bluuebunny/crossref_metadata_2025_split huggingface dataset:
timsTOF mass spectrometry-based immunopeptidomics refines tumor antigen identification
Authors: Gravel Naomi Hoenisch , Nelde Annika , Bauer Jens , Mühlenbruch Lena , Schroeder Sarah , Neidert Marian , Scheid Jonas , Lemke Steffen , Dubbelaar Marissa , Wacker Marcel , Dengler Anna , Klein Reinhild , Mauz Paul-Stefan , Löwenheim Hubert , Hauri-Hohl Mathias , Martin Roland , Hennenlotter Jörg , Stenzl Arnulf , Heitmann Jonas , Salih Helmut , Rammensee Hans-Georg , Walz Juliane 
Published: January 2023

Abstract
T cell recognition of human leukocyte antigen (HLA)-presented tumor-associated peptides is central for cancer immune surveillance. Mass spectrometry (MS)-based immunopeptidomics represents the only unbiased method for the direct identification and characterization of naturally presented tumor-associated peptides, a key prerequisite for the development of T cell-based immunotherapies. This study reports on the de novo implementation of ion mobility separation-based timsTOF MS for next-generation immunopeptidomics, enabling high-speed and sensitive detection of HLA-presented peptides. A direct comparison of timsTOF-based with state-of-the-art immunopeptidomics using orbitrap technology showed significantly increased HLA peptide identifications from benign and malignant primary samples of solid tissue and hematological origin. First application of timsTOF-based immunopeptidomics for tumor antigen discovery enabled (i) the expansion of benign reference immunopeptidome databases with > 150,000 HLA-presented peptides from 94 primary benign tissue samples, (ii) the refinement of previously described tumor antigens, and (iii) the identification of a vast array of novel tumor antigens, comprising low abundant neoepitopes, that might serve as targets for future cancer immunotherapy development.
Socioeconomic disparities in fertility treatments and associated likelihood of livebirth following In Vitro Fertilization
Authors: Manvelyan Evelina , Abittan Baruch , Weiwei Shan , Shahani Disha , Kwait Brittany , Rausch Mary , Blitz Matthew 
Published: January 2023

Abstract
Objective: To determine whether neighborhood-level socioeconomic characteristics are associated with the likelihood of livebirth (LB) following in vitro fertilization (IVF). Specifically, we evaluated neighborhood-level household income, unemployment rate, and educational attainment.
Design: A retrospective cross-sectional study was conducted for patients undergoing autologous IVF cycles.
Setting: Large academic health system.
Interventions: For each patient, ZIP code of residence was used as a proxy for neighborhood. Neighborhood characteristics were compared between patients with and without LB. Generalized estimating model was used to adjust the association between SES factors and likelihood of a live birth with respect to relevant clinical factors.
Results: A total of 4,942 autologous IVF cycles from 2,768 patients were included: 1,717 (62.0%) had at least one associated LB. Patients who achieved LB from IVF were younger, had higher anti-Mullerian hormone (AMH) levels, lower body mass index (BMI), and differed by ethnic background, primary language, and neighborhood socioeconomic characteristics. In a multivariable model, language, age, AMH, and BMI were associated with a live birth from IVF. None of the neighborhood-level socioeconomic variables were associated with the total number of IVF cycles or cycles required to achieve first LB.
Conclusion: Patients living in neighborhoods with lower annual household income have
lower odds of livebirth after IVF compared to those living in more affluent areas, despite undergoing the same number of IVF stimulation cycles.
What is the role of CHCHD2 in adrenal tumourigenesis?
Authors: Karapanagioti Angeliki , Nasiri-Ansari Narjes , Moustogiannis Athanasios , Trigas George C , Zografos Georgios , Aggeli Chrysanthi , Kyriakopoulos Georgios , Choreftaki Theodosia , Philippou Anastassios , Kaltsas Gregory , Kassi Eva , Angelousi A 
Published: January 2023

