bluuebunny/crossref_metadata_2025_split huggingface dataset:
Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS
Authors: Entila Frederickson , Han Xiaowei , Mine Akira , Schulze-Lefert Paul , Tsuda Kenichi 
Published: January 2024

AbstractDespite the plant health-promoting effects of plant microbiota, these assemblages also comprise potentially detrimental microbes. How plant immunity controls its microbiota to promote plant health under these conditions remains largely unknown. We find that commensal bacteria isolated from healthy Arabidopsis plants trigger diverse patterns of reactive oxygen species (ROS) production dependent on the immune receptors and completely on the NADPH oxidase RBOHD that selectively inhibited specific commensals, notably Xanthomonas L148. Through random mutagenesis, we find that L148 gspE, encoding a type II secretion system (T2SS) component, is required for the damaging effects of Xanthomonas L148 on rbohD mutant plants. In planta bacterial transcriptomics reveals that RBOHD suppresses most T2SS gene expression including gspE. L148 colonization protected plants against a bacterial pathogen, when gspE was inhibited by ROS or mutation. Thus, a negative feedback loop between Arabidopsis ROS and the bacterial T2SS tames a potentially detrimental leaf commensal and turns it into a microbe beneficial to the host.
Wide-range soft anisotropic thermistor with a direct wireless radio frequency interface
Authors: Wagih Mahmoud , Shi Junjie , Li Menglong , Komolafe Abiodun , Whittaker Thomas , Schneider Johannes , Kumar Shanmugam , Whittow William , Beeby Steve 
Published: January 2024

AbstractTemperature sensors are one of the most fundamental sensors and are found in industrial, environmental, and biomedical applications. The traditional approach of reading the resistive response of Positive Temperature Coefficient thermistors at DC hindered their adoption as wide-range temperature sensors. Here, we present a large-area thermistor, based on a flexible and stretchable short carbon fibre incorporated Polydimethylsiloxane composite, enabled by a radio frequency sensing interface. The radio frequency readout overcomes the decades-old sensing range limit of thermistors. The composite exhibits a resistance sensitivity over 1000 °C−1, while maintaining stability against bending (20,000 cycles) and stretching (1000 cycles). Leveraging its large-area processing, the anisotropic composite is used as a substrate for sub-6 GHz radio frequency components, where the thermistor-based microwave resonators achieve a wide temperature sensing range (30 to 205 °C) compared to reported flexible temperature sensors, and high sensitivity (3.2 MHz/°C) compared to radio frequency temperature sensors. Wireless sensing is demonstrated using a microstrip patch antenna based on a thermistor substrate, and a battery-less radio frequency identification tag. This radio frequency-based sensor readout technique could enable functional materials to be directly integrated in wireless sensing applications.
De novo biosynthesis of antiarrhythmic alkaloid ajmaline
Authors: Guo Jun , Gao Di , Lian Jiazhang , Qu Yang 
Published: January 2024

AbstractThe antiarrhythmic drug ajmaline is a monoterpenoid indole alkaloid (MIA) isolated from the Ayurvedic plant Rauvolfia serpentina (Indian Snakeroot). Research into the biosynthesis of ajmaline and another renowned MIA chemotherapeutic drug vinblastine has yielded pivotal advancements in the fields of plant specialized metabolism and engineering over recent decades. While the majority of vinblastine biosynthesis has been recently elucidated, the quest for comprehending ajmaline biosynthesis remains incomplete, marked by the absence of two critical enzymes. Here, we show the discovery and characterization of these two elusive reductases, alongside the identification of two physiologically relevant esterases that complete the biosynthesis of ajmaline. We show that ajmaline biosynthesis proceeds with vomilenine 1,2(R)-reduction followed by its 19,20(S)-reduction. This process is further modulated by two root-expressing esterases that deacetylate 17-O-acetylnorajmaline. Expanding upon the successful completion of the ajmaline biosynthetic pathway, we engineer the de novo biosynthesis of ajmaline in Baker’s yeast.
Immunological shifts during early-stage Parkinson’s disease identified with DNA methylation data on longitudinally collected blood samples
Authors: Pike Steven C. , Havrda Matthew , Gilli Francesca , Zhang Ze , Salas Lucas A. 
Published: January 2024

AbstractParkinson’s disease (PD) is the second most common neurodegenerative disease in the United States. Decades before motor symptoms manifest, non-motor symptoms such as hyposmia and rapid eye movement (REM) sleep behavior disorder are highly predictive of PD. Previous immune profiling studies have identified alterations to the proportions of immune cells in the blood of clinically defined PD patients. However, it remains unclear if these phenotypes manifest before the clinical diagnosis of PD. We utilized longitudinal DNA methylation (DNAm) microarray data from the Parkinson’s Progression Marker’s Initiative (PPMI) to perform immune profiling in clinically defined PD and prodromal PD patients (Prod). We identified previously reported changes in neutrophil, monocyte, and T cell numbers in PD patients. Additionally, we noted previously unrecognized decreases in the naive B cell compartment in the defined PD and Prod patient group. Over time, we observed the proportion of innate immune cells in PD blood increased, but the proportion of adaptive immune cells decreased. We identified decreases in T and B cell subsets associated with REM sleep disturbances and early cognitive decline. Lastly, we identified increases in B memory cells associated with both genetic (LRRK2 genotype) and infectious (cytomegalovirus seropositivity) risk factors of PD. Our analysis shows that the peripheral immune system is dynamic as the disease progresses. The study provides a platform to understand how and when peripheral immune alterations occur in PD and whether intervention at particular stages may be therapeutically advantageous.
A protective role of ABCA5 in response to elevated sphingomyelin levels in Parkinson’s disease
Authors: Fu YuHong , Pickford Russell , Galper Jasmin , Phan Katherine , Wu Ping , Li Hongyun , Kim Young-Bum , Dzamko Nicolas , Halliday Glenda M. , Kim Woojin Scott 
Published: January 2024

