bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotype information of large neuromuscular disease genes provided by linked-read sequencing has a potential to increase diagnostic yield
Authors: Lehtonen Johanna , Sulonen Anna-Maija , Almusa Henrikki , Lehtokari Vilma-Lotta , Johari Mridul , Palva Aino , Hakonen Anna H. , Wartiovaara Kirmo , Lehesjoki Anna-Elina , Udd Bjarne , Wallgren-Pettersson Carina , Pelin Katarina , Savarese Marco , Saarela Janna 
Published: February 2024

AbstractRare or novel missense variants in large genes such as TTN and NEB are frequent in the general population, which hampers the interpretation of putative disease-causing biallelic variants in patients with sporadic neuromuscular disorders. Often, when the first initial genetic analysis is performed, the reconstructed haplotype, i.e. phasing information of the variants is missing. Segregation analysis increases the diagnostic turnaround time and is not always possible if samples from family members are lacking. To overcome this difficulty, we investigated how well the linked-read technology succeeded to phase variants in these large genes, and whether it improved the identification of structural variants. Linked-read sequencing data of nemaline myopathy, distal myopathy, and proximal myopathy patients were analyzed for phasing, single nucleotide variants, and structural variants. Variant phasing was successful in the large muscle genes studied. The longest continuous phase blocks were gained using high-quality DNA samples with long DNA fragments. Homozygosity increased the number of phase blocks, especially in exome sequencing samples lacking intronic variation. In our cohort, linked-read sequencing added more information about the structural variation but did not lead to a molecular genetic diagnosis. The linked-read technology can support the clinical diagnosis of neuromuscular and other genetic disorders.
Impairment of unconscious emotional processing after unilateral medial temporal structure resection
Authors: Sato Wataru , Usui Naotaka , Kondo Akihiko , Kubota Yasutaka , Toichi Motomi , Inoue Yushi 
Published: February 2024

AbstractThe role of the amygdala in unconscious emotional processing remains a topic of debate. Past lesion studies have indicated that amygdala damage leads to impaired electrodermal activity in response to subliminally presented emotional stimuli. However, electrodermal activity can reflect both emotional and nonemotional processes. To provide behavioral evidence highlighting the critical role of the amygdala in unconscious emotional processing, we examined patients (n = 16) who had undergone unilateral resection of medial temporal lobe structures, including the amygdala. We utilized the subliminal affective priming paradigm in conjunction with unilateral visual presentation. Fearful or happy dynamic facial expressions were presented in unilateral visual fields for 30 ms, serving as negative or positive primes. Subsequently, neutral target faces were displayed, and participants were tasked with rating the valence of these targets. Positive primes, compared to negative ones, enhanced valence ratings of the target to a greater extent when they stimulated the intact hemisphere (i.e., were presented in the contralateral visual field of the intact hemisphere) than when they stimulated the resected hemisphere (i.e., were presented in the contralateral visual field of the resected hemisphere). These results suggest that the amygdala is causally involved in unconscious emotional processing.
Galacto-oligosaccharide preconditioning improves metabolic activity and engraftment of Limosilactobacillus reuteri and stimulates osteoblastogenesis ex vivo
Authors: De Bruyn Florac , Bonnet Nicolas , Baruchet Michaël , Sabatier Magalie , Breton Isabelle , Bourqui Bertrand , Jankovic Ivana , Horcajada Marie-Noëlle , Prioult Guénolée 
Published: February 2024

