bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of novel dual PTPN1 and PTPN2 inhibitors
Authors: Bosque Alberto , Howard J Natalie , Zaikos Thomas , Levinger Callie , Rivera Esteban , McMahon Elyse , Sanz Marta , Copertino Dennis , Wang Weisheng , Soriano-Sarabia Natalia , Jones R. Brad 
Published: July 2023

Abstract
Nonreceptor tyrosine phosphatases (NTPs) play an important role regulating protein phosphorylation and have been proposed as attractive therapeutic targets for different diseases. We have previously identified that 3-Hydroxy-1,2,3-benzotriazin-4(3H)-one (HODHBt) enhanced STAT activation upon cytokine treatment. Here, we demonstrated that HODHBt interacts and inhibits the catalytic domain of the NTPs PTPN1 and PTPN2. We confirmed that PTPN1 and PTPN2 specifically control the phosphorylation of STATs. PTPN1 and PTPN2 have been identified as intracellular checkpoint inhibitors that limit immune effector function. We validated that HODHBt enhanced CD8 and γδ-T cells immune effector functions. Finally, we identified a new family of compounds that act as dual PTPN1/PTPN2 inhibitors. Thus, our studies provide a new series of scaffold molecules for the development of specific PTPN1/PTPN2 inhibitors.
Crustal features of the Claritas Rise region indicate a mobile lithosphere on early Mars
Authors: Dohm James , Anderson Robert , Baker Victor , Spagnuolo Mauro , Karunatillake Suniti , Viviano Christina , Álvarez Orlando , Robbins Stuart , Williams Jean-Pierre , Fink Wolfgang , Hare Trent , Yin An , Mahaney William , Komatsu Goro , Schulze-Makuch Dirk , Yan Jiango , Judice Taylor , Fairén Alberto 
Published: July 2023

Abstract
Ancient Martian orogenesis remains controversial, ranging from mantle plumes to continental-scale gravity sliding to plate tectonism. Here, we consider Claritas Rise, an ancient, complex, Martian orogeny, as a case study in mountain building resulting from mobile lithospheric activity, using a geologic synthesis of comparative planetology. Claritas's juxtaposed serpentine and carbonate rocks, along a structurally controlled margin, compares to Earth's serpentine mélanges (e.g., Altai) that result from continental collisional processes. A less dense, older, deformed felsic/feldspathic crust may cause Claritas's gravity lows, as occurs in Earth's convergent plate boundary settings (e.g., Himalayas, Japan, Andes). This geochemically matches its regionally elevated incompatibles, potassium and thorium, relative to younger embaying lava flows. Claritas’ tectonic structures geometrically resemble the transtensional-extensional features of the Baikal Rift System located in southeastern Russia. Steeply dipping beds along a northeast-oriented ridge of Claritas also contain blocks resembling Earth's olistostromes. A mega-geomorphological pattern of landforms, including Claritas at its center, approximates that of the Western United States (i.e., where denser mafic Farallon Plate subducted beneath the buoyant, mafic/felsic North American Plate). An ancient mobile lithosphere offers a unifying explanation for these Earth counterparts on Mars while also addressing other features of interest, including crustal thickness differences across the topographic dichotomy and andesite-granite detections.
Controlled Growth of the Inorganic Backbone in Low-Dimensional Perovskites for Efficient, Stable, Semi-Transparent Wide Bandgap Perovskite Solar Cells
Authors: Zanetta Andrea , Vishal Badri , Faini Fabiola , Pica Giovanni , Marras Sergio , Yildirim Bumin , Babics Maxime , Ugur Esma , Aydin Erkan , De Wolf Stefaan , De Bastiani Michele , Grancini Giulia 
Published: July 2023

