bluuebunny/crossref_metadata_2025_split huggingface dataset:
Super-enhancer-associated LINC00963 promotes epithelial-mesenchymal transition in gastric cancer
Authors: Du Hong , Xiang Tingting , Xia Ying , Jin Yong , Deng Fahua , Xia Wansong , Li Hongyu , Cheng Shuqiang , Lan Bingxue , Wei Sixi , Song Cunfeng , Huang Hai 
Published: March 2024

Abstract
Background
In clinical practice, gastric cancer (GC) is a common malignancy with high morbidity. Accumulating research has revealed that lncRNAs are involved in the development and metastasis of tumor tissues in multiple cancers. As reported, LINC00963, a typical lncRNA is aberrantly expressed in gastric cancer. However, the underlying mechanisms of super-enhancers mediating remain unclear.
Materials and methods
The GC cell line enhancer-super-enhancer data were downloaded and analyzed from the NCBI database (GSE75595). Combined RT-qPCR and Sanger sequencing were employed to identify three variants of LINC00963 in gastric cell lines and peripheral blood samples from gastric cancer patients. The gene expression was detected through RT-qPCR, and their encoded protein expression levels were mesured by western blot. Transwell assayswere applied to assess the cell invasion and migration, while the apoptosis rate was tested by flow cytometry. A xenograft model was applied to simulate the tumor development process, during which the effect of LINC00963 on promoting tumorigenesis were investigated.
Results
Analysis of the GC cell line enhancer-super-enhancer data revealed a high expression of LINC00963 driven by super-enhancer. The variant 1 and variant 2 of LINC00963 exhibited high expression in GC cell line and the peripheral blood of gastric cancers. After down-regulated variant 1 of LINC00963, the results showed a significant increase in cell apoptosis rate. LINC00963 expression in GC cell line reduced upon exposure to a low dose of the bromodomain and extra-terminal inhibitor, JQ1, which resulted in a decrease of the protein levels of β-catenin and ZEB1. As a result, the protein expression levels of several marker proteins related to epithelial-mesenchymal transition (EMT), such as Vimentin, N-cadherin and Snail were observed to decrease, which may lead to an inhibition on GC cells metastasis, thereby suppressing tumor growth.
Conclusion
This study demonstrated that the Super-enhancer-associated LINC00963 is via a Wnt/β-catenin pathway that promotes EMT and tumor metastasis in gastric cancer.
Risk factors and the establishment of nomogram model for failure of air enema reduction in children with Ileocolic Intussusception
Authors: Xiong Jie , Wang Jun , Luo Bo , Zhao Yi , Qi Zhao-yang , Hu Gao-Lian , Zhou Ping-hui , Li Tian-Liang 
Published: March 2024

Abstract
Objective: This study aims to identify the risk factors associated with the failure of air enema reduction in children diagnosed with Ileocolic Intussusception, and subsequently develop a nomogram model to predict the likelihood of this failure.
Method:The retrospective analysis involved the examination of clinical data from 502 children diagnosed with intussusception who were admitted to the Children's Surgery Center of the First People's Hospital of Zigong City, Sichuan Province between June 2017 and June 2022. Out of these cases, 87 (17.3%) experienced failure in air enema reduction, while 100 cases (19.9%) required surgical intervention. Univariate and multivariate analyses were conducted to identify the risk factors associated with air enema reduction failure in children. Additionally, a nomogram was developed to establish a risk assessment model for predicting the likelihood of air enema reduction failure. Receiver operating characteristic curve (ROC) and AUC values were used to evaluate the accuracy of the model.
Results: The findings from the Univariate analysis indicate that several factors, including overweight, abdominal mass, abdominal distension, location of intussusception, length and diameter of intussusception, ileocecal valve edema, frequency of enema, and pathological factors, are significantly associated with the failure of intussusception air enema reduction in children (p < 0.05). The results of the multivariate analysis indicated that several factors were found to be independent risk factors for the failure of air enema reduction in children. These factors included overweight (OR=4.02, 95%CI 2.15-7.51, P < 0.001), location of intussusception (OR=3.39, 95%CI 1.31-8.77, P=0.012), times of enema (OR=2.18, 95%CI 1.27-3.77, P=0.005), and pathological factors (OR=2.54, 95%CI 1.17-5.49, P=0.018). The risk assessment model's nomogram had a total score of 260 points, and the area under the curve (AUC) value of the nomogram was 0.743.
Conclusion The failure of air enema in children can be attributed to various risk factors, including overweight, location of intussusception, the timing of enema, and pathological factors. Furthermore, the risk assessment model that has been developed exhibits promising clinical predictive capabilities.
Sustainability of opioid agonist therapy programmes in Belarus, the Republic of Moldova, Tajikistan and Ukraine in the context of transition from Global Fund support during 2020-2023
Authors: Stuikyte Raminta , Varentsov Ivan , Dvoriak Sergii , Filippovych Myroslava , Kralko Aleksei , Malikov Naimdzhon , Iatco Ala , Latypov Alisher , Cook Catherine 
Published: March 2024