AbstractA probiotic-related benefit for the host is inherently linked to metabolic activity and integration in the gut ecosystem. To facilitate these, probiotics are often combined with specific prebiotics in a synbiotic formulation. Here, we propose an approach for improving probiotic metabolic activity and engraftment. By cultivating the probiotic strain in the presence of a specific prebiotic (preconditioning), the bacterial enzymatic machinery is geared towards prebiotic consumption. Today, it is not known if preconditioning constitutes an advantage for the synbiotic concept. Therefore, we assessed the effects galacto-oligosaccharide (GOS) addition and preconditioning on GOS of Limosilactobacillus reuteri DSM 17938 on ex vivo colonic metabolic profiles, microbial community dynamics, and osteoblastogenesis. We show that adding GOS and preconditioning L. reuteri DSM 17938 act on different scales, yet both increase ex vivo short-chain fatty acid (SCFA) production and engraftment within the microbial community. Furthermore, preconditioned supernatants or SCFA cocktails mirroring these profiles decrease the migration speed of MC3T3-E1 osteoblasts, increase several osteogenic differentiation markers, and stimulate bone mineralization. Thus, our results demonstrate that preconditioning of L. reuteri with GOS may represent an incremental advantage for synbiotics by optimizing metabolite production, microbial engraftment, microbiome profile, and increased osteoblastogenesis.
Animal naming test stratifies the risk of falls and fall-related fractures in patients with cirrhosis
Authors: Miwa Takao , Hanai Tatsunori , Hirata Sachiyo , Nishimura Kayoko , Unome Shinji , Nakahata Yuki , Imai Kenji , Shirakami Yohei , Suetsugu Atsushi , Takai Koji , Shimizu Masahito 
Published: February 2024

AbstractThis study aimed to determine the relationship between animal naming test (ANT), falls, and fall-related fractures in patients with cirrhosis. Cognitive impairment and frailty were assessed using ANT and Karnofsky performance status (KPS), respectively. Factors stratifying the risk of previous falls and fall-related fractures within 1 year were assessed using a logistic regression model. Factors affecting patient performance in ANT were evaluated using multiple regression analysis. Of the 94 patients, 19% and 5% experienced falls and fall-related fractures, respectively. The performance in ANT was worse in patients who experienced falls (11 vs. 18; p < 0.001) and fall-related fractures (8 vs. 16; p < 0.001) than in those who did not. After adjustment, females, KPS, and ANT (odds ratio [OR], 0.78; 95% confidence interval [CI], 0.65–0.93; p = 0.005) were associated with falls, while ANT was significantly associated with fall-related fractures (OR, 0.56; 95% CI 0.35–0.88; p = 0.012). Age and education affected the performance in ANT, whereas the use of Oriental zodiac did not. The ANT is useful for stratifying the risk of falls and fall-related fractures in patients with cirrhosis. The effects of age and education should be considered when applying ANT in the Japanese population.
Performance analysis and knowledge-based quality assurance of critical organ auto-segmentation for pediatric craniospinal irradiation
Authors: Hanna Emeline M. , Sargent Emma , Hua Chia-ho , Merchant Thomas E. , Ates Ozgur 
Published: February 2024

AbstractCraniospinal irradiation (CSI) is a vital therapeutic approach utilized for young patients suffering from central nervous system disorders such as medulloblastoma. The task of accurately outlining the treatment area is particularly time-consuming due to the presence of several sensitive organs at risk (OAR) that can be affected by radiation. This study aimed to assess two different methods for automating the segmentation process: an atlas technique and a deep learning neural network approach. Additionally, a novel method was devised to prospectively evaluate the accuracy of automated segmentation as a knowledge-based quality assurance (QA) tool. Involving a patient cohort of 100, ranging in ages from 2 to 25 years with a median age of 8, this study employed quantitative metrics centered around overlap and distance calculations to determine the most effective approach for practical clinical application. The contours generated by two distinct methods of atlas and neural network were compared to ground truth contours approved by a radiation oncologist, utilizing 13 distinct metrics. Furthermore, an innovative QA tool was conceptualized, designed for forthcoming cases based on the baseline dataset of 100 patient cases. The calculated metrics indicated that, in the majority of cases (60.58%), the neural network method demonstrated a notably higher alignment with the ground truth. Instances where no difference was observed accounted for 31.25%, while utilization of the atlas method represented 8.17%. The QA tool results showed that the two approaches achieved 100% agreement in 39.4% of instances for the atlas method and in 50.6% of instances for the neural network auto-segmentation. The results indicate that the neural network approach showcases superior performance, and its significantly closer physical alignment to ground truth contours in the majority of cases. The metrics derived from overlap and distance measurements have enabled clinicians to discern the optimal choice for practical clinical application.
The exocyst complex and intracellular vesicles mediate soluble protein trafficking to the primary cilium
Authors: Niedziółka S. M. , Datta S. , Uśpieński T. , Baran B. , Skarżyńska W. , Humke E. W. , Rohatgi R. , Niewiadomski P. 
Published: February 2024

