bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins
Authors: Liu Wenzhe , Chen Limin , Yin Dongbao , Yang Zhiheng , Feng Jianfei , Sun Qi , Lai Luhua , Guo Xuefeng 
Published: August 2023

AbstractIntrinsically disordered proteins (IDPs) play crucial roles in cellular processes and hold promise as drug targets. However, the dynamic nature of IDPs remains poorly understood. Here, we construct a single-molecule electrical nanocircuit based on silicon nanowire field-effect transistors (SiNW-FETs) and functionalize it with an individual disordered c-Myc bHLH-LZ domain to enable label-free, in situ, and long-term measurements at the single-molecule level. We use the device to study c-Myc interaction with Max and/or small molecule inhibitors. We observe the self-folding/unfolding process of c-Myc and reveal its interaction mechanism with Max and inhibitors through ultrasensitive real-time monitoring. We capture a relatively stable encounter intermediate ensemble of c-Myc during its transition from the unbound state to the fully folded state. The c-Myc/Max and c-Myc/inhibitor dissociation constants derived are consistent with other ensemble experiments. These proof-of-concept results provide an understanding of the IDP-binding/folding mechanism and represent a promising nanotechnology for IDP conformation/interaction studies and drug discovery.
Maintenance of pig brain function under extracorporeal pulsatile circulatory control (EPCC)
Authors: Shariff Muhammed , Dobariya Aksharkumar , Albaghdadi Obada , Awkal Jacob , Moussa Hadi , Reyes Gabriel , Syed Mansur , Hart Robert , Longfellow Cameron , Douglass Debra , El Ahmadieh Tarek Y. , Good Levi B. , Jakkamsetti Vikram , Kathote Gauri , Angulo Gus , Ma Qian , Brown Ronnie , Dunbar Misha , Shelton John M. , Evers Bret M. , Patnaik Sourav , Hoffmann Ulrike , Hackmann Amy E. , Mickey Bruce , Peltz Matthias , Jessen Michael E. , Pascual Juan M. 
Published: August 2023

AbstractSelective vascular access to the brain is desirable in metabolic tracer, pharmacological and other studies aimed to characterize neural properties in isolation from somatic influences from chest, abdomen or limbs. However, current methods for artificial control of cerebral circulation can abolish pulsatility-dependent vascular signaling or neural network phenomena such as the electrocorticogram even while preserving individual neuronal activity. Thus, we set out to mechanically render cerebral hemodynamics fully regulable to replicate or modify native pig brain perfusion. To this end, blood flow to the head was surgically separated from the systemic circulation and full extracorporeal pulsatile circulatory control (EPCC) was delivered via a modified aorta or brachiocephalic artery. This control relied on a computerized algorithm that maintained, for several hours, blood pressure, flow and pulsatility at near-native values individually measured before EPCC. Continuous electrocorticography and brain depth electrode recordings were used to evaluate brain activity relative to the standard offered by awake human electrocorticography. Under EPCC, this activity remained unaltered or minimally perturbed compared to the native circulation state, as did cerebral oxygenation, pressure, temperature and microscopic structure. Thus, our approach enables the study of neural activity and its circulatory manipulation in independence of most of the rest of the organism.
The impact of time length to Boolean remission for tight disease activity control after acquisition in rheumatoid arthritis patients
Authors: Yoshii Ichiro , Chijiwa Tatsumi , Sawada Naoya 
Published: August 2023

AbstractClinical importance of time length from initiation under treat-to-target (T2T) strategy to acquisition of clinical remission (TL) in treating patients with rheumatoid arthritis (RA) on disease activity control, daily activities, and quality of life maintenance was investigated. In patients who achieved Boolean remission once or more, relationship between TL and patients’ background data at initiation, and relationship between TL and mean simplified disease activity score (SDAI), Health Assessment Questionnaire Disability Index (HAQ-DI) score, pain score with visual analog scale (PS-VAS), Sharp/van der Heijde Score (SHS) and quality of life score (QOLS) at the first remission and thereafter were evaluated statistically. Patients were divided into two groups whether TL was within 6 months or longer (G ≤ 6 and G > 6). Change of the parameters and Boolean remission rate (BRR) after the first remission between the two groups were compared statistically. In 465 patients, TL correlated significantly with the SDAI score, the HAQ score, PS-VAS, SHS, and the QOLS after the remission. The SDAI score and the BRR after the remission were significantly better in the G ≤ 6 than in the G > 6. TL is an important key to guarantee good and stable clinical course in treating under T2T.
Association of ERCC family mutations with prognosis and immune checkpoint inhibitors response in multiple cancers
Authors: Chen Chao , Liu Haozhen , Li Yanlin , Liu Jixian 
Published: August 2023

