bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial transition tensor of single cells
Authors: Zhou Peijie , Bocci Federico , Li Tiejun , Nie Qing 
Published: May 2024

AbstractSpatial transcriptomics and messenger RNA splicing encode extensive spatiotemporal information for cell states and transitions. The current lineage-inference methods either lack spatial dynamics for state transition or cannot capture different dynamics associated with multiple cell states and transition paths. Here we present spatial transition tensor (STT), a method that uses messenger RNA splicing and spatial transcriptomes through a multiscale dynamical model to characterize multistability in space. By learning a four-dimensional transition tensor and spatial-constrained random walk, STT reconstructs cell-state-specific dynamics and spatial state transitions via both short-time local tensor streamlines between cells and long-time transition paths among attractors. Benchmarking and applications of STT on several transcriptome datasets via multiple technologies on epithelial–mesenchymal transitions, blood development, spatially resolved mouse brain and chicken heart development, indicate STT’s capability in recovering cell-state-specific dynamics and their associated genes not seen using existing methods. Overall, STT provides a consistent multiscale description of single-cell transcriptome data across multiple spatiotemporal scales.
Prostate intra-fraction motion recorded by transperineal ultrasound
Authors: Ballhausen Hendrik , Belka Claus , Li Minglun 
Published: May 2024

AbstractInfra-fraction motion of the prostate was recorded during 3.423 fractions of image guided radiotherapy (IGRT) in 191 patients, 14 of which were treated by intensity modulated radiation therapy (IMRT), and 177 of which were treated by volumetric arc therapy (VMAT). The prostate was imaged by three-dimensional and time-resolved transperineal ultrasound (4D-US) of type Clarity by Elekta AB, Stockholm, Sweden. The prostate volume was registered and the prostate position (center of volume) was recorded at a frequency of 2.0 samples per second. This raw data set contains a total of 1.985.392 prostate and patient couch positions over a time span of 272 hours, 52 minutes and 34 seconds of life radiotherapy as exported by the instrument software. This data set has been used for the validation of models of prostate intra-fraction motion and for the estimation of the dosimetric impact of actual intra-fraction motion on treatment quality and side effects. We hope that this data set may be reused by other groups for similar purposes.
Improving the sustainability and effectiveness of photovoltaic evaporative cooling greenhouse in the Sahel
Authors: Djibrilla Alio Sanda M. , Rabani Adamou , Illyassou Karimoun M. , Abdoulkader Atto H. , Aissetou Drame Yaye 
Published: May 2024

AbstractAnthropogenic climate change has caused worldwide extreme weather events including droughts, floods and heatwaves. It disproportionately affects developing countries through food insecurity. Greenhouse is important and relevant to the food-energy-water security in many regions. This study investigates the thermal behavior of photovoltaic evaporative cooling greenhouse made with eco-friendly coolers. The cooling potential of local plant materials was assessed under ambient conditions. Experimental thermal data obtained from optimized evaporative cooling system equipped withHyphaene thebaicafibers (HF-pad) and conventional Celdek pad (C-pad), were used in heat and mass transfer equations to derive the greenhouse cooling performances. Computational fluid dynamics analysis software was used to investigate the refrigerant fluid distribution in the greenhouse. Cooler using HF-pad allows to keep the microclimate below 25 °C, with maximum moisture rate up to 80%, under harsh ambient conditions (temperature: 30–45 °C, humidity: 10–15%). HF-pad had the highest cooling coefficient of performance (COP = 9 against 6 for C-pad), the best cost to efficiency ratio (CER = 5; 4 times less than C-pad) and the lowest outlet temperature (20.0 °C). Due to higher outlet air velocity (1.116 m/s against 0.825 m/s for HF-pad), C-pad cooler spread cool air (20.5 °C) up to 1.25 m farther than its counterpart, creating higher pressure in the atmosphere (1.42 Pa against 0.71 Pa), with 2 times turbulent kinetic energy (0.014 J/kg). HF-pad presented cooling performances that compete with conventional pads. Moreover, optimization of HF-pad frame engineering and the technology scaling up to industrial level can allow better thermal and economic performances.
Formation of hydrogen bonding network of methane sulfonic acid at low degree of hydration (MSA)m·(H2O)n (m = 1–2 and n = 1–5)
Authors: Telfah Ahmad , Charifi Z. , latelli N. , Qattan Issam A. , Baaziz H. , Al-Bataineh Qais M. , Alsaad A. M. , Sabirianov R. F. 
Published: May 2024