Abstract

Background
Most national programmes of opioid agonist therapy (OAT) in Eastern Europe and Central Asia are at a critical juncture for building their sustainability due to decreasing support from the Global Fund and other international HIV funders. Therefore, it is timely to identify the status, trends, opportunities and risk factors of OAT preparedness in the face of donor transition.
Methods
The study assessed the OAT sustainability progress in 4 countries: Belarus, the Republic of Moldova, Tajikistan and Ukraine. The national assessments were conducted in 2020 and repeated during 2022–2023. In total, 363 sources were reviewed and used, 83 interviews with key informants and 13 focus groups were conducted with clients, using a joint methodology and a defined Framework with three dimensions: ‘Policy & Governance’; ‘Finance & Resources’; and, ‘Services’.
Results
All four countries have made improvements to increase OAT sustainability, though it varied. In 2022, Ukraine had a substantial degree of sustainability, followed by Belarus and Moldova with a moderate degree, while Tajikistan’s sustainability was at moderate-to-high risk. No country achieved a high degree of OAT sustainability in any of the three dimensions measured. However, a high degree of sustainability was reported for at least one indicator in Belarus, Moldova and Ukraine: ‘Medicines’; ‘Financial resources’; ‘Evidence and information systems’; ‘Service Accessibility’; or, ‘Service integration & quality’. On average, the greatest improvement between 2020 and 2022 was seen for ‘Availability & coverage’; ‘Financial resources’; ‘Service quality & integration’; and, ‘Service accessibility’. The highest risks across the countries, notably in Belarus and Tajikistan, were recorded for the indicator, ‘Availability and coverage’. Of concern is that the least progress, or even a decline, was found in ‘Human resources’ within the sustainability indicator.
Conclusions
OAT sustainability in 4 analysed countries remains at risk, although those countries are at a different point of donor transition. OAT resilience and ability to scale up depend upon multiple factors. Political will and continued funding are two of them, as demonstrated by Ukraine’s progress despite challenges posed by Russia’s full-scale invasion in 2022. The results show that both financial and programmatic areas are at risk and stagnating progress requires collective efforts.
Path Enumeration Solution for Evaluating Reliability, Based on the Path Algebra Framework
Authors: Prekas Stelios , Trakadas Panagiotis , Karkazis Panagiotis 
Published: March 2024

Abstract

The demand for connectivity in this fourth industrial revolution, is growing in an exponential rate. As the Fourth-Generation communication systems are replaced by the Fifth and Sixth-Generation ones, a plethora of fundamental performance issues need to constantly be addressed. Virtual network reliability is one of those main challenges for deploying resilient service-centric and user-centric scenarios in Next-Generation Networks. The need for strengthening critical applications dictates the emergence of mechanisms that could inherently produce more reliable resource allocations, either at the cloud or edge level. However, until the adoption of fully artificially intelligent management systems, the enhancement of existing resource evaluation and allocation mechanisms is mandatory during this transitional era. To reach this pressing milestone, we will have to revise the already deployed reliability frameworks, assessing their orchestrating stages. Our research focuses on providing a novel evaluation mechanism that could successfully replace traditional path choosing techniques in reliability prone algorithms, regardless of their orientation. The proposed synthesized metrics enumerate the candidate paths validly and optimally, by adhering to the Path Algebra fundamental properties of monotonicity and isotonicity. Such an implementation can be deployed seamlessly, either on legacy or modern architectures, cementing the innovative qualities of its design. The experimental results of our simulations indicate that the proposed solution favors substantially more reliable paths than its shortest-path counterpart.
An Optimised CRISPR Cas9 and Cas12a Toolkit for Barley and Wheat
Authors: Lawrenson Tom , Clarke Martha , Kirby Rachel , Forner Macarena , Steuernagel Burkhard , Harwood Wendy 
Published: March 2024