Abstract
Purpose
CHCHD2 is an anti-apoptotic mitochondrial protein acting through the BCL2/BAX pathway in various cancers. However, data on the regulatory role of CHCHD2 in adrenal tumourigenesis are scarce.
Methods
We studied the expression of CHCHD2, BCL2 and BAX in human adrenocortical tissues and SW-13 cells. mRNA and protein levels were analysed through qPCR and immunoblotting respectively in 16 benign adrenocortical neoplasms (BANs) and 10 adrenocortical carcinomas (ACCs) along with the adjacent normal adrenal tissues (controls). BCL2/BAX mRNA expression was also analyzed in SW-13 cells after CHCHD2 silencing. MTS, flow cytometry and scratch assays were performed to assess cell viability, apoptosis and invasion respectively.
Results
BCL2 and CHCHCD2 mRNA and protein expression was increased in BANs compared with normal adrenal tissues whereas BAX was decreased. BAX and CHCHD2 mRNA and protein levels were significantly down-regulated and up-regulated respectively in ACCs compared to either BANs or controls. Expression of the studied genes was not different among cortisol-secreting and non-functional ACAs. No significant association was found between genes’ expression and established prognostic markers of ACCs patients. In-vitro analysis showed that CHCHD2 silencing resulted in reduced cell viability and invasion as well as increased SW-13 cells apoptosis.
Conclusions
CHCHD2 expression seems to be implicated in adrenal tumourigenesis through BAX/BCL2 pathway similarly to other tumours. However, the exact mechanism needs to be further studied along with the possibility of being a potentional therapeutic target.
Comparison of pregnancy rates in antagonist cycles after luteal support with GnRH-agonist versus progesterone – prospective randomized study
Authors: Buhbut Eadit , Nabulsi Rinad , Avigdor Gilad , Ben-Ami Ido 
Published: January 2023

Abstract

Purpose: To compare pregnancy rates in GnRH-antagonist cycles triggered with hCG after luteal phase support with intranasal GnRH agonist as sole luteal phase support versus standard vaginal progesterone preparation.
Methods: Prospective randomized controlled study of patients who underwent antagonist-based IVF cycles triggered with hCG at university-affiliated tertiary medical center between 2020 and 2022. Patients meeting the inclusion criteria were randomly assigned to either intranasal GnRH-agonist or vaginal progesterone for luteal phase support. Pregnancy rates were the main outcome compared between the two study groups.
Results: A total of 150 patients underwent 164 cycles, 127 cycles of which were included in the study cohort. Of them, 64 (50.4%) and 63 (49.6%) cycles were treated with GnRH-agonist or progesterone respectively as sole luteal phase support. A significantly higher pregnancy rate was demonstrated in the GnRH-agonist group compared with the progesterone group. After adjustment of several potential confounders such as age, body mass index, past obstetric history, number of IVF cycles, oocyte retrieved and embryos transferred, GnRH-agonist was still associated with a higher pregnancy rate (odds ratio 3.4, 95% confidence interval 1.4-8.3). Ovarian hyperstimulation syndrome rates were similar between the groups.
Conclusions: This prospective study suggests that nasal GnRH-agonist for luteal phase support is associated with higher pregnancy rates compared with standard progesterone support in an antagonist-based protocol triggered with hCG, while maintaining a similar safety profile.
Slip-oscillate response in a synchronizing nonlinear micro-resonator
Authors: Shi Zhan , Pu Dong , Wang Xuefeng , Wei Xueyong , Huan Ronghua 
Published: January 2023

Abstract
Synchronization in phase feedback micro/nano systems are widely delved for its rich dynamics and prospective applications. As a key factor that affects the sensory performance, the synchronization transient process deserves much focus while few investigations on it so far. Here, we report the observation of the slipping and oscillation behavior of the frequency and phase of a nonlinear micro-oscillator injected by a harmonic perturbation in the synchronization region. The observed frequency and phase of the oscillator not monotonically approaches the synchronized state, yet experience a period of frequency and phase fluctuations which can be divided into two stages. The first stage time is influenced by the frequency detuning between the perturbation force and the oscillator. The second stage time is determined by the configuration of the potential well which is influenced by the nonlinearity terms. We found that the dynamic behavior of the frequency and phase can be regulated by the energy potential well of the nonlinear feedback system. By reconfigure the potential well pattern, we achieve 5 times suppression of the synchronization process, which have promising beneficial effects for the aspects of sensor application. Similar phenomena can be found in human body dynamics, which means that the observed mechanism can give some suggestions to study life science.
High flow nasal oxygen therapy compared with conventional oxygen therapy in hospitalised patients with respiratory illness: a systematic review and meta-analysis
Authors: Seow Daniel , Khor Yet H. , Khung Su-Wei , Smallwood David M , Ng Yvonne , Smallwood Natasha E 
Published: January 2023