AbstractThis study employs ab initio calculations based on density functional theory (DFT) to investigate the structural properties, 1H-NMR spectra, and vibrational spectra of methane sulfonic acid (MSA) at low degree of hydration. The findings reveal that energetically stable structures are formed by small clusters consisting of one or two MSA molecules (m = 1 and 2) and one or two water molecules in (MSA)m·(H2O)n (m = 1–2 and n = 1–5).These stable structures arise from the formation of strong cyclic hydrogen bonds between the proton of the hydroxyl (OH) group in MSA and the water molecules. However, clusters containing three or more water molecules (n > 2) exhibit proton transfer from MSA to water, resulting in the formation of ion-pairs composed of CH3SO3− and H3O+species. The measured 1H-NMR spectra demonstrate the presence of hydrogen-bonded interactions between MSA and water, with a single MSA molecule interacting with water molecules. This interaction model accurately represents the hydrogen bonding network, as supported by the agreement between the experimental and calculated NMR chemical shift results.
Telomere length is longer following diapause in two solitary bee species
Authors: Grula Courtney C. , Rinehart Joshua D. , Anacleto Angelo , Kittilson Jeffrey D. , Heidinger Britt J. , Greenlee Kendra J. , Rinehart Joseph P. , Bowsher Julia H. 
Published: May 2024

AbstractThe mechanisms that underlie senescence are not well understood in insects. Telomeres are conserved repetitive sequences at chromosome ends that protect DNA during replication. In many vertebrates, telomeres shorten during cell division and in response to stress and are often used as a cellular marker of senescence. However, little is known about telomere dynamics across the lifespan in invertebrates. We measured telomere length in larvae, prepupae, pupae, and adults of two species of solitary bees, Osmia lignaria and Megachile rotundata. Contrary to our predictions, telomere length was longer in later developmental stages in both O. lignaria and M. rotundata. Longer telomeres occurred after emergence from diapause, which is a physiological state with increased tolerance to stress. In O. lignaria, telomeres were longer in adults when they emerged following diapause. In M. rotundata, telomeres were longer in the pupal stage and subsequent adult stage, which occurs after prepupal diapause. In both species, telomere length did not change during the 8 months of diapause. Telomere length did not differ by mass similarly across species or sex. We also did not see a difference in telomere length after adult O. lignaria were exposed to a nutritional stress, nor did length change during their adult lifespan. Taken together, these results suggest that telomere dynamics in solitary bees differ from what is commonly reported in vertebrates and suggest that insect diapause may influence telomere dynamics.
Impact of the COVID-19 pandemic on pediatric out-of-hospital cardiac arrest outcomes in Japan
Authors: Chida-Nagai Ayako , Sato Hiroki , Yamazawa Hirokuni , Takeda Atsuhito , Yonemoto Naohiro , Tahara Yoshio , lkeda Takanori 
Published: May 2024

AbstractThis study investigates the impact of the COVID-19 pandemic on pediatric out-of-hospital cardiac arrest (OHCA) outcomes in Japan, aiming to address a critical research gap. Analyzing data from the All-Japan Utstein registry covering pediatric OHCA cases from 2018 to 2021, the study observed no significant changes in one-month survival, neurological outcomes, or overall performance when comparing the pre-pandemic (2018–2019) and pandemic (2020–2021) periods among 6765 cases. However, a notable reduction in pre-hospital return of spontaneous circulation (ROSC) during the pandemic (15.1–13.1%, p = .020) was identified. Bystander-initiated chest compressions and rescue breaths declined (71.1–65.8%, 22.3–13.0%, respectively; both p < .001), while bystander-initiated automated external defibrillator (AED) use increased (3.7–4.9%, p = .029). Multivariate logistic regression analyses identified factors associated with reduced pre-hospital ROSC during the pandemic. Post-pandemic, there was no noticeable change in the one-month survival rate. The lack of significant change in survival may be attributed to the negative effects of reduced chest compressions and ventilation being offset by the positive impact of widespread AED availability in Japan. These findings underscore the importance of innovative tools and systems for safe bystander cardiopulmonary resuscitation during a pandemic, providing insights to optimize pediatric OHCA care.
Impaired signaling pathways on Berardinelli–Seip congenital lipodystrophy macrophages during Leishmania infantum infection
Authors: Nogueira Viviane Brito , de Oliveira Mendes-Aguiar Carolina , Teixeira Diego Gomes , Freire-Neto Francisco Paulo , Tassi Leo Zenon , Ferreira Leonardo Capistrano , Wilson Mary Edythe , Lima Josivan Gomes , Jeronimo Selma Maria Bezerra 
Published: May 2024