AbstractThe efficient transport of proteins into the primary cilium is a crucial step for many signaling pathways. Dysfunction of this process can lead to the disruption of signaling cascades or cilium assembly, resulting in developmental disorders and cancer. Previous studies on the protein delivery to the cilium were mostly focused on the membrane-embedded receptors. In contrast, how soluble proteins are delivered into the cilium is poorly understood. In our work, we identify the exocyst complex as a key player in the ciliary trafficking of soluble Gli transcription factors. In line with the known function of the exocyst in intracellular vesicle transport, we demonstrate that soluble proteins, including Gli2/3 and Lkb1, can use the endosome recycling machinery for their delivery to the primary cilium. Finally, we identify GTPases: Rab14, Rab18, Rab23, and Arf4 that are involved in vesicle-mediated Gli protein ciliary trafficking. Our data pave the way for a better understanding of ciliary transport and uncover transport mechanisms inside the cell.
Development of a 3D tracking system for multiple marmosets under free-moving conditions
Authors: Yurimoto Terumi , Kumita Wakako , Sato Kenya , Kikuchi Rika , Oka Gohei , Shibuki Yusuke , Hashimoto Rino , Kamioka Michiko , Hayasegawa Yumi , Yamazaki Eiko , Kurotaki Yoko , Goda Norio , Kitakami Junichi , Fujita Tatsuya , Inoue Takashi , Sasaki Erika 
Published: February 2024

AbstractAssessment of social interactions and behavioral changes in nonhuman primates is useful for understanding brain function changes during life events and pathogenesis of neurological diseases. The common marmoset (Callithrix jacchus), which lives in a nuclear family like humans, is a useful model, but longitudinal automated behavioral observation of multiple animals has not been achieved. Here, we developed a Full Monitoring and Animal Identification (FulMAI) system for longitudinal detection of three-dimensional (3D) trajectories of each individual in multiple marmosets under free-moving conditions by combining video tracking, Light Detection and Ranging, and deep learning. Using this system, identification of each animal was more than 97% accurate. Location preferences and inter-individual distance could be calculated, and deep learning could detect grooming behavior. The FulMAI system allows us to analyze the natural behavior of individuals in a family over their lifetime and understand how behavior changes due to life events together with other data.
On the stability of canonical correlation analysis and partial least squares with application to brain-behavior associations
Authors: Helmer Markus , Warrington Shaun , Mohammadi-Nejad Ali-Reza , Ji Jie Lisa , Howell Amber , Rosand Benjamin , Anticevic Alan , Sotiropoulos Stamatios N. , Murray John D. 
Published: February 2024

AbstractAssociations between datasets can be discovered through multivariate methods like Canonical Correlation Analysis (CCA) or Partial Least Squares (PLS). A requisite property for interpretability and generalizability of CCA/PLS associations is stability of their feature patterns. However, stability of CCA/PLS in high-dimensional datasets is questionable, as found in empirical characterizations. To study these issues systematically, we developed a generative modeling framework to simulate synthetic datasets. We found that when sample size is relatively small, but comparable to typical studies, CCA/PLS associations are highly unstable and inaccurate; both in their magnitude and importantly in the feature pattern underlying the association. We confirmed these trends across two neuroimaging modalities and in independent datasets with n ≈ 1000 and n = 20,000, and found that only the latter comprised sufficient observations for stable mappings between imaging-derived and behavioral features. We further developed a power calculator to provide sample sizes required for stability and reliability of multivariate analyses. Collectively, we characterize how to limit detrimental effects of overfitting on CCA/PLS stability, and provide recommendations for future studies.
Dynamical localization transition in the non-Hermitian lattice gauge theory
Authors: Cheng Jun-Qing , Yin Shuai , Yao Dao-Xin 
Published: February 2024