Abstract

Background
CRISPR Cas9 and Cas12a are the two most frequently used programmable nucleases reported in plant systems. There is now a wide range of component parts for both which likely have varying degrees of effectiveness and potentially applicability to different species. Our aim was to develop and optimise Cas9 and Cas12a based systems for highly efficient genome editing in the monocotyledons barley and wheat and produce a user-friendly toolbox facilitating simplex and multiplex editing in the cereal community.
Results
We identified a Zea mays codon optimised Cas9 with 13 introns in conjunction with arrayed guides driven by U6 and U3 promoters as the best performer in barley where 100% of T0 plants were simultaneously edited in all three target genes. When this system was used in wheat >90% of T0 plants were edited in all three subgenome targets. For Cas12a, an Arabidopsiscodon optimised sequence with 8 introns gave the best editing efficiency in barley when combined with a tRNA based multiguide array, resulting in 90% mutant alleles in three simultaneously targeted genes. When we applied this Cas12a system in wheat 86% & 93% of T0 plants were mutated in two genes simultaneously targeted. We show that not all introns contribute equally to enhanced mutagenesis when inserted into a Cas12a coding sequence and that there is rational for including multiple introns. We also show the combined effect of two features which boost Cas12a mutagenesis efficiency (D156R mutation and introns) is more than the sum of the features applied separately.
Conclusion
Based on the results of our testing, we describe and provide a GoldenGate modular cloning system for Cas9 and Cas12a use in barley and wheat. Proven Cas nuclease and guide expression cassette options found in the toolkit will facilitate highly efficient simplex and multiplex mutagenesis in both species. We incorporate GRF-GIF transformation boosting cassettes in wheat options to maximise workflow efficiency.
Nonlocal abstract Stokes equations and applications
Authors: Shakhmurov Veli 
Published: March 2024

Abstract
In this paper, the Cauchy problem for the stationary and instationary nonlocal imcompressible abstract Stokes equation is considered. The equation involve a convolution term and an abstract operator in a Banach space E on leading part. The existence, uniqueness and coercive estimates are derived in Lp spaces. We, can obtain different classes of Stokes equations by choosing the space E and the linear operator A which occur in a wide variety of physical systems. In application the existence, uniqueness and Lp-maximal regularity properties to solution of initial value problems for nonlocal degenerate Stokes equations and nonlocal Stokes equations with discontinuous coefficients are established
AMS: 35Q30, 76D05, 34G10, 35J25
​Durna: Achieving Cloud of Clouds by integrating Blockchain and Software Defined Storage
Authors: Dinparast Saber , Mohasefi Jamshid Bagherzadeh , Javan Morteza Sargolzaei , Sardroud Asghar Asl Asgharian 
Published: March 2024

Abstract

This paper proposes a new architecture which addresses the challenge of creating a unified storage cloud out of multiple independent cloud storage by developing a decentralized configuration management system named Durna. Durna integrates blockchain and software defined storage technologies and creates a unified decentralized service while preserving each autonomous unit independent. Durna is capable of generating, distributing, and applying configuration files among nodes in the storage network in a stable, and decentralized manner. By achieving this, the software defined storage gains the decentralized management capability, while still benefiting from its established capabilities in guaranteeing storage service quality. To ensure the system's effectiveness and prevent unforeseen problems, a formal model of the decentralized configuration management system was created and evaluated using model-checking. At the end, we discussed our experience of deploying the primitive Durna hyper-cloud system.
Accuracy of the Gross-Pitaevskii Equation in a Double-Well Potential
Authors: Sakhel Asaad R. , Ragan Robert J. , Mullin William J. 
Published: March 2024

