bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk
Authors: Shao Xin , Li Chengyu , Yang Haihong , Lu Xiaoyan , Liao Jie , Qian Jingyang , Wang Kai , Cheng Junyun , Yang Penghui , Chen Huajun , Xu Xiao , Fan Xiaohui 
Published: July 2022

AbstractSpatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics.
Photochemical and thermochemical pathways to S2 and polysulfur formation in the atmosphere of Venus
Authors: Francés-Monerris Antonio , Carmona-García Javier , Trabelsi Tarek , Saiz-Lopez Alfonso , Lyons James R. , Francisco Joseph S. , Roca-Sanjuán Daniel 
Published: July 2022

AbstractPolysulfur species have been proposed to be the unknown near-UV absorber in the atmosphere of Venus. Recent work argues that photolysis of one of the (SO)2 isomers, cis-OSSO, directly yields S2 with a branching ratio of about 10%. If correct, this pathway dominates polysulfur formation by several orders of magnitude, and by addition reactions yields significant quantities of S3, S4, and S8. We report here the results of high-level ab-initio quantum-chemistry computations that demonstrate that S2 is not a product in cis-OSSO photolysis. Instead, we establish a novel mechanism in which S2 is formed in a two-step process. Firstly, the intermediate S2O is produced by the coupling between the S and Cl atmospheric chemistries (in particular, SO reaction with ClS) and in a lesser extension by O-abstraction reactions from cis-OSSO. Secondly, S2O reacts with SO. This modified chemistry yields S2 and subsequent polysulfur abundances comparable to the photolytic cis-OSSO mechanism through a more plausible pathway. Ab initio quantification of the photodissociations at play fills a critical data void in current atmospheric models of Venus.
Evidence accumulation occurs locally in the parietal cortex
Authors: Zhang Zhewei , Yin Chaoqun , Yang Tianming 
Published: July 2022

AbstractDecision making often entails evidence accumulation, a process that is represented by neural activities in a network of multiple brain areas. Yet, it has not been identified where exactly the accumulation originates. We reason that a candidate brain area should both represent evidence accumulation and information that is used to compute evidence. Therefore, we designed a two-stage probabilistic reasoning task in which the evidence for accumulation had to be first determined from sensory signals orthogonal to decisions. With a linear encoding model, we decomposed the responses of posterior parietal neurons to each stimulus into an early and a late component that represented two dissociable stages of decision making. The former reflected the transformation from sensory inputs to accumulable evidence, and the latter reflected the accumulation of evidence and the formation of decisions. The presence of both computational stages indicates that evidence accumulation signal in the parietal cortex is computed locally.
Structural basis for assembly and disassembly of the IGF/IGFBP/ALS ternary complex
Authors: Kim Hyojin , Fu Yaoyao , Hong Ho Jeong , Lee Seong-Gyu , Lee Dong Sun , Kim Ho Min 
Published: July 2022

AbstractInsulin-like growth factors (IGFs) have pleiotropic roles in embryonic and postnatal growth and differentiation. Most serum IGFs are bound in a ternary complex with IGF-binding protein 3 (IGFBP3) and acid-labile subunit (ALS), extending the serum half-life of IGFs and regulating their availability. Here, we report cryo-EM structure of the human IGF1/IGFBP3/ALS ternary complex, revealing the detailed architecture of a parachute-like ternary complex and crucial determinants for their sequential and specific assembly. In vitro biochemical studies show that proteolysis at the central linker domain of IGFBP3 induces release of its C-terminal domain rather than IGF1 release from the ternary complex, yielding an intermediate complex that enhances IGF1 bioavailability. Our results provide mechanistic insight into IGF/IGFBP3/ALS ternary complex assembly and its disassembly upon proteolysis for IGF bioavailability, suggesting a structural basis for human diseases associated with IGF1 and IGFALS gene mutations such as complete ALS deficiency (ACLSD) and IGF1 deficiency.
Learning to rank Higgs boson candidates
Authors: Köppel Marius , Segner Alexander , Wagener Martin , Pensel Lukas , Karwath Andreas , Schmitt Christian , Kramer Stefan 
Published: July 2022