Abstract
Wide bandgap (WB) perovskites are of interest for envisioned applications in coloured and semi-transparent solar cells. For this, phase pure low dimensional perovskites (LDP) are of promise as they pair a tuneable wide bandgap with stability. However, so far, the power conversion efficiency (PCE) of LDP solar cells barely touched a few percentages, mainly due to inefficient charge transport being the inorganic layer spaced by organic sheets. To overcome such limit is essential to control the growth of the crystalline backbone, which is dictated by the alignment of the inorganic planes. Here, we demonstrate an effective strategy, based on the judicious choice of additives and controlled seed growth in the perovskite solution, to guide the crystallization of phase pure LDPs inorganic layers perpendicularly to the substrate. The vertically aligned LDP solar cells with only two inorganic layers held together (refereed to n = 2) and a bandgap of 2.0 eV, outperformed their non-oriented 2D counterpart, boosting the PCE to a record value of 9.4%. Furthermore, this sets a benchmark for the stability of WB PSCs, where 80% of the initial performance was retained after ~ 100 h illumination. To broaden the scope of our method, we fabricated semi-transparent LDP devices (transmittance > 30%) with a PCE of 6% paving the way for the development of tuneable smart solar devices.
Denaturing mass photometry for straightforward optimization of protein-protein cross-linking reactions at single-molecule level
Authors: Cianferani Sarag , Gizardin-Fredon Hugo , Santo Paulo , Chagot Marie-Eve , Charpentier Bruno , Banderas Tiago , Manival Xavier , Hernandez-Alba Oscar 
Published: July 2023

Abstract

Mass photometry (MP) is a versatile, fast and low sample-consuming biophysical technique that gained interest in structural biology to study noncovalent assemblies in native conditions. We report here on a novel method to perform MP analysis in denaturing conditions (dMP) and its application for fast, accurate and straightforward optimization of chemical reactions in cross-linking mass spectrometry (XL-MS) workflows. dMP consists in a robust 2-step protocol that ensures 95% of irreversible denaturation within only 5 min. The proposed single-molecule method clearly overcomes the limitations and outperforms gold standard SDS-PAGE, as illustrated on several biological complexes. dMP provides an unprecedented and unmatched in-solution quantification of all coexisting XL species, including sub-complexes and non-specific XL aggregates, along with identification of significantly higher numbers of XL dipeptides in MS. We anticipate single-molecule dMP to be a high-impact game-changer for the XL-MS community with the potential to leverage the quality and reliability of XL-MS datasets.
Sequence-to-expression approach to identify etiological non-coding DNA variations in P53 and cMYC-driven diseases
Authors: Kin Katherine , Bhogale Shounak , Zhu Lisha , Thomas Derrick , Bertol Jessica , Zheng W. Jim , Sinha Saurabh , Fakhouri Walid D. 
Published: July 2023

Abstract
Background and methods
Disease risk prediction based on DNA sequence and transcriptional profile can improve disease screening, prevention, and potential therapeutic approaches by revealing contributing genetic factors and altered regulatory networks. Despite identifying many disease-associated DNA variants through genome-wide association studies, distinguishing deleterious non-coding DNA variations remains poor for most common diseases. We previously reported that non-coding variations disrupting cis-overlapping motifs (CisOMs) of opposing transcription factors significantly affect enhancer activity. We designed in vitro experiments to uncover the significance of the co-occupancy and competitive binding and inhibition between P53 and cMYC on common target gene expression.
Results
Analyzing publicly available ChIP-seq data for P53 and cMYC in human embryonic stem cells and mouse embryonic cells showed that ~ 344–366 genomic regions are co-occupied by P53 and cMYC. We identified, on average, two CisOMs per region, suggesting that co-occupancy is evolutionarily conserved in vertebrates. Our data showed that treating U2OS cells with doxorubicin increased P53 protein level while reducing cMYC level. In contrast, no change in protein levels was observed in Raji cells. ChIP-seq analysis illustrated that 16–922 genomic regions were co-occupied by P53 and cMYC before and after treatment, and substitutions of cMYC signals by P53 were detected after doxorubicin treatment in U2OS. Around 187 expressed genes near co-occupied regions were altered at mRNA level according to RNA-seq data. We utilized a computational motif-matching approach to determine that changes in predicted P53 binding affinity by DNA variations in CisOMs of co-occupied elements significantly correlate with alterations in reporter gene expression. We performed a similar analysis using SNPs mapped in CisOMs for P53 and cMYC from ChIP-seq data in U2OS and Raji, and expression of target genes from the GTEx portal.
Conclusions
We found a significant correlation between change in motif-predicted cMYC binding affinity by SNPs in CisOMs and altered gene expression. Our study brings us closer to developing a generally applicable approach to filter etiological non-coding variations associated with P53 and cMYC-dependent diseases.
Effects of European Propolis administration on the growth performance, health status, selected blood biochemical and immunological variables of pre-weaning calves
Authors: Ahmadi Fatemeh , Mudroň Pavol , Ivančová Petra , Mohri Mehrdad , Ahmadi Saba , Gomulec Pavel , Kremeň Jozef , Mekková Simona , Maryan Kadasi , Dolník Michal 
Published: July 2023