AbstractLocal constraint in the lattice gauge theory provides an exotic mechanism that facilitates the disorder-free localization. However, the understanding of nonequilibrium dynamics in the non-Hermitian lattice gauge model remains limited. Here, we investigate the quench dynamics in a system of spinless fermions with nonreciprocal hopping in the $${{\mathbb{Z}}}_{2}$$

Z

2

gauge field. By employing a duality mapping, we systematically explore the non-Hermitian skin effect, localization-delocalization transition, and real-complex transition. Through the identification of diverse scaling behaviors of quantum mutual information for fermions and spins, we propose that the non-Hermitian quantum disentangled liquids exist both in the localized and delocalized phases, the former originates from the $${{\mathbb{Z}}}_{2}$$

Z

2

gauge field and the latter arises from the non-Hermitian skin effect. Furthermore, we demonstrate that the nonreciprocal dissipation causes the flow of quantum information. Our results provide valuable insights into the nonequilibrium dynamics in the gauge field, and may be experimentally validated using quantum simulators.
From flocking to glassiness in dense disordered polar active matter
Authors: Paoluzzi Matteo , Levis Demian , Pagonabarraga Ignacio 
Published: February 2024

AbstractLiving materials such as biological tissues or bacterial colonies are collections of heterogeneous entities of different sizes, capable of autonomous motion, and often capable of cooperating. Such a degree of complexity brings to collective motion on large scales. However, how the competition between geometrical frustration, autonomous motion, and the tendency to move cooperatively impact large-scale behavior remains an open question. We implement those three ingredients in a model of active matter and show that the system, in forming migratory patterns, can arrange in bands or develop long-range order, depending on the density of the system. We also show that the active material undergoes a reentrant glass transition triggered by the alignment interaction that typically causes only collective migratory motion. Finally, we observe that polar order destroys active phase separation, producing homogeneous, disordered moving configurations.
Electric-field-aligned liquid crystal polymer for doubling anisotropic thermal conductivity
Authors: Li Maohua , Gong Ping , Zhang Zhenbang , Li Linhong , Chen Yapeng , Qin Yue , Guo Yingying , Yang Rongjie , Zhang Jianxiang , Zhou Yiwei , Xu Kang , Wang Yandong , Do Hainam , Jia Xiaofei , Cai Tao , Lin Cheng-Te , Jiang Nan , Yu Jinhong 
Published: February 2024

AbstractHigh thermal conductive polymers have become more important because equipment requires high performance, high-energy density, and high integration. There are different strategies to make high thermal conductive polymers, among which is the synthesis of polymers in the liquid crystal phase. However, the thermal conductivity of such material is rarely beyond 1 W m−1 K−1 because of the disordered molecular directionality. The disordered directionality between crystal zones limits the thermal conductivity in a specific direction. Here, we show a method for unifying the direction of crystal zones by applying an external electric field on the liquid crystal monomers. Meanwhile, by exposing the transparent equipment and specially designed photopolymerisable monomer in UV light, the liquid crystal monomer is in situ polymerised into a liquid crystal polymer with a high intrinsic thermal conductivity of 1.02 W m−1 K−1. The molecular alignment was characterised and resulted in the resultant high conductivity.
Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding
Authors: Rossouw Emma I. , Landschoff Jannes , Ndhlovu Andrew , Neef Götz , Miya Masaki , Courtaillac Kira-Lee , Brokensha Rouane , von der Heyden Sophie 
Published: February 2024

AbstractEnvironmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.
PGC-1α integrates insulin signaling with mitochondrial physiology and behavior in a Drosophila model of Fragile X Syndrome
Authors: Weisz Eliana D. , Fenton Adam R. , Jongens Thomas A. 
Published: February 2024