AbstractIn the extensive search for new physics, the precise measurement of the Higgs boson continues to play an important role. To this end, machine learning techniques have been recently applied to processes like the Higgs production via vector-boson fusion. In this paper, we propose to use algorithms for learning to rank, i.e., to rank events into a sorting order, first signal, then background, instead of algorithms for the classification into two classes, for this task. The fact that training is then performed on pairwise comparisons of signal and background events can effectively increase the amount of training data due to the quadratic number of possible combinations. This makes it robust to unbalanced data set scenarios and can improve the overall performance compared to pointwise models like the state-of-the-art boosted decision tree approach. In this work we compare our pairwise neural network algorithm, which is a combination of a convolutional neural network and the DirectRanker, with convolutional neural networks, multilayer perceptrons or boosted decision trees, which are commonly used algorithms in multiple Higgs production channels. Furthermore, we use so-called transfer learning techniques to improve overall performance on different data types.
IL-7/IL7R axis dysfunction in adults with severe community-acquired pneumonia (CAP): a cross-sectional study
Authors: Ampuero Sandra , Bahamonde Guillermo , Tempio Fabián , Garmendia María Luisa , Ruiz Mauricio , Pizarro Rolando , Rossi Patricio , Huenchur Lucía , Lizama Luis , López Mercedes , Avendaño Luis F. , Luchsinger Vivian 
Published: July 2022

AbstractCommunity-acquired pneumonia (CAP) is a worldwide leading cause of death. Recognized risk factors in some severe cases have not been identified. Lymphocytopenia has been frequently described in CAP. Since IL-7, membrane-bound receptor (IL7Rα;CD127) and soluble IL7Rα (sIL7R) are critical in lymphocytes homeostasis, in this work we aimed to evaluate the involvement of the IL-7/IL7Rα axis in the severity of adult CAP, since it has not been explored. The IL7Rα SNPs rs6897932, rs987106, and rs3194051 SNPs in IL7α were genotyped, the systemic expression of the IL7R gene, sIL7R, IL-7, and levels of peripheral IL7Rα+ T lymphocytes were quantified in 202 hospitalized CAP cases. rs3194051GG was more frequent in non-survivors than in survivors; rs987106TT was more frequent and rs3194051AA less frequent in patients at intensive care unit (ICU) than in those not admitted to ICU. IL7Rα gene expression was lower in non-survivors than in survivors, and in severe than in mild cases. CD3+CD127+ lymphocytes were lower in severe than in mild cases; in non-survivors than in survivors and in ICU than in non- ICU admitted cases. sIL7Rα plasmatic levels were higher in non-survivors than in survivors, and in severe than in mild cases. rs6897932CC, rs987106AA and rs3194051GG carriers showed the highest while rs6897932TT showed the lowest sIL7Rα levels. The AUC of sIL7Rα levels predicting 30-day mortality was 0.71. Plasma IL-7 levels were lower in ICU-admitted than in not ICU-admitted and in non-survivors than in survivors. No additional association was detected. In conclusion, rs3194051GG and rs987106TT IL7R genotypes were associated with a poorer prognosis. A significant association between sIL7R levels and SNPs of the IL7R gene is described for the first time in adult CAP. Increased plasmatic sIL7R could contribute to identifying adult CAP cases at risk of death.
Neurophysiological correlates of automatic integration of voice and gender information during grammatical processing
Authors: Alekseeva Maria , Myachykov Andriy , Bermudez-Margaretto Beatriz , Shtyrov Yury 
Published: July 2022

AbstractDuring verbal communication, interlocutors rely on both linguistic (e.g., words, syntax) and extralinguistic (e.g., voice quality) information. The neural mechanisms of extralinguistic information processing are particularly poorly understood. To address this, we used EEG and recorded event-related brain potentials while participants listened to Russian pronoun–verb phrases presented in either male or female voice. Crucially, we manipulated congruency between the grammatical gender signaled by the verbs’ ending and the speakers’ apparent gender. To focus on putative automatic integration of extralinguistic information into syntactic processing and avoid confounds arising from secondary top-down processes, we used passive non-attend auditory presentation with visual distraction and no stimulus-related task. Most expressed neural responses were found at both early (150 ms, ELAN-like) and late (400 ms, N400-like) phrase processing stages. Crucially, both of these brain responses exhibited sensitivity to extralinguistic information and were significantly enhanced for phrases whose voice and grammatical gender were incongruent, similar to what is known for ERPs effects related to overt grammatical violations. Our data suggest a high degree of automaticity in processing extralinguistic information during spoken language comprehension which indicates existence of a rapid automatic syntactic integration mechanism sensitive to both linguistic and extralinguistic information.
Chemometric approach to evaluate the chemical behavior of rainwater at high altitude in Shaune Garang catchment, Western Himalaya
Authors: Kumar Ramesh , Kumar Rajesh , Singh Atar , Arif Mohammad , Kumar Pankaj , Kumari Anupma 
Published: July 2022