Abstract
The present study aimed to investigate the effects of oral European Propolis supplementation on health status, growth performance, hematological, and serum biochemical variables of neonatal dairy calves. Twenty-four neonatal dairy calves were enrolled in this study from 48 hours after birth until seven days old. A complete clinical examination was performed daily during the study, by the same person. Blood sampling, body measurements, and lung ultrasonography were conducted on days 0,7,14 and 28. The concentrations of albumin, total protein, total immunoglobulin, triglyceride, total cholesterol, urea, creatinine, inorganic phosphate, and activities of aspartate aminotransferase, alanine aminotransferase, and gamma-glutamyl transferase were measured. PEE supplementation had no significant effect on body weight, daily weight gain, length, and height (P > 0.05). Pulmonary examination scores by ultrasonography for subclinical pneumonia in this study showed a significant difference at different times of examination. However, no significant difference between treatment and control groups. Days with navel ill infection were significantly lower in the propolis treatment group in comparison with control (P value = 0.016). There was not any significant difference concerning days in fever and diarrhea between trial groups (P value = 0.44 and 0.15, respectively). There was not a significant difference in hematological and biochemical variables between trial groups. Our results suggest that European Propolis had no positive effects on growth performance, hematological, and biochemical blood variables. In conclusion, supplementation of the Propolis may be beneficial for better navel ill diseases control in new- born dairy calves. Even though, further studies are needed to clarify propolis effects.
Geochemical fractionation of trace metals and ecological risk assessment of surface sediments for a simulated dredging area in Sepetiba Bay - Brazil
Authors: Vicente Murilo de Carvalho , Trevisan Cleuza Leatriz , de Carvalho Ângelo Cezar Borges , de Oliveira Braulio Cherene Vaz , de Rezende Carlos Eduardo , Machado Wilson , Wasserman Julio Cesar 
Published: July 2023

Abstract
The Sepetiba Bay (Southeast Brazil) is a known Cd and Zn contaminated site that received spills of a large slag pile leachate from a Zn smelter. With important harbors, Sepetiba Bay demands periodic dredging operations which affect directly on the mobility of the metals. The main goal of this work was to assess metal mobility in sediments of a simulated dredging area in this tropical bay. To achieve this goal 18 superficial sediment samples were collected within this simulated area. pH and Eh of the interstitial water were measured in situ, while the sediments were analyzed for grain size, organic carbon and total nitrogen, total metals. Metal mobility assessment was evaluated with a sequential extraction procedure, proposed by the European Community Bureau of Reference (BCR). The results demonstrate that Cd and Zn are mainly associated with the exchangeable fraction (mean concentrations 1.4 mg kg− 1 and 149.4 mg kg− 1 respectively) and reducible fractions (mean concentrations 0.27 mg kg− 1 and 65.54 mg kg− 1 respectively), while Fe, Cr, Cu, Ni, and Al are associated with the residual fraction. Metals that are associated with the residual fraction are probably related to the mineral assembly of the sediment and should not represent a considerable environmental risk for the biota. The two metals associated with the exchangeable and reducible fraction respond to strongly reducing characteristics on surface sediments, which are affected by reduced hydrodynamics and high organic matter input. However, Cd and Zn could constitute a risk, mainly during resuspension events, when alterations of pH, and Eh, promoted by oxygenation of sediments can release them to the water column and result in increased association to the exchangeable fraction.
Brief, unmoderated cross-partisan discussions can reduce political polarization
Authors: de Jong Jona 
Published: July 2023

