bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence type analysis and recombinational tests (START)
Authors: Jolley K. A. , Feil E. J. , Chan M.-S. , Maiden M. C. J. 
Published: July 2002

Abstract
Summary: The 32-bit Windows application START is implemented using Visual Basic and C++ and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection.
Availability: START is available at http://outbreak.ceid.ox.ac.uk/software.htm.
Contact: keith.jolley@ceid.ox.ac.uk
* To whom correspondence should be addressed.
Predicting protein–protein interactions from primary

structure
Authors: Bock Joel R. , Gough David A. 
Published: July 2002

Abstract
Motivation: An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. The expectation is that this will provide a fuller appreciation of cellular processes and networks at the protein level, ultimately leading to a better understanding of disease mechanisms and suggesting new means for intervention. This paper addresses the question: can protein–protein interactions be predicted directly from primary structure and associated data? Using a diverse database of known protein interactions, a Support Vector Machine (SVM) learning system was trained to recognize and predict interactions based solely on primary structure and associated physicochemical properties.
Results: Inductive accuracy of the trained system, defined here as the percentage of correct protein interaction predictions for previously unseen test sets, averaged 80% for the ensemble of statistical experiments. Future proteomics studies may benefit from this research by proceeding directly from the automated identification of a cell’s gene products to prediction of protein interaction pairs.
Contact: dgough@bioeng.ucsd.edu
* To whom correspondence should be addressed.
The PYRIN domain: A member of the death domain‐fold superfamily
Authors: Fairbrother Wayne J. , Gordon Nathaniel C. , Humke Eric W. , O'Rourke Karen M. , Starovasnik Melissa A. , Yin Jian‐Ping , Dixit Vishva M. 
Published: July 2002

AbstractPYRIN domains were identified recently as putative protein–protein interaction domains at the N‐termini of several proteins thought to function in apoptotic and inflammatory signaling pathways. The ∼95 residue PYRIN domains have no statistically significant sequence homology to proteins with known three‐dimensional structure. Using secondary structure prediction and potential‐based fold recognition methods, however, the PYRIN domain is predicted to be a member of the six‐helix bundle death domain‐fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain‐fold superfamily are well established mediators of protein–protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. An homology model of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1, a member of the Apaf‐1/Ced‐4 family of proteins, was constructed using the three‐dimensional structures of the FADD and p75 neurotrophin receptor DDs, and of the Apaf‐1 and caspase‐9 CARDs, as templates. Validation of the model using a variety of computational techniques indicates that the fold prediction is consistent with the sequence. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain‐fold provides experimental support for the structure prediction.
Trends of Randomized Clinical Trials Citing Prior Systematic Reviews, 2007-2021
Authors: Jia Yuanxi , Li Bingli , Yang Zhirong , Li Fuxiao , Zhao Ziyi , Wei Chang , Yang Xuhao , Jin Qianyi , Liu Di , Wei Xin , Yost Jennifer , Lund Hans , Tang Jinling , Robinson Karen A. 
Published: March 2023

ImportanceSystematic reviews can help to justify a new randomized clinical trial (RCT), inform its design, and interpret its results in the context of prior evidence.ObjectiveTo assess trends and factors associated with citing (a marker of the use of) prior systematic reviews in RCT reports.Design, Setting, and ParticipantsThis cross-sectional study investigated 737 Cochrane reviews assessing health interventions to identify 4003 eligible RCTs, defined as those included in an updated version but not in the first version of a Cochrane review and published 2 years after the first version of the Cochrane review was published.Main Outcomes and MeasuresThe primary outcome was the citation of prior systematic reviews, Cochrane or others, as determined by screening references of eligible RCTs. Factors that may be associated with the citation of prior systematic reviews were also examined.ResultsAmong 4003 eligible RCTs, 1241 studies (31.0%) cited Cochrane reviews, 1698 studies (42.4%) cited prior non-Cochrane reviews, and 2265 studies (56.6%) cited either type of systematic review or both; 1738 RCTs (43.4%) cited no systematic reviews. The percentage of RCTs citing prior Cochrane reviews, non-Cochrane reviews, and either or both types of review increased from 28 studies (15.3%), 46 studies (25.1%), and 65 studies (35.5%) of 183 RCTs before 2008 to 42 studies (40.8%), 65 studies (64.1%), and 73 studies (71.8%) of 102 RCTs since 2020, respectively; the annual increases were 1.9% (95% CI, 1.4%-2.3%), 3.3% (95% CI, 2.9%-3.7%), and 3.0% (95% CI, 2.5%-3.5%), respectively. The proportion of RCTs citating prior systematic reviews varied considerably across clinical specialties, ranging from 28 of 106 RCTs (26.4%) in ophthalmology to 386 of 553 RCTs (69.8%) in psychiatry (P &amp;lt; .001). RCTs with 100 participants or more (risk ratio [RR], 1.16; 95% CI, 1.03-1.30), nonindustry funding (RR, 1.43; 95% CI, 1.27-1.61), and authors from high-income countries (RR, 1.10; 95% CI, 1.03-1.17) were more likely to cite systematic reviews than those with fewer than 100 participants, industry funding, and authors from low- and middle-income countries, respectively. A journal requirement to cite systematic reviews was not associated with the likelihood of citing a systematic review.Conclusions and RelevanceThis study found that the citation of prior systematic reviews in RCT reports improved over time, but approximately 40% of RCTs failed to do so. These findings suggest that reference to prior evidence for initiating, designing, and reporting RCTs should be further emphasized to assure clinical relevance, improve methodological quality, and facilitate interpretation of new results.
Histamine and Histamine Receptor Ligands
Authors: Ghamari Nakisa , Stark Holger , Hamzeh‐Mivehroud Maryam 
Published: March 2023