AbstractThe proteins encoded by the excision repair cross-complementing (ERCC) family are pivotal in DNA damage repair and maintaining genome stability. However, the precise role of the ERCC family in tumor prognosis and the effectiveness of immune checkpoint inhibitors (ICI) therapy remain uncertain. This study aimed to explore the connection between ERCC mutations and prognosis as well as the response to ICI. We observed that patients with ERCC mutations exhibited enhanced progression-free survival (PFS) and overall survival (OS) in two independent pan-cancer cohorts. Furthermore, this mutant subgroup showed higher tumor mutation burden (TMB) compared to the wild-type subgroup. Notably, ERCC mutations were associated with better OS (HR 0.54, 95% CI 0.42–0.70; P < 0.001) in pan-cancer patients who underwent ICI therapy (N = 1661). These findings were validated in a separate cohort, where patients in the ERCC mutant subgroup demonstrated improved clinical outcomes (HR 0.56, 95% CI 0.37–0.84; P = 0.03) and higher response rates (51.9% vs. 26.8%) than the wild-type subgroup. Further analysis revealed that patients with ERCC mutations displayed elevated tumor neoantigen burden (TNB) levels and increased infiltration of immune-response cells. Our study suggests that ERCC mutations are linked to enhanced immunogenicity and improved ICI efficacy, thus potentially serving as a biomarker for ICI therapy.
Bio-organic fertilizers promote yield, chemical composition, and antioxidant and antimicrobial activities of essential oil in fennel (Foeniculum vulgare) seeds
Authors: Abdelbaky Ahmed S. , Mohamed Abir M. H. A. , Abd El-Mageed Taia A. , Rady Mostafa M. , Alshehri Fatma , El-Saadony Mohamed T. , AbuQamar Synan F. , El-Tarabily Khaled A. , Al-Elwany Omar A. A. 
Published: August 2023

AbstractThe aromatic fennel plant (Foeniculum vulgareMiller) is cultivated worldwide due to its high nutritional and medicinal values. The aim of the current study was to determine the effect of the application of bio-organic fertilization (BOF), farmyard manure (FM) or poultry manure (PM), either individually or combined withLactobacillus plantarum(LP) and/orLactococcus lactis(LL) on the yield, chemical composition, and antioxidative and antimicrobial activities of fennel seed essential oil (FSEO). In general, PM + LP + LL and FM + LP + LL showed the best results compared to any of the applications of BOF. Among the seventeen identified FSEO components,trans-anethole (78.90 and 91.4%), fenchone (3.35 and 10.10%), limonene (2.94 and 8.62%), and estragole (0.50 and 4.29%) were highly abundant in PM + LP + LL and FM + LP + LL, respectively. In addition, PM + LP + LL and FM + LP + LL exhibited the lowest half-maximal inhibitory concentration (IC50) values of 8.11 and 9.01 μg mL−1, respectively, compared tol-ascorbic acid (IC50 = 35.90 μg mL−1). We also observed a significant (P > 0.05) difference in the free radical scavenging activity of FSEO in the triple treatments. The in vitro study using FSEO obtained from PM + LP + LL or FM + LP + LL showed the largest inhibition zones against all tested Gram positive and Gram negative bacterial strains as well as pathogenic fungi. This suggests that the triple application has suppressive effects against a wide range of foodborne bacterial and fungal pathogens. This study provides the first in-depth analysis of Egyptian fennel seeds processed utilizing BOF treatments, yielding high-quality FSEO that could be used in industrial applications.
Phase angle is related to physical function and quality of life in preoperative patients with lumbar spinal stenosis
Authors: Otsubo Ryota , Hashida Ryuki , Murotani Kenta , Iwanaga Sohei , Hirota Keisuke , Koya Shunji , Tsukada Yuya , Ogata Yuta , Yokosuka Kimiaki , Yoshida Tatsuhiro , Nakae Ichiro , Fudo Takuma , Morito Shinji , Shimazaki Takahiro , Yamada Kei , Sato Kimiaki , Matsuse Hiroo , Shiba Naoto , Hiraoka Koji 
Published: August 2023