Abstract
Background
This systematic review aims to summarise the evidence regarding any benefits of high flow nasal oxygen (HFNO) therapy compared to conventional oxygen therapy (COT) in hospitalised patients with acute or chronic respiratory illnesses.
Methods
A comprehensive search was performed across three databases for studies that reported any of: escalation to invasive mechanical ventilation (IMV), mortality, length of stay, carbon dioxide levels, disability, or admission rates.
Results
In patients with acute respiratory illnesses, pooled RCT data revealed no significant differences between HFNO and COT in overall need for IMV (RR = 0.82, 95% CI = 0.65–1.05; p = 0.11; n = 15 RCTs) or in-hospital mortality (RR = 1.00, 95% CI 0.85–1.17; p = 1.00; n = 5). Similarly, for patients with chronic respiratory illnesses, RCT data revealed no significant difference in overall need for IMV (RR = 0.86, 95% CI = 0.33–2.23; p = 0.76; n = 4) or in-hospital mortality (RR = 0.40, 95% CI = 0.04–4.10; p = 0.44; n = 1) for HFNO compared to COT. Patients with COVID-19 receiving HFNO had a significantly reduced need for IMV (RR = 0.72, 95% CI = 0.63–0.82; p < 0.001), short-term mortality (RR = 0.62, 95% CI = 0.48–0.79; p < 0.001), and long-term mortality (RR = 0.67, 95% CI = 0.48–0.92; p = 0.01).
Conclusion
HFNO did not significantly reduce the need for IMV escalation or in-hospital mortality in patients with acute or chronic respiratory illnesses, except for patients with COVID-19.
Scanless two-photon voltage imaging
Authors: Sims Ruth , Bendifallah Imane , Grimm Christiane , Lafirdeen Aysha , Lu Xiaoyu , St-Pierre François , Papagiakoumou Eirini , Emiliani Valentina 
Published: January 2023

Abstract

Parallel light-sculpting methods have been used to perform scanless two-photon photostimulation of multiple neurons simultaneously during all-optical neurophysiology experiments. We demonstrate that scanless two-photon excitation also enables high-resolution, high-contrast, voltage imaging by efficiently exciting fluorescence in a large fraction of the cellular soma. We present a thorough characterisation of scanless two-photon voltage imaging using existing parallel approaches and lasers with different repetition rates. We demonstrate voltage recordings of high frequency spike trains and sub-threshold depolarizations in intact brain tissue from neurons expressing the soma-targeted genetically encoded voltage indicator JEDI-2P-kv. Using a low repetition-rate laser, we perform recordings from up to ten neurons simultaneously. Finally, by co-expressing JEDI-2P-kv and the channelrhodopsin ChroME-ST in neurons of hippocampal organotypic slices, we perform single-beam, simultaneous, two-photon voltage imaging and photostimulation. This enables in-situ validation of the precise number and timing of light evoked action potentials and will pave the way for rapid and scalable identification of functional brain connections in intact neural circuits.
An assessment of the strategies for the energy-critical elements necessary for the development of sustainable energy sources
Authors: Krishna RAM , Dhass Avithi Desappan , Arya Abhishek , Prasad Ranjit , Colak Ilhami 
Published: January 2023

Abstract
There have been several strategies developed in order to increase the diversified supply of energy so that it can meet all of the demands for energy in the future. As a result, to ensure a healthy and sustainable energy future, it is imperative to warrant reliable and diverse energy supply sources if the “green energy economy” is to be realized. The purpose of developing and deploying clean energy technologies is to improve our overall energy security, reduce carbon footprint, and ensure that the generation of energy is secure and reliable in the future, making sure that we are in a position to spur economic growth in the future. In this paper, advancements in alternative sources of energy sustainability and strategies will be examined, so as to ensure there will be enough fuel to supply all of the future demands for energy. Several emerging clean energy technologies rely heavily on the availability of materials that exhibit unique properties that are necessary for their development. This paper examines the role that materials, such as rare earth metals and other critical materials, play in securing a clean energy economy and the development of clean energy economies in general. In order for the development of these technologies to be successful and sustainable, a number of these energy-critical materials are at risk of becoming unavailable. This is due to their limited availability, disruptions in supply, and the lack of suitable resources for their development. An action plan focusing on producing energy-critical materials in energy-efficient ways is discussed as part of an initiative to advance the development of clean and sustainable energy.
Post-depositional Hg transformation processes in an open boreal peatland constrained by Hg stable isotopes
Authors: Li Chuxian , Jiskra Martin , Nilsson Mats B. , Osterwalder Stefan , Zhu Wei , Mauquoy Dmitri , Skyllberg Ulf , Enrico Maxime , Peng Haijun , Song Yu , Björn Erik , Bishop Kevin 
Published: January 2023