Abstract

Histamine belongs to the group of biogenic amines and exerts its biological properties mainly mediated by four different G‐protein‐coupled receptor class A subtypes, named H
1
–H
4
receptors. While selective agonists are mainly used for pharmacological experiments, antagonists are widely used in different therapeutic fields. Different generations of H
1
receptor antagonists are mainly used for the treatment of allergic diseases and sleep disturbances, whereas H
2
receptor antagonists became blockbuster drugs in the treatment of stomach ulcers. With the detection of the H
3
receptor, the neurotransmitter properties of histamine have been proven. Despite several approaches, so far only one H
3
receptor antagonist (Pitolisant) got market approval for the orphan disease narcolepsy and for obstructive sleep apnea. The immunomodulatory and anti‐inflammatory properties of H
4
receptor antagonists have raised hopes for new therapeutic approaches in the near future.
Development of a log file analysis tool for proton patient QA, system performance tracking, and delivered dose reconstruction
Authors: Ates Ozgur , Pirlepesov Fakhriddin , Zhao Li , Hua Chia‐ho , Merchant Thomas E. 
Published: March 2023

AbstractPurpose/Objective(s)To describe a log file–based patient‐specific quality assurance (QA) method and develop an in‐house tool for system performance tracking and dose reconstruction in pencil‐beam scanning proton therapy that can be used for pre‐treatment plan review.Materials/MethodsThe software extracts beam‐specific information from the treatment delivery log file and automatically compares the monitor units (MU), lateral position, and size of each spot against the intended values in the treatment plan to identify any discrepancies in the beam delivery. The software has been used to analyze 992 patients, 2004 plans, 4865 fields, and more than 32 million proton spots from 2016 to 2021. The composite doses of 10 craniospinal irradiation (CSI) plans were reconstructed based on the delivered spots and compared with the original plans as an offline plan review method.ResultsOver the course of 6 years, the proton delivery system has proved stable in delivering patient QA fields with proton energies of 69.4–221.3 MeV and an MU range of 0.003–1.473 MU per spot. The planned mean and standard deviation (SD) of the energy and spot MU were 114.4 ± 26.4 MeV and 0.010 ± 0.009 MU, respectively. The mean and SD of the differences in MU and position between the delivered and planned spots were 9.56 × 10−8 ± 2.0 × 10−4 MU and 0.029/−0.007 ± 0.049/0.044 mm on the X/Y‐axis for random differences and 0.005/0.125 ± 0.189/0.175 mm on the X/Y‐axis for systematic differences. The mean and SD of the difference between the commissioning and delivered spot sizes were 0.086/0.089 ± 0.131/0.166 mm on the X/Y‐axis.ConclusionA tool has been developed to extract crucial information about the performance of the proton delivery and monitor system and provide a dose reconstruction based on delivered spots for quality improvement. Each patient's plan was verified before treatment to ensure accurate and safe delivery within the delivery tolerance of the machine.
Toward a Novel Energy‐Dissipation Metamaterial with Tensegrity Architecture
Authors: A. Santos Filipe 
Published: March 2023