AbstractBerardinelli–Seip congenital lipodystrophy (CGL), a rare autosomal recessive disorder, is characterized by a lack of adipose tissue. Infections are one of the major causes of CGL individuals’ premature death. The mechanisms that predispose to infections are poorly understood. We used Leishmania infantum as an in vitro model of intracellular infection to explore mechanisms underlying the CGL infection processes, and to understand the impact of host mutations on Leishmania survival, since this pathogen enters macrophages through specialized membrane lipid domains. The transcriptomic profiles of both uninfected and infected monocyte-derived macrophages (MDMs) from CGL (types 1 and 2) and controls were studied. MDMs infected with L. infantum showed significantly downregulated expression of genes associated with infection-response pathways (MHC-I, TCR-CD3, and granzymes). There was a transcriptomic signature in CGL cells associated with impaired membrane trafficking and signaling in response to infection, with concomitant changes in the expression of membrane-associated genes in parasites (e.g. δ-amastins). We identified pathways suggesting the lipid storage dysfunction led to changes in phospholipids expression and impaired responses to infection, including immune synapse (antigen presentation, IFN-γ signaling, JAK/STAT); endocytosis; NF-kappaB signaling; and phosphatidylinositol biosynthesis. In summary, lipid metabolism of the host plays an important role in determining antigen presentation pathways.
Entanglement and quantum coherence of two YIG spheres in a hybrid Laguerre–Gaussian cavity optomechanics
Authors: Hidki Abdelkader , Peng Jia-Xin , Singh S. K. , Khalid M. , Asjad M. 
Published: May 2024

AbstractWe theoretically investigate continuous variable entanglement and macroscopic quantum coherence in the hybrid L–G rotational cavity optomechanical system containing two YIG spheres. In this system, a single L–G cavity mode and both magnon modes (which are due to the collective excitation of spins in two YIG spheres) are coupled through the magnetic dipole interaction whereas the L–G cavity mode can also exchange orbital angular momentum (OAM) with the rotating mirror (RM). We study in detail the effects of various physical parameters like cavity and both magnon detunings, environment temperature, optorotational and magnon coupling strengths on the bipartite entanglement and the macroscopic quantum coherence as well. We also explore parameter regimes to achieve maximum values for both of these quantum correlations. We also observed that the parameters regime for achieving maximum bipartite entanglement is completely different from macroscopic quantum coherence. So, our present study shall provide a method to control various nonclassical quantum correlations of macroscopic objects in the hybrid L–G rotational cavity optomechanical system and have potential applications in quantum sensing, quantum meteorology, and quantum information science.
Water-dispersable photoreactors based on core–shell mesoporous silica particles
Authors: Baliś Andrzej , Lorens Dominika , Gut Arkadiusz , Zapotoczny Szczepan 
Published: May 2024

AbstractRobust solid-core silica particles with submicrometer size and anthracene-containing mesoporous shell were obtained and studied as model water-dispersable photoreactors. An anthracene derivative containing a triethoxysilyl group was synthesized and co-condensed with tetraethoxysilane in various ratios to form a photoactive mesoporous shell with a thickness up to approximately 80 nm on previously prepared solid silica particles. Mesopores of as-synthesized particles, without a commonly applied removal of the micellar templates, offered a confined space for solubilization of hydrophobic molecules. Efficient excitation energy transfer from anthracene chromophores to both hydrophobic (perylene) and hydrophilic (fluoresceine) encapsulated acceptors was observed in an aqueous dispersion of the particles. Photosensitized oxidation of encapsulated perylene was shown to proceed efficiently in such systems serving as water-dispersable photoreactors. Importantly, the designed core–shell systems were found to be stable for a long time (at least 24 months) and robust enough, thanks to the presence of solid cores, to be handled by centrifugation in aqueous dispersions. All these features make them promising candidates for reusable systems for the photosensitized degradation of water pollutants, especially hydrophobic pollutants.
Revealing the hierarchical structure of microbial communities
Authors: Ruth Beatrice , Peter Stephan , Ibrahim Bashar , Dittrich Peter 
Published: May 2024