Abstract
Peatland vegetation constantly takes up mercury (Hg) from the atmosphere, typically contributing to net production and export of neurotoxic Methyl-Hg to downstream ecosystems. Chemical reduction processes can slow down Methyl-Hg production by releasing Hg from peat back to the atmosphere. The extent of these processes remain, however, unclear. Here we present results from a comprehensive study covering concentrations and isotopic signatures of Hg in an open boreal peatland system to identify post-depositional Hg transformation processes. Isotope mass balances suggest photoreduction of HgII is the predominant process by which 30% of annually deposited Hg is emitted back to the atmosphere. Isotopic analyses indicate that dark abiotic oxidation decreases peat soil gaseous Hg0 concentrations above the water table, and that supersaturated gaseous Hg below the water table was likely created more by photoreduction of rainfall rather than release from peat soil. These findings constrain the possibilities for mobilizing previously deposited Hg. Identification and quantification of these processes further advance our understanding of the fate of Hg in peatlands and their export of Methyl-Hg to downstream ecosystems.
Intraspecific inflorescence and palynological variations in the morphotypes of Amorphophallus paeoniifolius
Authors: Anil Shirly Raichal , Devi A. Asha , Asha K.I. , Beevy S. Suhara , Siril Elengikkal Avarachan 
Published: January 2023

Abstract
The genus Amorphophallus Blume ex Decne. is a vast and widespread group of aroids belonging to Araceae which is taxonomically and botanically distinct due to the frequency of emergence of inflorescences and their relatively short active period of existence. Amorphophallus paeoniifolius var. campanulatus or the elephant foot yam is an important tuber crop due to its high productivity and popularity as a vegetable in various delicious cuisines and medicinal properties. Wild congenerics of the cultivated A. paeoniifolius known as A. paeoniifolius Nicolson var. paeoniifolius (Decne.) Sivad. possess powerful therapeutic action against piles and gastro-intestinal disorders. The wide visible morphological variation observed in wild A. paeoniifolius morphotypes (morphological variants) available in the Western Ghats especially in the vegetative as well as inflorescence characters led to the present investigation to analyze and appraise the inflorescence diversity in comparison with other aspects, among the wild relatives of Amorphophallus paeoniifolius. Variation in the surface pattern of petiole and spathe is the main difference found within the species. The shape of appendix, the colour and pattern of spathe, scale leaves (bract) subtending the spathe, the male zone, female zone, the pollen morphology as assessed by SEM and pollen fertility showed distinct variation within the species revealing six distinct morphotypes. The mitotic chromosome studies indicated structural variation which was reflected in the karyomorphology. The ISSR markers, inflorescence /floral markers and vegetative morphological descriptors also indicated clear distinction between the morphotypes in addition to the variation seen in pollen morphology
Uplink Interference Mitigation in HetNets with Q-Learning Algorithm
Authors: Abbasi-Moghadam Dariush , Etminan Khatereh , Kalantarinejad Nazanin 
Published: January 2023

Abstract
Interference cancellation is one of the important issues in Heterogeneous networks (HetNets), due to the density of the network. In this paper, we investigate the problem of interference cancellation and resource allocation with the Q-learning approach. We consider the Inter-interference and Intra-interference between the femtocell and macro cells in the uplink scenario. With the aim of maximizing the QoS of the macro user equipment (MUE) and minimizing the interference of the MUE, a new reward function was proposed. The simulation results show the improvement of the proposed algorithm in two strong interference and increasing distance scenarios.
A Radioactive and Fluorescent Dual Modality Cysteine Cathepsin-B Activity-Based Probe for Cancer Theranostic
Authors: Zhou Lianbo , He Feng , Xiang Xing , Dong Chuning , Xiang Tian , Li Xian , Li Hong , Bu HongLi , Wang Yunhua , Ma Xiaowei 
Published: January 2023