Abstract

The Gross-Pitaevskii equation (GPE) in a double well potential produces solutions that break the symmetry of the underlying non-interacting Hamiltonian, i.e., asymmetric solutions. The GPE is derived from the more general second-quantized Fock Schrödinger equation (FSE). We investigate whether such solutions appear in the more general case or are artifacts of the GPE. We use two-mode analyses for a variational treatment of the GPE and to treat the Fock equation. An exact diagonalization of the FSE in dual-condensates yields degenerate ground states that are very accurately fitted by phase-state representations of the degenerate asymmetric states found in the GPE. The superposition of degenerate asymmetrical states forms a cat state. An alternative form of cat state results from a change of the two-mode basis set.
Psychosocial factors contribute to the disability and distress associated with chronic pain in ambulatory patients attending an Australian cancer center
Authors: Glare Paul A , Pugliano Lina , Sequeira Amit A. , Asghari Ali , Nicholas Michael K. 
Published: March 2024

Abstract

Purpose: The prevalence, characteristics, and optimal management of chronic pain in cancer survivors remain uncertain. This study aimed to estimate its prevalence, origin, and severity, while examining the role of mood and unhelpful thoughts and beliefs in pain-related distress and disability.
Methods: Ambulatory adults visiting the cancer center of a university teaching hospital in Sydney, Australia, were invited to participate in a de-identified cross-sectional survey. The survey included demographics, clinical information, and responses to validated pain questionnaires.
Results: Out of 362 patients attending the center during the survey period, 346 (96%) returned completed surveys. Among them, 120 (35%) believed they were cured or in remission. 60 (17%, 95%CI 14%-20%) reported pain persisting for more than three months, with 35 (57% of those in pain) attributing it to unrelated comorbidities. 39 (11% of survey participants) reported moderate to severe interference with functioning due to pain. Pain interference correlated in the expected direction with depression, pain catastrophizing, and low pain self-efficacy (all p<0.01). Low pain self-efficacy significantly contributed to physical interference even when controlling for pain intensity. Similarly, pain catastrophizing contributed to pain-related distress.
Conclusion: Chronic pain was prevalent in those surveyed, often stemming from comorbidities. Over 10% of respondents reported high-impact chronic pain, linked to depressed mood, low pain self-efficacy, and pain catastrophizing.
Cosmic quenching and scaling laws for evolution of galaxies and SMBHs
Authors: Xu Zhijie (Jay) 
Published: March 2024

Abstract

Observations suggest a tight coupling between spuermassive black hole (SMBH) growth and star formation in the host galaxy. Based on Illustris simulations and astronomical observations, a cosmic quenching over the cosmic time scale is proposed to regulate the synchronized evolution of both SMBH and host. A central quantity of cosmic quenching is the parameter 𝜀𝑏 (unit: 𝑚2/𝑠3) that describes the rate of mass and energy flow of gases along the bulge radial direction. The parameter 𝜀𝑏 also controls the efficiency of gas cooling and the supply of cold gas. The value 𝜀𝑏 ≈ 10−4 (1 + 𝑧)5/2𝑚2/𝑠3 can be determined which decreases with time. For a larger 𝜀𝑏 in the early universe, gas cooling is more efficient in providing a richer supply of cold gas for a rapid initial evolution of both SMBH and host. At lower redshifts, a smaller 𝜀𝑏 means less efficient gas cooling, less cold gas supply, and slower star formation and black hole growth (quenched). The rate of mass accretion naturally exhibits a peak at 𝑧 ≈ 2 due to the decrease in 𝜀𝑏. Scaling laws involving 𝜀𝑏 are identified that govern the evolution of both SMBHs and their hosts. For host galaxies, we identify the mass-size relation 𝑀𝑏 ∝ 𝜀2/3 𝑏 𝑟5/3 𝑏 𝐺−1 and the dispersion-size relation 𝜎2 𝑏 ∝ (𝜀𝑏𝑟𝑏)2/3 ∝ (1 + 𝑧), where 𝑟𝑏 ∝ (1 + 𝑧)−1 is the bulge size. For SMBH, an initial rapid growth is identified with a sharp increase in luminosity 𝐿𝐵 ∝ (𝜀𝑏𝑀𝐵𝐻)4/5𝐺−1/5𝑐, followed by a transition stage with a decreasing luminosity 𝐿𝐵 ∝ 𝜀2𝑏𝑀𝐵𝐻 ∝ (1 + 𝑧)5, and a dormant stage with 𝐿𝐵 ∝ (𝜀𝑏𝑀𝐵𝐻)4/3𝐺1/3𝑐−5/3. Here 𝐺 is the gravitational constant, 𝑐 is the speed of light, 𝑀𝐵𝐻 is the mass of BH. For SMBH-galaxy co-evolution, the observed M-σ correlation can be analytically derived as 𝑀𝐵𝐻 ∝ 𝜎5 𝑏 /(𝜀𝑏𝐺). Using these scaling laws, analytical solutions are formulated for the evolution of the SMBH mass function Φ𝐵𝐻 (𝑀, 𝑧), the AGN mass function Φ𝐴𝐺𝑁 (𝑀, 𝑧), duty cycle 𝑈(𝑀, 𝑧), and the Eddington ratio distribution. The model predicts Φ𝐿 ∝ 𝐿−1/5 for the faint-end quasar luminosity function, Φ𝐴𝐺𝑁 ∝ 𝑀−1/5 for a small-mass-end AGN mass function, and 𝑈 ∝ 𝑀−1/5 for the duty cycle at high redshift. Finally, the complete redshift evolution of some observed high-redshift SMBHs can be modeled. The results suggest an initial super-Eddington growth in a short period when the SMBHs are still small, followed by a slow growth due to cosmic quenching when the SMBHs become large.
Dismantle and rebuild: The importance of preparedness and self-efficacy before, during, and after allogeneic haematopoietic cell transplantation
Authors: Holmberg Katarina , Bergkvist Karin , Wengström Yvonne , Hagelin Carina Lundh 
Published: March 2024