AbstractLumbar spinal stenosis (LSS) can interfere with daily life and quality of life (QOL). Evaluating physical function and QOL and helping patients to improve is the focus of rehabilitation. Phase angle (PhA) assessment is widely used to measure body composition and is considered an indicator of physical function and QOL. This study investigated the relationship between PhA and physical function, physical activity, and QOL in patients with LSS. PhA, handgrip strength, walking speed, Timed Up and Go test (TUG), Life Space Assessment (LSA), Prognostic Nutritional Index (PNI), Japanese Orthopaedic Association Back Pain Evaluation Questionnaire (JOABPEQ), and EQ-5D were assessed and statistically analyzed. The study included 133 patients with LSS. Multiple regression analysis of PhA adjusted for age, sex, and body mass index (Model 1) and for Model 1 + PNI (Model 2) showed significant correlations (P < 0.05) with handgrip strength, walking speed, TUG, and LSA. Regarding QOL, PhA was significantly correlated (P < 0.05) with lumbar function in JOABPEQ. PhA was associated with physical function and QOL in patients with LSS and might be a new clinical indicator in this population.
Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content
Authors: Pandey Jeewan , Thompson Dalton , Joshi Madhumita , Scheuring Douglas C. , Koym Jeffrey W. , Joshi Vijay , Vales M. Isabel 
Published: August 2023

AbstractFree amino acids in potato tubers contribute to their nutritional value and processing quality. Exploring the natural variation in their accumulation in tubers across diverse genetic backgrounds is critical to potato breeding programs aiming to enhance or partition their distribution effectively. This study assessed variation in the tuber-bound free amino acids in a diversity panel of tetraploid potato clones developed and maintained by the Texas A&M Potato Breeding Program to explore their genetic basis and to obtain genomic-estimated breeding values for applied breeding purposes. Free amino acids content was evaluated in tubers of 217 tetraploid potato clones collected from Dalhart, Texas in 2019 and 2020, and Springlake, Texas in 2020. Most tuber amino acids were not affected by growing location, except histidine and proline, which were significantly lower (− 59.0%) and higher (+ 129.0%), respectively, at Springlake, Texas (a location that regularly suffers from abiotic stresses, mainly high-temperature stress). Single nucleotide polymorphism markers were used for genome-wide association studies and genomic selection of clones based on amino acid content. Most amino acids showed significant variations among potato clones and moderate to high heritabilities. Principal component analysis separated fresh from processing potato market classes based on amino acids distribution patterns. Genome-wide association studies discovered 33 QTL associated with 13 free amino acids. Genomic-estimated breeding values were calculated and are recommended for practical potato breeding applications to select parents and advance clones with the desired free amino acid content.
A highly efficient scheme for library preparation from single-stranded DNA
Authors: Miura Fumihito , Kanzawa-Kiriyama Hideaki , Hisano Osamu , Miura Miki , Shibata Yukiko , Adachi Noboru , Kakuda Tsuneo , Shinoda Ken-ichi , Ito Takashi 
Published: August 2023

AbstractAlthough methods for sequencing library preparation from double-stranded DNA are well established, those from single-stranded DNA (ssDNA) have not been well studied. Further, the existing methods have limitations in efficiency and yield. Therefore, we developed a highly efficient procedure for sequencing library preparation from ssDNA. In this method, the first adaptor tagging of ssDNA is performed using terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation, which we reported recently. After complementary strand synthesis using the adaptor-tagged ssDNA, second adaptor tagging via Vaccinia virus topoisomerase I (VTopoI or TOPO)-based adaptor ligation is performed. With additional steps for degradation, repression, and removal of the adaptor dimer, the proposed TACS-TOPO scheme realizes adaptor dimer-free sequencing library preparation from ssDNA samples of 24 pg. The TACS-TOPO scheme was successfully applied to cell-free DNA analysis with amplification-free library preparation from 50 µL of human serum. A modified TACS-TOPO scheme was also applied to DNA extracted from ancient human bones, bringing two to eight times more library yields than those using a conventional library preparation protocol. The procedures for preparing VTopoI and its complex with a double-stranded oligonucleotide adaptor are also described. Overall, the proposed TACS-TOPO scheme can facilitate practical and sensitive sequencing analysis of ssDNA.
Novel CAF-identifiers via transcriptomic and protein level analysis in HNSC patients
Authors: Dwivedi Nehanjali , Shukla Nidhi , Prathima K. M. , Das Manjula , Dhar Sujan K. 
Published: August 2023