Abstract

Purpose: Cysteine cathepsin B (CTS-B) is a crucial enzyme that is overexpressed in numerous malignancies and contributes to the invasion and metastasis of cancer. Therefore, this study set out to develop and evaluate an activity-based multi-modality theranostic agent targeting CTS-B for cancer imaging and therapy.
Methods: A CTS-B activity-based probe, BMX2, was synthesized and labeled efficiently with 68Ga and 90Y to produce 68Ga-BMX2 for multi-modality imaging and 90Y-BMX2 for radiation therapy. The affinity and specificity of the BMX2 binding with the CTS-B enzyme were determined by fluorescent western blot using recombined active human CTS-B enzyme (rh-CTS-B) and four cancer cell lines including HeLa, HepG2, MCF7, and U87MG with CA074 as CTS-B inhibitor for control. Confocal laser scanning microscope imaging and cell uptake measurement was also performed. Then in vivo PET imaging and fluorescence imaging were acquired on HeLa xenografts. Finally, the therapeutic effect of 90Y-BMX2 was tested.
Results: BMX2 could be specifically activated by rh-CTS-B and stably bound to the enzyme. The binding of BMX2 with CTS-B has a time-dependent and enzyme concentration-dependent manner. Although CTS-B expression varied between cell lines, all showed significant uptake of BMX2 and 68Ga-BMX2. In vivo optical and PET imaging showed high tumor uptake of BMX2 and 68Ga-BMX2 and accumulated for more than 24 hours. The 90Y-BMX2 could significantly inhibit HeLa tumor growth.
Conclusion: The development of 68Ga/90Y-BMX2, a radioactive and fluorescent dual modality theranostic agent, demonstrated an effective theranostic approach for PET diagnostic imaging, fluorescence imaging, and radionuclide therapy of cancers, which may have a potential for clinical translation for cancer theranostic in the future.
Machine learning based routing protocol (MLBRP) for Mobile Internet of Things networks
Authors: Larouci Nour El Houda , Sahraoui Somia , Djeffal Abdelhamid 
Published: January 2023

Abstract
Massive volumes of data generated by large numbers of connected Internet of Things (IoT) devices impact both IoT service and network performance. Packet routing is an ever-important networking feature that enables the transmission of data packets across interconnected IoT networks. Usually, classical proactive and reactive routing protocols use the information of their neighbours to build a global view of the network by the mean of control messages and then calculate a path to the destination. After a packet has been delivered, history is discarded, and only actual information is used to determine new paths. In the present research work, we propose applying a Machine Learning (ML) approach to take advantage of previously successfully taken routing decisions and build new decision models that nodes can use to make intelligent routing decisions. In our proposal, we integrate three machine learning techniques: Decision Trees(DT), Support Vector Machines (SVM), and Artificial Neural Networks (ANN) into the well-known Ad hoc On-demand Distance Vector (AODV) routing protocol and evaluate the efficiency of solution variants for packets routing in IoT-connected smart city scenario. The assessment results show that the proposed ML-based routing solutions outperform the AODV protocol and decrease the use of control messages to more than 50% of the overall communication overhead. Therefore, network performances are more optimized, and network lifetime is also increased.
Resistance mechanism to Notch inhibition and combination therapy in human T cell acute lymphoblastic leukemia
Authors: Radtke Freddy , Cao Linlin , Buendía Gustavo Ruiz , Fournier Nadine , Liu Yuanlong , Armand Florence , Hamelin Romain , Pavlou Maria 
Published: January 2023

Abstract
Gain-of-function mutations in NOTCH1 are among the most frequent genetic alterations in T cell acute lymphoblastic leukemia (T-ALL), making the Notch signaling pathway a promising therapeutic target for personalized medicine. Yet, a major limitation for long-term success of targeted therapy is relapse due to tumor heterogeneity or acquired resistance. Thus, we performed a genome-wide CRISPR-Cas9 screen to identify prospective resistance mechanisms to pharmacological NOTCH inhibitors and novel targeted combination therapies to efficiently combat T-ALL. Mutational loss of Phosphoinositide-3-Kinase regulatory subunit 1 (PIK3R1) causes resistance to Notch inhibition. PIK3R1 deficiency leads to increased PI3K/AKT signaling which regulates the cell cycle and spliceosome machinery, both at the transcriptional and post-translational level. Moreover, several therapeutic combinations have been identified, where simultaneous targeting of the cyclin-dependent kinases 4 and 6 (CDK4/6) and NOTCH proved to be the most efficacious in T-ALL xenotransplantation models.