AbstractThe interest in novel energy‐dissipation devices that offer advanced functionalities for optimal performance in state‐of‐the‐art engineering applications is growing. In this regard, a highly tunable and innovative dissipator is developed. This dissipator features movement amplification capabilities resulting from the radial replication of a unit‐cell with tensegrity architecture. The kinematic response of the dissipator is analyzed for several layouts, by varying the number of unit‐cells within the device, their internal geometry, and identifying the corresponding locking configurations. A fully operational 3D‐printed prototype is presented, demonstrating its excellent performance in terms of damping capabilities and feasibility. The experimental results are used to validate a numerical model of the flower unit. This model demonstrates the importance of pre‐strain on the overall stiffness and dissipative features of the proposed system. By utilizing these numerical models, it is shown that the proposed device can be used as a building block for more complex assemblies such as periodic metamaterials with tensegrity architecture.
Development of Folate‐Superparamagnetic Nanoconjugates for Inhibition of Cancer Cell Proliferation
Authors: Ferjaoui Zied , Nahle Sara , Schneider Raphaël , Kerdjoudj Halima , Mertz Damien , Quilès Fabienne , Ferji Khalid , Gaffet Eric , Alem Halima 
Published: March 2023

AbstractHere, a versatile strategy to engineer smart theranostic nanocarriers is reported. The core/shell nanosystem is composed of a superparamagnetic iron oxide (Fe3−δO4) nanoparticle (NP) core bearing the biocompatible thermo‐responsive poly(2‐(2‐methoxy)ethyl methacrylate‐oligo(ethylene glycol methacrylate), P(MEO2MAx‐OEGMA100−x) copolymer (where x and 100‐x represent the molar fractions of MEO2MA and OEGMA, respectively). Folic acid (FA) is end‐conjugated to the P(MEO2MAx‐OEGMA100−x) copolymer, leading to Fe3−δO4@P(MEO2MAx‐OEGMA100−x)‐FA, to facilitate active targeting of NPs to cancer cells. A highly potent hydrophobic anticancer agent doxorubicin (DOX) is incorporated in the thermo‐responsive P(MEO2MAx‐OEGMAy) brushes via supramolecular interactions to increase its solubility and the assessment of therapeutic potentials. These experiments confirm the magnetic hyperthermia properties of nanocarrier and reveal that only a small amount (10% ± 4%) of DOX is diffused at room temperature, while almost full drug (100%) is released after 52 h at 41 °C. Interestingly, it is found that P(MEO2MA60‐OEGMA40) polymers offer to NPs a promising stealth behavior against Human Serum Albumin and Fibrinogen model proteins.
Controlled Patterning of Complex Resistance Gradients in Conducting Polymers with Bipolar Electrochemistry
Authors: Salinas Gerardo , Arnaboldi Serena , Garrigue Patrick , Kuhn Alexander 
Published: March 2023

AbstractConducting polymers have gained considerable attention for the possible design of localized electroactive patterns for microelectronics. In this work, the authors take advantage of the properties of polypyrrole, in synergy with a wireless polarization, triggered by bipolar electrochemistry, to produce localized resistance gradient patterns. The physicochemical modification is caused by the reduction and overoxidation of polypyrrole, which produces highly resistive regions at different positions along the conducting substrate at predefined locations. Due to the outstanding flexibility of polypyrrole, U‐, S‐, and E‐shaped bipolar electrodes can be formed for prove‐of‐concept experiments, and electrochemically modified in order to generate well‐defined resistance gradients. Energy‐dispersive X‐ray spectroscopy analysis of the samples confirms the localized physicochemical modifications. This approach presents as main advantages the wireless nature of bipolar electrochemistry and the possible fine‐tuning of the spatial distribution of the electrochemical modification, in comparison with more conventional patterning methods.
An Indoor Light‐Powered Sensor System Integrated with Organic Photovoltaics
Authors: Kim Woojo , Cho Kyounguk , Lee Jung‐Hyun , Ko Doo‐Hyun , Jung Sungjune 
Published: March 2023