Abstract

Purpose The aim of this study was to explore patients’ experiences of being prepared for allogenic haematopoietic cell transplantation and to explore their perceived self-efficacy and preparedness for self-care after allogenic haematopoietic cell transplantation.
Methods Qualitative descriptive design was adopted using content analysis to analyse individual interviews.
Results An overarching theme, Life is taken apart, then you have to know how to put the pieces together, and four sub themes, Convert information into something understandable, Taking responsibility, maintaining and preparing for an uncertain time in life, Fumbling independence, and Reorientating in an altered body places new demands on self-care illustrates the dismantlement of life during treatment and how actions and approaches can build a new life.
Conclusions Emphasis was placed on preparation before admission, this applied to both healthcare professionals and participants. However, during admission, preparation decreased and the time was not used for preparatory learning. This meant that participants were well prepared for the acute phase but unprepared for life after completion of treatment. Self-efficacy was perceived as high among the participants who sought information about taking care of their health.
Implication for cancer survivors This study provides insight into, and knowledge about, how patients prepare before, during, and after treatment. This knowledge should primarily be directed towards healthcare professionals to be used for future patients who may need advice and support, as well as continued preparation for a life after transplantation.
Genetic evaluation of the patients with clinically diagnosed inborn errors of immunity by whole exome sequencing: Results from a specialized research center for immunodeficiency in Türkiye
Authors: Erman Baran , Aba Umran , Ipsir Canberk , Pehlivan Damla , Aytekin Caner , Cildir Gokhan , Cicek Begum , Bozkurt Ceren , Tekeoglu Sidem , Kaya Melisa , Aydogmus Cigdem , Cipe Funda , Sucak Gulsan , Eltan Sevgi Bilgic , Ozen Ahmet , Barıs Safa , Karakoc-Aydiner Elif , Kıykım Ayca , Karaatmaca Betul , Kose Hulya , Uygun Dilara Fatma Kocacık , Celmeli Fatih , Arikoglu Tugba , Ozcan Dilek , Keskin Ozlem , Arık Elif , Aytekin Elif Soyak , Cesur Mahmut , Kucukosmanoglu Ercan , Kılıc Mehmet , Yuksek Mutlu , Bıcakcı Zafer , Esenboga Saliha , Ayvaz Deniz Cagdas , Sefer Asena Pınar , Guler Sukru Nail , Keles Sevgi , Reisli Ismail , Musabak Ugur , Demirbas Nazlı Deveci , Haskologlu Sule , Kilic Sara Sebnem , Metin Ayse , Dogu Figen , Ikinciogullari Aydan , Tezcan Ilhan 
Published: March 2024

Abstract

Molecular diagnosis of inborn errors of immunity (IEI) poses critical implications for patient’s long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.