Abstract
Can cross-partisan discussions reduce political polarization? Existing research studies lengthy, moderated interactions that avoid substantive disagreement. This focus hampers scalability, limits understanding of how effects are achieved, and leaves open whether results travel to real-world, polarized contexts. This article reports results from an experiment in which 580 UK Labour and Conservative party voters were matched to have a ten-minute, unmoderated chat discussion about a contentious policy issue. The discussion immediately reduced affective polarization, moderated issue opinions, and durably increased willingness to engage in cross-partisan discussions. Absent moderation, most respondents naturally engaged in conciliatory behaviour by sharing personal experiences, including each other in the discussion and attempting to find common ground. I also show that this type of discussion exercise is scalable. The platform was voluntarily used by more than 100.000 people in the five weeks before the Dutch 2021 parliamentary elections, though almost no data was collected.
SNPRS:Stacked Neural network for predicting Polygenic Risk Score
Authors: Kim Sun bin , Kang Joon Ho , Cheon MyeongJae , Kim Dong Jun , Lee Byung-Chul 
Published: July 2023

Abstract
In recent years, polygenic risk scores (PRS) have increasingly been used to predict disease susceptibility from genome-wide association studies (GWAS) outcomes. However, these models are limited by overfitting and potential overestimation of the effect size of correlated variants. To address these issues, this study presents a novel Stacked Neural Network Polygenic Risk Score (SNPRS) approach. SNPRS combines outputs from multiple neural network models trained using genetic variants selected across a wide range of p-value thresholds, thus capturing a broader spectrum of genetic variants and more accurately determining the effect size of variant combinations. We tested SNPRS using real data from the UK Biobank to predict the genetic risk of breast and prostate cancer. The results show that SNPRS outperforms conventional models and a single deep neural network model, suggesting that it can significantly enhance the predictive accuracy and relevance of PRS in genetic research.
Electronic and Optical Properties of Zinc-BlendeB x Ga 1−x N and Al x Ga 1−x N Ternary Alloys ByAlchemical Mixing of Pseudopotentials
Authors: Bamgbose M. K. , Adebayo G. A. 
Published: July 2023

Abstract
Density Functional Theory-Generalised Gradient Approximation (DFT-GGA)is employed to study electronic and optical properties of B x Ga 1−x N and Al x Ga 1−x Nternary alloys. The properties determined are equilibrium lattice parameter,bulk modulus, band structure, density of states(DOS), band gap, real and imagi-nary dielectric functions, static dielectric function, refractive index, static refrac-tive index, absorption coefficient, and intrinsic interband absorption. The directband gaps of these alloys are tuned up to 2.95eV for B x Ga 1−x N and 3.12eV forAl x Ga 1−x N . The results obtained in this work are in excellent agreement withother theoretical and experimental works. The calculation indicates that thesealloys are potential candidates of ultraviolet Light Emitting Diodes(LEDs) andultraviolet Laser Diodes(LDs).
Shoreline Dynamics During 1972-2022, and Its Implications, Vedaranniyam Region, Tamil Nadu, India
Authors: Anandhan VIJAY , Jayaraman Saravanavel , Somasundaram Ramasamy 
Published: July 2023