AbstractEnergy harvesting systems are attracting significant attention as a new power‐supply technology to overcome the limitations of internet of things (IoT) devices usually established in an indoor environment such as power consumption, size, and usage time. Organic photovoltaics (OPVs) with high absorption coefficients at indoor light wavelengths are a promising energy source for the IoT‐based sensors. However, OPVs in sensor platforms are not well addressed because of their insufficient and inconsistent power supply under indoor circumstance. Herein, a self‐powered sensor system that combines highlyefficient indoor OPV modules with a boost converter for real‐time temperature measurements is demonstrated. The OPV module with a ternary blend is devised to achieve suitable morphology for low‐intensity indoor operation resulting in high efficiency and stability under 1000 lux 3000 K light‐emitting diode illumination. Moreover, the voltage of the OPV modules is effectively boosted through an optimized converter to adequately operate the sensor platform. The sensor system integrated with the OPV modules and boost converter successfully measures the real‐time changes in temperature in indoor environments. This study proposes an ideal self‐powered sensor platform that can be used in smart‐home systems using indoor lighting.
Two Calix[3]Phenothiazine‐Based Amorphous Pure Organic Room‐Temperature Phosphorescent Supramolecules Mediated by Guest
Authors: Sun Yonghui , Jiang Linnan , Liu Lijuan , Chen Yong , Xu Wen‐Wen , Niu Jie , Qin Yuexiu , Xu Xiufang , Liu Yu 
Published: March 2023

AbstractHerein, two kinds of amorphous solid‐state supramolecular systems with purely organic room temperature phosphorescence (RTP) from calix[3]phenothiazine (C[3]Pz) activated by 1,2‐/1,3‐dicyanobenzene (1,2‐/1,3‐DCB) are reported. Different from macrocycle‐confined guest phosphorescence emission, RTP of these two amorphous solid‐state supramolecular systems is entirely from the 1,2‐/1,3‐DCB rivets C[3]Pz cavity to form dense supramolecular complex through CH…π interactions, leading to two different phosphorescence emissions at 566/524 nm under 430 nm excitation, respectively. Although C[3]Pz shows a regular arrangement in the crystal, the vibration dissipation of the benzene ring results in C[3]Pz emitting only fluorescence at 508 nm at room temperature. 1,2‐DCB and 1,3‐DCB can act as molecular rivets to fix the C[3]Pz to inhibit molecular vibration so as to reduce nonradiative relaxation, which enables C[3]Pz to achieve effective RTP emission with 20.8–36.8% quantum yields. This kind of guest‐activated host RTP, which is fairly rare in supramolecular systems, is successfully used for color QR codes and information encryption.
Blockade of Activin Receptor IIB Protects Arthritis Pathogenesis by Non‐Amplification of Activin A‐ACVR2B‐NOX4 Axis Pathway
Authors: Jeon Jimin , Lee Hyemi , Jeon Min‐Seung , Kim Seok‐Jung , Choi Cham , Kim Ki Woo , Yang Dong Joo , Lee Sangho , Bae Yong‐Soo , Choi Won Il , Jung Juyeon , Eyun Seong‐il , Yang Siyoung 
Published: March 2023

AbstractAlthough activin receptor IIB (ACVR2B) is emerging as a novel pathogenic receptor, its ligand and assembled components (or assembly) are totally unknown in the context of osteoarthritis (OA) pathogenesis. The present results suggest that upregulation of ACVR2B and its assembly could affect osteoarthritic cartilage destruction. It is shown that the ACVR2B ligand, activin A, regulates catabolic factor expression through ACVR2B in OA development. Activin A Tg mice (Col2a1‐Inhba) exhibit enhanced cartilage destruction, whereas heterozygous activin A KO mice (Inhba+/−) show protection from cartilage destruction. In silico analysis suggests that the Activin A‐ACVR2B axis is involved in Nox4‐dependent ROS production. Activin A Tg:Nox4 KO (Col2a1‐Inhba:Nox4−/−) mice show inhibition of experimental OA pathogenesis. NOX4 directly binds to the C‐terminal binding site on ACVR2B‐ACVR1B and amplifies the pathogenic signal for cartilage destruction through SMAD2/3 signaling. Together, the findings reveal that the ACVR2B assembly, which comprises Activin A, ACVR2B, ACVR1B, Nox4, and AP‐1‐induced HIF‐2α, accelerates OA development. Furthermore, it is shown that shRNA‐mediated ACVR2B knockdown or trapping ligands of ACVR2B abrogate OA development by competitively disrupting the ACVR2B‐Activin A interaction. These results suggest that the ACVR2B assembly is required to amplify osteoarthritic cartilage destruction and could be a potential therapeutic target in efforts to treat OA.
Artificial Leaf for Solar‐Driven Ammonia Conversion at Milligram‐Scale Using Triple Junction III‐V Photoelectrode
Authors: Huang Hao , Periyanagounder Dharmaraj , Chen Cailing , Li Zhongxiao , Lei Qiong , Han Yu , Huang Kuo‐Wei , He Jr‐Hau 
Published: March 2023