AbstractThe present research has been performed to analyze the chemical behavior of rainwater of the Shaune Garang catchment (32.19° N, 78.20° E) in the Baspa basin, located at a high elevation (4221 m above mean sea level) in the Himachal Himalaya, India. During the study period, sixteen rainwater samples were collected from the Shaune Garang catchment at five different sites. The volume-weighted mean (VWM) pH value of rainwater ranged between 4.59 and 6.73, with an average value of 5.47 ± 0.69, indicating the alkaline nature of rainfall. The total ionic strength in the rainwater ranged from 113.4 to 263.3 µeq/l with an average value of 169.1 ± 40.4 µeq/l. The major dominant cations were Ca2+ (43.10%) and Na+ (31.97%) and anions were Cl− (37.68%), SO42− (28.71%) and NO3− (23.85%) in rainwater. The ionic ratios were calculated among all the ions. The fraction of (NO3−  +Cl−) with SO42− was measured as 2.3, which specifies sour faces of rainwater due to HNO3, H2SO4, and HCl. A multivariate statistical assessment of rainwater chemistry through Principal Component Analysis (PCA) shows the significance of four factors controlling 78.37% of the total variance, including four-component (PC1 explained 27.89%, PC2 explained 24.98%, PC3 explained 14.64%, PC4 explained 10.85%). However, the individual contribution of Factor 1(PC1) explains 27.89% of the total variance (78.37%) and displays a strong optimistic loading for Ca2+ and Cl−. Further, high loading of Ca2+ and NO3− and moderate loading of SO42− signify the contribution of burning fossil fuel and soil dust. Anthropogenic and natural pollutants influence the composition of rainwater in the pristine Himalayas due to local and long-distance transportation. The study area receives precipitation from the West and North-West, transporting dust and fossil fuel emissions from the Thar Desert and Northwestern countries.
DJ-1 controls T cell differentiation and osteoclastogenesis in rheumatoid arthritis
Authors: Min Hong Ki , Kim Se Hee , Lee Ji-Yeon , Lee Sang-Heon , Kim Hae-Rim 
Published: July 2022

AbstractHerein, we investigated the effect of DJ-1 on helper T cell differentiation, fibroblast-like synoviocyte (FLS) activation, and osteoclastogenesis in rheumatoid arthritis (RA). Serum and synovial fluid (SF) of RA and osteoarthritis (OA) patients were collected, and DJ-1 and H2O2 levels were investigated. CD4+ cells from peripheral blood mononuclear cells (PBMCs) were cultured under type 17 helper T cell (Th17) polarization conditions, and CD4+ T cell differentiation, pro-inflammatory cytokine levels, and soluble receptor activator of nuclear factor kappa-Β ligand (RANKL) were assessed. RA-FLSs were stimulated with 50 μM H2O2, and DJ-1 (10, 50, 100 ng/mL) to evaluate MMP-9, VEGF, TNF-α, and sRANKL production, while RANKL+ FLSs were assessed using flow cytometry. Monocytes were cultured with RANKL or IL-17A with or without DJ-1 and H2O2-pretreated RA-FLS, and tartrate-resistant acid phosphatase (TRAP) staining and RT-qPCR of osteoclast-related genes were performed. The levels of DJ-1 and H2O2 in serum and SF of RA patients were higher than those of OA patients. Under Th17-polarizing conditions, CD4+RANKL+ and CD4+CCR4+CCR6+CXCR3- T cells decreased, whereas CD4+CD25highFoxp3+ T cell increased after DJ-1 administration. Additionally, IL-17A, TNF-α, and sRANKL levels decreased in DJ-1-treated groups. DJ-1 lowered MMP-9, VEGF, TNF-α, and sRANKL levels, and RANKL+ FLS in ROS-stimulated RA-FLS. Both RANKL and IL-17A stimulated osteoclast differentiation, DJ-1 decreased TRAP+ cell count, and the expression levels of TRAP, ATP6v0d2, NFATc1, and CTSK. These findings were also observed in in vitro osteoclastogenesis with DJ-1 pretreated RA-FLS. As DJ-1 regulates Th17/Treg imbalance, pro-inflammatory cytokine production, RA-FLS activation, and osteoclastogenesis, it holds potential for RA therapy.
Evidence for isotropic s-wave superconductivity in high-entropy alloys
Authors: Leung Casey K. W. , Zhang Xiaofu , von Rohr Fabian , Lortz Rolf , Jäck Berthold 
Published: July 2022