AbstractCancer-associated fibroblasts (CAFs), a prominent component of the tumor microenvironment, play an important role in tumor development, invasion, and drug resistance. The expression of distinct “CAF-markers” which separates CAFs from normal fibroblasts and epithelial cells, have traditionally been used to identify them. These commonly used CAF-markers have been reported to differ greatly across different CAF subpopulations, even within a cancer type. Using an unbiased -omic approach from public data and in-house RNAseq data from patient derived novel CAF cells, TIMP-1, SPARC, COL1A2, COL3A1 and COL1A1 were identified as potential CAF-markers by differential gene expression analysis using publicly available single cell sequencing data and in-house RNAseq data to distinguish CAF populations from tumor epithelia and normal oral fibroblasts. Experimental validation using qPCR and immunofluorescence revealed CAF-specific higher expression of TIMP-1 and COL1A2 as compared to other markers in 5 novel CAF cells, derived from patients of diverse gender, habits and different locations of head and neck squamous cell carcinoma (HNSC). Upon immunohistochemical (IHC) analysis of FFPE blocks however, COL1A2 showed better differential staining between tumor epithelia and tumor stroma. Similar data science driven approach utilizing single cell sequencing and RNAseq data from stabilized CAFs can be employed to identify CAF-markers in various cancers.
Photonic helicoid-like surface states in chiral metamaterials
Authors: Chern Ruey-Lin 
Published: August 2023

AbstractWe investigate the photonic topological phases in chiral metamaterials characterized by the magnetoelectric tensors with diagonal chirality components. The underlying medium is considered a photonic analogue of the topological semimetal featured with a Weyl cone and a cylindrical surface in the frequency-wave vector space. As the ’spin’-degenerate condition is satisfied, the photonic system can be rearranged as two hybrid modes that are completely decoupled. By introducing the pseudospin states as the basis for the hybrid modes, the photonic system is described by two subsystems in the form of spin-orbit Hamiltonians of spin 1, which result in nonzero spin Chern numbers that determine the topological properties. Surface modes at the interface between vacuum and the chiral metamaterial exist in their common gap in the wave vector space, which are analytically formulated by algebraic equations. In particular, the surface modes form a pair of spiral surface sheets wrapping around the Weyl cone, resembling the helicoid surface states that occur in topological semimetals. At the Weyl frequency, the surface modes contain two Fermi arc-like states that concatenate to yield a straight line segment.
Estrous cycle dependent expression of oxycodone conditioned reward in rats
Authors: Babb Jessica A. , Constantino Nicholas J. , Kaplan Gary B. , Chartoff Elena H. 
Published: August 2023

AbstractOxycodone is one of the most widely prescribed and misused opioid painkillers in the United States. Evidence suggests that biological sex and hormonal status can impact drug reward in humans and rodents, but the extent to which these factors can influence the rewarding effects of oxycodone is unclear. The purpose of this study was to utilize place conditioning to determine the effects of sex and female hormonal status on the expression of oxycodone conditioned reward in rats. Gonadally intact adult Sprague-Dawley male and female rats were used to test: (1) whether both sexes express conditioned reward to oxycodone at similar doses, (2) the impact of conditioning session length on oxycodone conditioned reward expression in both sexes, and (3) the influence of female estrous cycle stage on oxycodone conditioned reward expression. Both sexes expressed conditioned reward at the same doses of oxycodone. Increasing the length of conditioning sessions did not reveal an effect of sex and resulted in lower magnitude conditioned reward expression. Importantly however, female stage of estrous cycle significantly influenced oxycodone conditioned reward expression. These results suggest that female hormonal status can impact the rewarding effects of opioids and thus have important implications for prescription opioid treatment practices.
PDI augments kainic acid-induced seizure activity and neuronal death by inhibiting PP2A-GluA2-PICK1-mediated AMPA receptor internalization in the mouse hippocampus
Authors: Lee Duk-Shin , Kim Tae-Hyun , Park Hana , Kim Ji-Eun 
Published: August 2023