AbstractDeveloping a green and energy‐saving alternative to the traditional Haber‐Bosch process for converting nitrogen into ammonia is urgently needed. Imitating from biological nitrogen fixation and photosynthesis processes, this work develops a monolithic artificial leaf based on triple junction (3J) InGaP/GaAs/Ge cell for solar‐driven ammonia conversion under ambient conditions. A gold layer serves as the catalytic site for nitrogen fixation with photogenerated electrons. The Au/Ti/3J InGaP/GaAs/Ge photoelectrochemical (PEC) device achieves high ammonia production rates and Faradaic efficiencies in a two‐electrode system without applying external potential. For example, at 0.2 sunlight intensity, the solar‐to‐ammonia (STA) conversion efficiency reaches 1.11% and the corresponding Faradaic efficiency is up to 28.9%. By integrating a Ni foil on the anode side for the oxygen evolution reaction (OER), the monolithic artificial leaf exhibits an ammonia production rate of 8.5 µg cm−2 h at 1.5 sunlight intensity. Additionally, a 3 × 3 cm unassisted wireless PEC device is fabricated that produces 1.0039 mg of ammonia in the 36‐h durability test. Thus, the new artificial leaf can successfully and directly convert solar energy into chemical energy and generate useful products in an environmentally friendly approach.
ANPELA: Significantly Enhanced Quantification Tool for Cytometry‐Based Single‐Cell Proteomics
Authors: Zhang Ying , Sun Huaicheng , Lian Xichen , Tang Jing , Zhu Feng 
Published: March 2023

AbstractANPELA is widely used for quantifying traditional bulk proteomic data. Recently, there is a clear shift from bulk proteomics to the single‐cell ones (SCP), for which powerful cytometry techniques demonstrate the fantastic capacity of capturing cellular heterogeneity that is completely overlooked by traditional bulk profiling. However, the in‐depth and high‐quality quantification of SCP data is still challenging and severely affected by the large numbers of quantification workflows and extreme performance dependence on the studied datasets. In other words, the proper selection of well‐performing workflow(s) for any studied dataset is elusory, and it is urgently needed to have a significantly enhanced and accelerated tool to address this issue. However, no such tool is developed yet. Herein, ANPELA is therefore updated to its 2.0 version (https://idrblab.org/anpela/), which is unique in providing the most comprehensive set of quantification alternatives (>1000 workflows) among all existing tools, enabling systematic performance evaluation from multiple perspectives based on machine learning, and identifying the optimal workflow(s) using overall performance ranking together with the parallel computation. Extensive validation on different benchmark datasets and representative application scenarios suggest the great application potential of ANPELA in current SCP research for gaining more accurate and reliable biological insights.
A Review of Gut Microbiota‐Derived Metabolites in Tumor Progression and Cancer Therapy
Authors: Yang Qiqing , Wang Bin , Zheng Qinghui , Li Heyu , Meng Xuli , Zhou Fangfang , Zhang Long 
Published: March 2023

AbstractGut microbiota‐derived metabolites are key hubs connecting the gut microbiome and cancer progression, primarily by remodeling the tumor microenvironment and regulating key signaling pathways in cancer cells and multiple immune cells. The use of microbial metabolites in radiotherapy and chemotherapy mitigates the severe side effects from treatment and improves the efficacy of treatment. Immunotherapy combined with microbial metabolites effectively activates the immune system to kill tumors and overcomes drug resistance. Consequently, various novel strategies have been developed to modulate microbial metabolites. Manipulation of genes involved in microbial metabolism using synthetic biology approaches directly affects levels of microbial metabolites, while fecal microbial transplantation and phage strategies affect levels of microbial metabolites by altering the composition of the microbiome. However, some microbial metabolites harbor paradoxical functions depending on the context (e.g., type of cancer). Furthermore, the metabolic effects of microorganisms on certain anticancer drugs such as irinotecan and gemcitabine, render the drugs ineffective or exacerbate their adverse effects. Therefore, a personalized and comprehensive consideration of the patient's condition is required when employing microbial metabolites to treat cancer. The purpose of this review is to summarize the correlation between gut microbiota‐derived metabolites and cancer, and to provide fresh ideas for future scientific research.