AbstractHigh-entropy alloys (HEA) form through the random arrangement of five or more chemical elements on a crystalline lattice. Despite the significant amount of resulting compositional disorder, a subset of HEAs enters a superconducting state below critical temperatures, $$T_{\text{c}}<10\,$$

T
c

<
10

K. The superconducting properties of the known HEAs seem to suffice a Bardeen–Cooper–Schrieffer (BCS) description, but little is known about their superconducting order parameter and the microscopic role of disorder. We report on magnetic susceptibility measurements on films of the superconducting HEA (TaNb)$$_{1-x}$$

1
-
x

(ZrHfTi)$$_{x}$$

x

for characterizing the lower and upper critical fields $$H_{\text{c,1}}(T)$$

H
c,1

(
T
)

and $$H_{\text{c,2}}(T)$$

H
c,2

(
T
)

, respectively as a function of temperature T. Our resulting analysis of the Ginzburg–Landau coherence length and penetration depth demonstrates that HEAs of this type are single-band isotropic s-wave superconductors in the dirty limit. Despite a significant difference in the elemental composition between the $$x=0.35$$

x
=
0.35

and $$x=0.71$$

x
=
0.71

films, we find that the observed $$T_{\text{c}}$$

T
c

variations cannot be explained by disorder effects.
Predictors of fulvestrant long-term benefit in hormone receptor-positive/HER2 negative advanced breast cancer
Authors: Torrisi Rosalba , Vaira Valentina , Giordano Laura , Destro Annarita , Basilico Vera , Mazzara Saveria , Salvini Piermario , Gaudioso Gabriella , Fernandes Bethania , Rudini Noemi , Masci Giovanna , Santoro Armando 
Published: July 2022

AbstractWe retrospectively investigated in women treated with fulvestrant for HR+/HER2 negative advanced breast cancer clinical, pathological and molecular features associated with long-term benefit from treatment defined as being progression-free at 18 months. Specifically, we analyzed on formalin-fixed paraffin-embedded tumor samples ESR1 and PI3KCA mutations and miRNAs profiles. 59 patients were evaluable (median age of 67 years, range 32–92). 18-month PFS rate was 27%; the lack of visceral metastases significantly predicted the likelihood of being progression-free at 18 months, while PI3KCA mutations, found in 36% of patients, were not associated with 18-month PFS. As of miRNAs, miR-549a, miR-644a, miR-16-5p were negatively while let-7c-5p was positively associated with 18-month PFS. In addition, miR-520d-3p and miR-548g-3p values were significantly lower while miR-603, miR-181a-5p and miR-199a-miR-199b-3p values were significantly higher in patients achieving 18-month PFS. In silico analysis of targets modulated by these two latter groups of miRNAs show that in patients achieving 18-month PFS the Hippo and Wnt signaling pathways were predicted to be upregulated while endocrine resistance was potentially repressed by miR-603, miR-181a-5p and miR-199a-miR-199b-3p. Our results provide additional clues on the molecular mechanisms involved in fulvestrant activity and resistance. Underlying pathways should be further elucidated and confirmed in larger cohorts.
Intervention is a better predictor of tDCS mind-wandering effects than subjective beliefs about experimental results
Authors: Gordon Matilda S. , Seeto Jennifer X. W. , Dux Paul E. , Filmer Hannah L. 
Published: July 2022