Abstract

The coastal zones always remain dynamically active with continued land building and land loss activities, as these form the provinces where various tectonic, fluvial, Aeolian, coastal and marine geomorphic processes interface with each other in varying dynamism and duration. Such morphological changes along the coasts do only control the environment of the coastal systems. In this connection, the east of India is unique with the complex tectonic and geomorphic processes, and thus the dynamically changing morphologies. Amongst various processes, the littoral currents are one of the dynamic processes along the east coast of India which move clockwisely all along the coast from Cape Comorin in the south to Andamans in the north during the non- northeast monsoonic months (Mar-Oct) and anticlockwisely from Andamans to down south of Tamil Nadu coast during northeast monsoonic months (Nov-Feb). This causes continued erosion and deposition all along the coast. This has been discretely seen in the form of rapid land growth in Vedaranniyam nose region in the centre and the land loss or erosion both in the northern and southern sectors of the Vedaranniyam nose region. The detailed mapping of the shorelines and the quantitative studies on the erosion/ deposition phenomenon from the shorelines of different periods deduced from the satellite Infra-red & Near Infra-red data of 1972, 1997, 2004,2006, 2009, 2016, 2018 & 2022 periods showed that the land has grown to an average area of 1.27 sq.km. from 1972–2022 in the central Vedaranniyam nose region with the land loss or the erosion on the northern and southern sectors. The Areal extent of the land growth was further visualised for every 500 years viz 2500, 3000, 3500 and so on. This indicated that, in the context of the current sea bed topography observed in GEBCO data in-between the Vedaranniyam nose and Jaffna peninsula, these two lands will get connected by a land bridge in another 10,000 or 12,000 years. Such land bridging will also lead to the formation of a caught-up sea to its south which may become a land in-between Rameswaram coast in the west and Jaffna coast in the east in course of time.
Factors influencing the first and the fifth years adherence to adjuvant endocrine therapy in breast cancer patients in a low income country
Authors: Nicoletti Antonio Pedro , Damin Andréa 
Published: July 2023

Abstract
PURPOSE: breast cancer is the leading cause of cancer death in Brazil and in many countries around the world. In order to minimize the risk of recurrence and death, adjuvant endocrine therapy (AET) is used in women whose tumors express hormone receptors; however, the therapy is associated with low rates of compliance. Therefore, we sought to evaluate the proportion of patients who are adherent/non-adherent to AET at the beginning of the therapy (1st year) and at its end (5th year).
METHODS: cross-sectional study assessing adherence through the Brief Medication Questionnaire.
RESULTS: it was identified that eventual failures in maintaining the correct adherence to the treatment have risen from 23% of patients in the 1st year of treatment to 35% of patients in the 5th year (p=0.005). In both groups, use of aromatase inhibitors, polypharmacy of at least 3 mediations and the previous diagnosis of DM or SAH have contributed to low adherence among patients.
CONCLUSION: the proportion of patients who are not adherent to AET was high in both cohorts, and the rate of non-adherent patients rises over time. It is essential to incorporate screening methods for lack of compliance to AET, as well as measures to try to reduce non-persistence to the treatment, such as educating the patients on the benefits of the treatment, managing comorbidities through lifestyle changes and, therefore, reducing polypharmacy and, above all, detecting and treating very early the adverse effects of AET that might interfere with its correct use
A genome-wide association study reveals human genetic impact on the nasal microbial diversity, taxa and functions
Authors: Zhang Tao , Liu Xiaomin , Tong Xin , Zou Leying , Ju Yanmei , Liu Mingliang , Han Mo , Lu Haorong , Yang Huanming , Wang Jian , Zong Yang , Liu Weibin , Xu Xun , Jin Xin , Xiao Liang , Jia Huijue , Guo Ruijin 
Published: July 2023

Abstract
The nasal cavity harbors diverse microbiota that contribute to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1,401 healthy individuals, we demonstrated that host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10− 10): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational and Mendelian randomization analyses consistently revealed that several metabolites such as cystine, cystathionine, and glutamic acid play crucial roles in the host metabolism-nasal microbiota interplays. This study indicates that the contribution of the host genome to the nasal microbiome is not weaker than that of other host factors.