AbstractFragile X Syndrome (FXS) is the most prevalent monogenetic form of intellectual disability and autism. Recently, dysregulation of insulin signaling (IS) and aberrations in mitochondrial function have emerged as robust, evolutionarily conserved components of FXS pathophysiology. However, the mechanisms by which altered IS and mitochondrial dysfunction impact behavior in the context of FXS remain elusive. Here, we show that normalization of IS improves mitochondrial volume and function in flies that lack expression of dfmr1, the Drosophila homolog of the causal gene of FXS in humans. Further, we demonstrate that dysregulation of IS underlies diminished expression of the mitochondrial master regulator PGC-1α/Spargel in dfmr1 mutant flies. These results are behaviorally relevant, as we show that pan-neuronal augmentation of PGC-1α/Spargel improves circadian behavior in dfmr1 mutants. Notably, we also show that modulation of PGC-1α/Spargel expression in wild-type flies phenocopies the dfmr1 mutant circadian defect. Taken together, the results presented herein provide a mechanistic link between mitochondrial function and circadian behavior both in FXS pathogenesis as well as more broadly at the interface between metabolism and behavioral output.
Ionic liquids for the green synthesis of 1,2,3-triazoles: a systematic review
Authors: Kumar Aman , Kumar Vijay , Singh Prashant , Tittal Ram Kumar , Lal Kashmiri 
Published: February 2024

This review focuses on the use of ionic liquids (ILs) in green synthesis of 1,2,3-triazoles which critically screened, and summarized in two sections i.e., from alkynes and substrates other than alkynes using ILs as solvent, as catalyst and as both.
Prevalence and Predicting Factors of Pretreatment Dysphagia in Veterans With Head and Neck Cancer: A Pilot Study
Authors: Warner Heather L. , Romanelli Lauren , Adams Katherine , Xiao Jingyuan , Young Nwanmegha 
Published: February 2024

Background:
Dysphagia is a common sequela in individuals with a diagnosis of head and neck cancer. However, the prevalence and predicting factors for pretreatment dysphagia have not been well identified in the literature. A priori knowledge of the presence of a pretreatment dysphagia is advantageous and can have clinically significant implications for management of this patient population. The ability to predict pretreatment dysphagia in this population would allow more targeted interventions and potential improvements in clinical outcomes.

Participants:
This pilot study investigated the prevalence and predicting factors of pretreatment dysphagia in 67 veterans with head and neck cancer through the West Haven, CT, Veterans Affairs cancer database.

Method:
Data for this study were acquired via retrospective medical record review.

Results:
The prevalence of pretreatment dysphagia in our sample was found to be 49.3%. Age and pretreatment percutaneous endoscopic gastrostomy placement were found to have a statistically significant relationship with pretreatment dysphagia. Stage of cancer diagnosis and the diagnosis of pretreatment dysphagia were found to have a statistically significant relationship with posttreatment dysphagia.

Conclusions:
Findings offer important preliminary data and clinical considerations about this issue and serve as a foundation for future research. There are a limited number of factors associated with pretreatment dysphagia, and clinicians should consider a conservative referral approach when considering the need for dysphagia assessment prior to the initiation of oncologic treatment.
Narbenentstörung
Authors: Jahn Claus , Rathay Uwe , Zhang Zheng , von Löwensprung Natalie Rosenhauer 
Published: February 2024

Summary4 Expert*innen stellen Ihnen Behandlungsstrategien der Narbenentstörung aus der Komplexmittelhomöopathie, der Neuraltherapie, der TCM und der Anthroposophischen Medizin vor.
Auf den Spuren der Samtpfoten
Authors: Bastian Petra 
Published: February 2024

SummaryMögliche Blockaden oder Barrieren, die den ausgewählten Therapieansätzen entgegenwirken, müssen in der Praxis ergründet werden. Der Fallbericht beschreibt einen solchen Prozess. Bei der kleinen Patientin mit Neurodermitisschüben und wiederkehrenden Bronchitiden hing die Blockade mit geopathischen Störfeldern zusammen. Den Hinweis auf diesen Ursprung gab ausgerechnet das Verhalten einer Katze, von dem die Mutter des Mädchens fast beiläufig berichtete.