AbstractProtein disulfide isomerase (PDI) is a redox-active enzyme and also serves as a nitric oxide donor causingS-nitrosylation of cysteine residues in various proteins. Although PDI knockdown reducesα-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor (AMPAR)-mediated neuronal activity, the underlying mechanisms are largely unknown. In the present study, we found that under physiological condition PDI knockdown increased CaMKII activity (phosphorylation) in the mouse hippocampus. However, PDI siRNA inhibited protein phosphatase (PP) 2A-mediated GluA2 S880 dephosphorylation by increasing PP2A oxidation, independent ofS-nitrosylation. PDI siRNA also enhanced glutamate ionotropic receptor AMPA type subunit 1 (GluA1) S831 and GluA2 S880, but not GluA1 S845 and GluA2 Y869/Y873/Y876 phosphorylations, concomitant with the enhanced protein interacting with C kinase 1 (PICK1)-mediated AMPAR internalization. Furthermore, PDI knockdown attenuated seizure activity and neuronal damage in response to kainic acid (a non-desensitizing agonist of AMPAR). Therefore, these findings suggest that PDI may regulate surface AMPAR expression through PP2A-GluA2-PICK1 signaling pathway, and that PDI may be one of the therapeutic targets for epilepsy via AMPAR internalization without altering basal neurotransmission.
Impact of malaria on glutathione peroxidase levels: a systematic review and meta-analysis
Authors: Kotepui Manas , Mahittikorn Aongart , Anabire Nsoh Godwin , Kotepui Kwuntida Uthaisar 
Published: August 2023

AbstractThe primary antioxidant, glutathione peroxidase (GPx), is hypothesized to contribute to the pathophysiology of malaria. This current study conducted a meta-analysis to examine variations in GPx blood levels in malaria patients. Seven electronic databases—ProQuest, Scopus, Embase, MEDLINE, PubMed, Ovid, and Google Scholar—were searched for relevant studies with no limitations to publication language or publication date. The Joanna Briggs Institute critical appraisal tools were used to appraise the risk of bias among the included studies critically. The meta-analysis was conducted by pooling the effect estimates and Hedges’s g using a random-effects model. Search results returned 1253 articles, of which 16 studies were used for syntheses. Results of the meta-analysis indicated that malaria patients had decreased blood levels of GPx compared to uninfected individuals (P < 0.01, Hedges’ g: − 4.06, 95% CI − 5.49–(− 2.63), I2: 99.07%, 1278 malaria patients/627 uninfected individuals, 15 studies). Subgroup analyses indicated that peripheral levels of GPx were significantly diminished in patients with P. falciparum malaria compared to uninfected controls (P < 0.01, Hedges’ g: − 3.06, 95% CI − 4.46–(− 1.65), I2: 98.39%, 9 studies) but not in patients with P. vivax malaria (P = 0.15, Hedges’ g: − 2.05, 95% CI − 4.83–0.74), I2: 98.64%, 2 studies) Overall, malaria is associated with declined levels of GPx, particularly in patients with P. falciparum malaria. The finding provides valuable insights that prompt the need to investigate the role of GPx depletion in malaria pathogenesis.
NADH and NADPH peroxidases as antioxidant defense mechanisms in intestinal sulfate-reducing bacteria
Authors: Kushkevych Ivan , Dordević Dani , Alberfkani Mohammad I. , Gajdács Márió , Ostorházi Eszter , Vítězová Monika , Rittmann Simon K.-M. R. 
Published: August 2023

AbstractAnimal and human feces typically include intestinal sulfate-reducing bacteria (SRB). Hydrogen sulfide and acetate are the end products of their dissimilatory sulfate reduction and may create a synergistic effect. Here, we report NADH and NADPH peroxidase activities from intestinal SRB Desulfomicrobium orale and Desulfovibrio piger. We sought to compare enzymatic activities under the influence of various temperature and pH regimes, as well as to carry out kinetic analyses of enzymatic reaction rates, maximum amounts of the reaction product, reaction times, maximum rates of the enzyme reactions, and Michaelis constants in cell-free extracts of intestinal SRB, D. piger Vib-7, and D. orale Rod-9, collected from exponential and stationary growth phases. The optimal temperature (35 °C) and pH (7.0) for both enzyme’s activity were determined. The difference in trends of Michaelis constants (Km) during exponential and stationary phases are noticeable between D. piger Vib-7 and D. orale Rod-9; D. orale Rod-9 showed much higher Km (the exception is NADH peroxidase of D. piger Vib-7: 1.42 ± 0.11 mM) during the both monitored phases. Studies of the NADH and NADPH peroxidases—as putative antioxidant defense systems of intestinal SRB and detailed data on the kinetic properties of this enzyme, as expressed by the decomposition of hydrogen peroxide—could be important for clarifying evolutionary mechanisms of antioxidant defense systems, their etiological role in the process of dissimilatory sulfate reduction, and their possible role in the development of bowel diseases.