrate the challenges of estimating complex introgression histories and provide an example of how indirect and direct introgression can be distinguished.
Yunfuconcha new genus, a possible stem-archiheterodont bivalve from the Ordovician of Guangdong, South China
Authors: Zhang Ren-jie , Johnston Paul A , Niu Zhi-jun , Li Chu-an , Wang Zhi-hong , Hu Kun , Song Fang , He Yao-yan , He Jin-lan , Lin Xiao-ming , Yang Wen-qiang 
Published: October 2024

ABSTRACT
Yunfuconcha bimenta, a new genus and species of bivalve from the Ordovician of western Guangdong, China, is described. Its unusual hinge consists of a palaeotaxodont-like dentition anteriorly and a heteroconch-like dentition posteriorly. The posterior hinge area exhibits a remarkable, broad, deeply inset, concave ligament area, which is reminiscent of the ventrally expanded ligament of some Recent and fossil lucinoids and the triangular resilifer in late Palaeozoic crassatellid heteroconchs. Lamellar posterior teeth and sockets complete the posterior dentition. The unusual combination of features, normally associated with either the Order Cardiolariatida (used here in place of Order ‘Afghanodesmatida’—the type genus Afghanodesma, is known only from wax impressions rendering it and its nominal higher taxa invalid) or various crassatelloids and lucinoids, make systematic placement of Yunfuconcha n. gen. uncertain below subclass rank. In view of presumed derived heteroconch-like characters of the posterior hinge, we place Yunfuconcha n. gen. in the Subclass Autobranchia, possibly as a stem archiheterodont or a stem heteroconch.
THE MOLECULAR HISTORY OF IDH-MUTANT ASTROCYTOMAS WITHOUT ADJUVANT TREATMENT
Authors: Ng Prof Ho Keung , Shi Dr Zhi-Feng , Li Dr Kay 
Published: October 2024

Abstract

AIMS
Hypermutation and malignant transformation are potential complications arising from temozolomide treatment of IDH-mutant gliomas. However, the natural history of IDH-mutant low-grade gliomas without temozolomide treatment is relatively un-studied. We set out to study the molecular history of paired IDH-mutant astrocytomas without adjuvant treatment in the interim.

METHOD
We retrieved retrospectively from our hospitals paired tumors from 19 patients with IDH-mutant, 1p19q noncodeleted Grade 2 astrocytomas where no interim adjuvant treatment with either temozolomide or radiotherapy was given between primary and ﬁrst recurrences. Two patients had multiple resected recurrences and radiotherapy but not temozolomide was given before the last specimens were resected. We studied the natural molecular history of these low-grade IDH-mutant astrocytomas without pressure of temozolomide with methylation proﬁling and copy number variation (CNV) analyses, target DNA sequencing, TERTp sequencing, FISH for ALT and selected biomarkers.

RESULTS
Recurrences were mostly higher grades (15/19 patients) and characterized by new CNVs not present in the primary tumors (17/19 cases). Few novel mutations were identiﬁed in recurrences. Tumors from 17/19 (89.5%) patients showed either CDKN2A homozygous deletion, MYC or PDGFRA ampliﬁcation at recurrences. There was no case of hypermutation. Phylogenetic trees constructed for tumors for the two patients with multiple recurrences showed a conserved evolution pattern.

CONCLUSION
In summary, our studies demonstrated in contrast to the phenomenon of temozolomide-induced hypermutation, IDH-mutant, 1p19q non-codeleted Grade 2 astrocytomas which were not treated by temozolomide instead acquired new CNVs at tumor recurrences. These ﬁndings improve our understanding of the molecular life history of IDH-mutant astrocytomas.
DEVELOPING CEREBROSPINAL ﬂUID METABOLOMIC BIOMARKERS FOR MINIMAL RESIDUAL DISEASE AND RELAPSE IN EPENDYMOMA AND MEDULLOBLASTOMA
Authors: Whitby Dr Alison , Shastri Mrs Bhoomi , Halsey Prof Christina , Grundy Prof Richard , Kim Dr Dong-Hyun , Dandapani Dr Madhumita 
Published: October 2024

Abstract

AIMS
Relapse rates of 30% and 50% in medulloblastoma and ependymoma lead to poor outcomes for paediatric brain tumours. Occurring usually within two years, relapses imply minimal residual disease (MRD) is present below the imaging detection threshold. Patient outcomes might be improved by diagnosing MRD using a sensitive, minimally invasive cerebrospinal ﬂuid (CSF) liquid biopsy, as CSF is proximal to tumour. Metabolites arising from aberrant cancer metabolism may be biomarkers in CSF.

METHOD
With only 25µl CSF, extracted with 75µl methanol, liquid chromatography coupled with tandem high-resolution mass spectrometry (LC-MS/MS) could differentiate these paediatric brain tumours (n=47; day 14 post-surgery) from controls (n=49).

RESULTS
Fourteen metabolites were increased in abundance in tumours and four decreased compared to controls. These included amino acids and derivatives (n=8), metabolites in one carbon metabolism (n=1), carnitine cycle (n=2), aerobic glycolysis (n=2), purine catabolism (n=2), ascorbate degradation (n=1) and creatinine synthesis (n=2). From those, betaine/creatinine ratio gave an area under the curve (AUC) of 0.96 (excellent) in receiver operating curve analysis. Using a cut-off ratio of 0.1775 for discriminating brain tumours from controls, had sensitivity and speciﬁcity of 92% and 89%. Speciﬁcally identifying tumours, a ratio of betaine/threonate with cut-off 2.1514 discriminated ependymomas from controls (sensitivity/speciﬁcity 92%/91%). A ratio of malic acid/hypoxanthine with cut-off 0.04429 discriminated medulloblastomas from controls (sensitivity/speciﬁcity 100%/98%). Medulloblastomas (n=14) were largely similar to ependymomas (n=33); nevertheless, three metabolites met the criteria of corrected p&lt;0.05. A ratio of glutarate semialdehyde/malic acid with cut-off 0.04243 discriminated ependymomas from medulloblastomas (sensitivity/speciﬁcity 79%/82%) in a good model (AUC 0.85).

CONCLUSION
This is the ﬁrst report of CSF metabolites in ependymoma. Ratios between metabolites levels could be useful as biomarkers to detect brain tumours and distinguish brain tumour type speciﬁcally and sensitively. Further work to develop a liquid biopsy test for the detection of MRD is ongoing.