AbstractMeasuring the dynamics of microbial communities results in high-dimensional measurements of taxa abundances over time and space, which is difficult to analyze due to complex changes in taxonomic compositions. This paper presents a new method to investigate and visualize the intrinsic hierarchical community structure implied by the measurements. The basic idea is to identify significant intersection sets, which can be seen as sub-communities making up the measured communities. Using the subset relationship, the intersection sets together with the measurements form a hierarchical structure visualized as a Hasse diagram. Chemical organization theory (COT) is used to relate the hierarchy of the sets of taxa to potential taxa interactions and to their potential dynamical persistence. The approach is demonstrated on a data set of community data obtained from bacterial 16S rRNA gene sequencing for samples collected monthly from four groundwater wells over a nearly 3-year period (n = 114) along a hillslope area. The significance of the hierarchies derived from the data is evaluated by showing that they significantly deviate from a random model. Furthermore, it is demonstrated how the hierarchy is related to temporal and spatial factors; and how the idea of a core microbiome can be extended to a set of interrelated core microbiomes. Together the results suggest that the approach can support developing models of taxa interactions in the future.
Immune profiling of dedifferentiated liposarcoma and identification of novel antigens for targeted immunotherapy
Authors: Jirovec Anna , Flaman Ashley , Godbout Elena , Serrano Daniel , Werier Joel , Purgina Bibianna , Diallo Jean-Simon 
Published: May 2024

AbstractDedifferentiated liposarcoma (DDLS) is an aggressive, recurring sarcoma with limited treatments. T-cell immunotherapies selectively target malignant cells, holding promise against DDLS. The development of successful immunotherapy for DDLS requires a thorough evaluation of the tumor immune microenvironment and the identification and characterization of targetable immunogenic tumor antigens. To assess the complexity of the human DDLS tumor immune microenvironment and to identify target antigens, we used the nCounter NanoString platform, analyzing gene expression profiles across 29 DDLS and 10 healthy adipose tissue samples. Hierarchical clustering of tumors based on expression of tumor inflammation signature genes revealed two distinct groups, consisting of 15 inflamed tumors and 14 non-inflamed tumors, demonstrating tumor heterogeneity within this sarcoma subtype. Among the identified antigens, PBK and TTK exhibited substantial upregulation in mRNA expression compared to healthy adipose tissue controls, further corroborated by positive protein expression by IHC. This data shows considerable inter-tumoral heterogeneity of inflammation, which should be taken into consideration when designing an immunotherapy for DDLS, and provides a novel targetable antigen in DDLS. The results of this study lay the groundwork for the development of a novel immunotherapy for this highly aggressive sarcoma.
Influence of Li concentration on structural, morphological and electrochemical properties of anatase-TiO2 nanoparticles
Authors: Putjuso Thanin , Putjuso Sasitorn , Karaphun Attaphol , Swatsitang Ekaphan 
Published: May 2024

AbstractLithium-doped anatase-TiO2 nanoparticles (LixTi1-xO2 NPs, x = 0, 0.05, 0.10, 0.15 and 0.20) could be synthesized by a simple sol–gel process. X-ray diffraction (XRD) results displayed the tetragonal (space group: I41/amd) of polycrystalline TiO2 anatase phase. The spectroscopy results of Raman and FT-IR confirmed the anatase phase of TiO2 through the specific modes of metal oxides vibration in the crystalline TiO2. Surfaces micrographs by scanning electron microscope (SEM) of agglomerated LixTi1-xO2 NPs showed a spongy like morphology. Transmission electron microscope (TEM) illustrated a cuboidal shape of dispersed NPs with particle size distributed in a narrow range 5–10 nm. Bruanauer Emmett-Teller (BET) results showed the increased surface area of LixTi1−xO2 NPs with increasing Li content. LixTi1-xO2 NPs (x = 0.05–0.20) working electrodes illustrated a pseudocapacitive behavior with excellent electrochemical properties through the whole cycles of GCD test. Interestingly, Li0.1Ti0.9O2 NPs electrode illustrated a high performance in terms of maximum specific capacitance 822 F g−1 at 1.5 A g−1 in 0.5 M Li2SO4 electrolyte, with excellent capacitive retention 92.6% after 5000 cycles GCD test.
Efficacy and safety of netupitant/palonosetron in preventing nausea and vomiting in diffuse large B cell lymphoma patients undergoing R–CHOP chemotherapy
Authors: Kwak Kunye , Park Yong , Kim Byung Soo , Kang Ka-Won 
Published: May 2024

AbstractDiffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin’s lymphoma, for which cyclophosphamide, doxorubicin, vincristine, and prednisone with rituximab(R–CHOP) is one of the standard regimens. Given that R–CHOP is highly emetogenic, chemotherapy-induced nausea and vomiting (CINV) prevention is clinically important. However, there is a paucity of studies focusing on these patients. This study aimed to ascertain the effectiveness of an oral fixed-dose combination of netupitant and palonosetron (NEPA) in preventing CINV in patients with DLBCL undergoing first-line R-CHOP chemotherapy. Seventy patients were enrolled in this single-center prospective non-comparative study conducted between November 2020 and May 2023 in South Korea. NEPA was administered 1 h prior to chemotherapy initiation on day 1. The primary endpoint of the study was the complete response rate (no emesis, and no rescue medication) during the acute, delayed, and overall phases, which were assessed over a period of 120 h post-chemotherapy. The complete response rates for NEPA were 90.0% [95% CI 80.5, 95.9] for the acute phase, 85.7% [95% CI 75.3, 92.9] for the delayed phase, and 84.3% [95% CI 73.6, 91.9] for the overall phase, with no-emesis rates (acute: 97.1% [95% CI 97.1, 99.7], delayed: 95.7% [95% CI 88.0, 99.1], overall: 92.9% [95% CI 84.1, 97.6]). NEPA was well tolerated with no severe treatment-emergent adverse events. NEPA exhibited substantial efficacy in mitigating CINV in DLBCL patients undergoing R–CHOP chemotherapy, demonstrating high CR and no-emesis rates, and favorable safety profiles.
Patient-centricity in digital measure development: co-evolution of best practice and regulatory guidance
Authors: Aryal Suvekshya , Blankenship Jennifer M. , Bachman Shelby L. , Hwang Soohyun , Zhai Yaya , Richards Jennifer C. , Clay Ieuan , Lyden Kate 
Published: May 2024

AbstractDigital health technologies (DHTs) have the potential to modernize drug development and clinical trial operations by remotely, passively, and continuously collecting ecologically valid evidence that is meaningful to patients’ lived experiences. Such evidence holds potential for all drug development stakeholders, including regulatory agencies, as it will help create a stronger evidentiary link between approval of new therapeutics and the ultimate aim of improving patient lives. However, only a very small number of novel digital measures have matured from exploratory usage into regulatory qualification or efficacy endpoints. This shows that despite the clear potential, actually gaining regulatory agreement that a new measure is both fit-for-purpose and delivers value remains a serious challenge. One of the key stumbling blocks for developers has been the requirement to demonstrate that a digital measure is meaningful to patients. This viewpoint aims to examine the co-evolution of regulatory guidance in the United States (U.S.) and best practice for integration of DHTs into the development of clinical outcome assessments. Contextualizing guidance on meaningfulness within the larger shift towards a patient-centric drug development approach, this paper reviews the U.S. Food and Drug Administration (FDA) guidance and existing literature surrounding the development of meaningful digital measures and patient engagement, including the recent examples of rejections by the FDA that further emphasize patient-centricity in digital measures. Finally, this paper highlights remaining hurdles and provides insights into the established frameworks for development and adoption of digital measures in clinical research.
Dual function of a highly conserved bacteriophage tail completion protein essential for bacteriophage infectivity
Authors: Auzat Isabelle , Ouldali Malika , Jacquet Eric , Fauler Beatrix , Mielke Thorsten , Tavares Paulo 
Published: May 2024

AbstractInfection of bacteria by phages is a complex multi-step process that includes specific recognition of the host cell, creation of a temporary breach in the host envelope, and ejection of viral DNA into the bacterial cytoplasm. These steps must be perfectly regulated to ensure efficient infection. Here we report the dual function of the tail completion protein gp16.1 of bacteriophage SPP1. First, gp16.1 has an auxiliary role in assembly of the tail interface that binds to the capsid connector. Second, gp16.1 is necessary to ensure correct routing of phage DNA to the bacterial cytoplasm. Viral particles assembled without gp16.1 are indistinguishable from wild-type virions and eject DNA normally in vitro. However, they release their DNA to the extracellular space upon interaction with the host bacterium. The study shows that a highly conserved tail completion protein has distinct functions at two essential steps of the virus life cycle in long-tailed phages.