AbstractBlinding in non-invasive brain stimulation research is a topic of intense debate, especially regarding the efficacy of sham-controlled methods for transcranial direct current stimulation (tDCS). A common approach to assess blinding success is the inclusion of correct guess rate. However, this method cannot provide insight into the effect of unblinding on observed stimulation outcomes. Thus, the implementation of measures to systematically evaluate subjective expectation regarding stimulation is needed. Previous work evaluated subjective effects in an earlier study which reported a mind-wandering and tDCS data set and concluded that subjective belief drove the pattern of results observed. Here we consider the subjective and objective intervention effects in a key contrast from that data set—2 mA vs. sham—which was not examined in the reanalysis. In addition, we examine another key contrast from a different tDCS mind-wandering study that employed similar methodology. Our findings support objective intervention as the strongest predictor of the observed effects of mind-wandering in both re-analyses, over and above that of subjective intervention. However, it is important to control for and understand the possible inadequacies of sham-controlled methods.
Rosmarinus officinalis L. hexane extract: phytochemical analysis, nanoencapsulation, and in silico, in vitro, and in vivo anti-photoaging potential evaluation
Authors: Ibrahim Nehal , Abbas Haidy , El-Sayed Nesrine S. , Gad Heba A. 
Published: July 2022

AbstractA shift towards natural anti-aging ingredients has spurred the research to valorize traditionally used plants. In this context,Rosmarinus officinalisL. was evaluated for its photoprotective, antioxidant, anti-inflammatory, and anti-wrinkling properties. GC/MS and LC-ESI-HRMS based phytochemical profiling of rosemary leaves hexane extract resulted in the identification of 47 and 31 compounds, respectively and revealed rich content in triterpenoids, monoterpenoids and phenolic diterpenes. In vitro assays confirmed the antioxidant, anti-aging, and wound healing potential of rosemary extract along with a good safety profile, encouraging further development. A systematic molecular modelling study was conducted to elucidate the mechanistic background of rosemary anti-aging properties through the inhibitory effects of its major constituents against key anti-aging targets viz. elastase, collagenase, and hyaluronidase. Development of rosemary extract lipid nanocapsules-based mucoadhesive gels was performed to improve skin contact, permeation, and bioavailability prior to in vivo testing. The developed formulae demonstrated small particle size (56.55–66.13 nm), homogenous distribution (PDI of 0.207–0.249), and negatively charged Zeta potential (− 13.4 to − 15.6). In UVB-irradiated rat model, topical rosemary hexane extract-loaded lipid nanocapsules-based gel provided photoprotection, restored the antioxidant biochemical state, improved epidermal and dermal histological features, and decreased the level of inflammatory and wrinkling markers. The use of rosemary hexane extract in anti-aging and photoprotective cosmeceuticals represents a safe, efficient, and cost-effective approach.
Significance of concentration-dependent viscosity on the dynamics of tangent hyperbolic nanofluid subject to motile microorganisms over a non-linear stretching surface
Authors: Siddique Imran , Abdal Sohaib , Din Irfan Saif Ud , Awrejcewicz Jan , Pawłowski Witold , Hussain Sajjad 
Published: July 2022

AbstractThe communication describes a theoretical framework for tangent hyperbolic fluid of nano-biofilm due to an extending or shrinking sheet that comprises a stagnation point flow, chemical reaction with activation energy, and bioconvection of gyrotactic microorganisms. The varying transport features due to dynamic viscosity, thermal conductivity, nano-particle mass permeability and microbe organisms diffusivity are taken into account for the novelty of this work. The inspiration is developed to enhance heat transfer. A set of leading partial differential equations is formed along with appropriate boundary constraints. Using similarity transformations, the basic formulation is transitioned into non-linear differential equations. To produce observational data, the shooting technique and Runge-Kutta fourth order method are employed. The coding of numerical scheme is developed in Matlab script. The visual representation of the effects of diverse fluid transport properties and distinctive parameters on speed, temperature, concentration and motile density are evaluated. The velocity become faster when the parameters $$\omega $$
ω
, $$\lambda $$
λ
, $$\epsilon $$
ϵ
and $$V_0$$

V
0

are enhanced. Brownian motion, thermal conductivity, heat generation as well as thermophoresis factors all strengthen the temperature distribution, however the nano-particle concentration profile is enhanced as the nano-particle mass conductivity variable, activation energy as well as the thermophoresis variable are boosted. The microorganism density improves significantly when the microorganism diffusivity factor increases. The skin friction, Sherwood number, Nusselt number and motile density number decline against the incremented transport parameters.