AbstractParkinson’s disease (PD) is a chronic neurodegenerative disorder that affects the motor system. Increasing evidence indicates that lysosomal dysfunction is pivotal in the pathogenesis of PD, typically characterized by dysregulation of sphingolipids in lysosomes. ATP-binding cassette subfamily A member 5 (ABCA5) is a lysosomal transporter that mediates the removal of excess sphingomyelin from lysosomes. We therefore investigated whether the expression levels of ABCA5 are associated with sphingomyelin levels and α-synuclein pathology in PD. Firstly, we undertook a comprehensive assessment of the six sphingolipid classes that are part of the lysosomal salvage pathway in the disease-affected amygdala and disease-unaffected visual cortex using liquid chromatography-mass spectrometry. We found that sphingomyelin levels were significantly increased in PD compared to controls and correlated with disease duration only in the amygdala, whereas, the five other sphingolipid classes were slightly altered or unaltered. Concomitantly, the expression of ABCA5 was upregulated in the PD amygdala compared to controls and correlated strongly with sphingomyelin levels. Using neuronal cells, we further verified that the expression of ABCA5 was dependent on cellular levels of sphingomyelin. Interestingly, sphingomyelin levels were strongly associated with α-synuclein in the amygdala and were related to α-synuclein expression. Finally, we revealed that sphingomyelin levels were also increased in PD plasma compared to controls, and that five identical sphingomyelin species were increased in both the brain and the plasma. When put together, these results suggest that in regions accumulating α-synuclein in PD, ABCA5 is upregulated to reduce lysosomal sphingomyelin levels potentially as a protective measure. This process may provide new targets for therapeutic intervention and biomarker development for PD.
Hamiltonian phase error in resonantly driven CNOT gate above the fault-tolerant threshold
Authors: Wu Yi-Hsien , Camenzind Leon C. , Noiri Akito , Takeda Kenta , Nakajima Takashi , Kobayashi Takashi , Chang Chien-Yuan , Sammak Amir , Scappucci Giordano , Goan Hsi-Sheng , Tarucha Seigo 
Published: January 2024

AbstractBecause of their long coherence time and compatibility with industrial foundry processes, electron spin qubits are a promising platform for scalable quantum processors. A full-fledged quantum computer will need quantum error correction, which requires high-fidelity quantum gates. Analyzing and mitigating gate errors are useful to improve gate fidelity. Here, we demonstrate a simple yet reliable calibration procedure for a high-fidelity controlled-rotation gate in an exchange-always-on Silicon quantum processor, allowing operation above the fault-tolerance threshold of quantum error correction. We find that the fidelity of our uncalibrated controlled-rotation gate is limited by coherent errors in the form of controlled phases and present a method to measure and correct these phase errors. We then verify the improvement in our gate fidelities by randomized benchmark and gate-set tomography protocols. Finally, we use our phase correction protocol to implement a virtual, high-fidelity, controlled-phase gate.
Individual honey bee tracking in a beehive environment using deep learning and Kalman filter
Authors: Kongsilp Panadda , Taetragool Unchalisa , Duangphakdee Orawan 
Published: January 2024

AbstractThe honey bee is the most essential pollinator and a key contributor to the natural ecosystem. There are numerous ways for thousands of bees in a hive to communicate with one another. Individual trajectories and social interactions are thus complex behavioral features that can provide valuable information for an ecological study. To study honey bee behavior, the key challenges that have resulted from unreliable studies include complexity (high density of similar objects, small objects, and occlusion), the variety of background scenes, the dynamism of individual bee movements, and the similarity between the bee body and the background in the beehive. This study investigated the tracking of individual bees in a beehive environment using a deep learning approach and a Kalman filter. Detection of multiple bees and individual object segmentation were performed using Mask R-CNN with a ResNet-101 backbone network. Subsequently, the Kalman filter was employed for tracking multiple bees by tracking the body of each bee across a sequence of image frames. Three metrics were used to assess the proposed framework: mean average precision (mAP) for multiple-object detection and segmentation tasks, CLEAR MOT for multiple object tracking tasks, and MOTS for multiple object tracking and segmentation tasks. For CLEAR MOT and MOTS metrics, accuracy (MOTA and MOTSA) and precision (MOTP and MOTSP) are considered. By employing videos from a custom-designed observation beehive, recorded at a frame rate of 30 frames per second (fps) and utilizing a continuous frame rate of 10 fps as input data, our system displayed impressive performance. It yielded satisfactory outcomes for tasks involving segmentation and tracking of multiple instances of bee behavior. For the multiple-object segmentation task based on Mask R-CNN, we achieved a 0.85 mAP. For the multiple-object-tracking task with the Kalman filter, we achieved 77.48% MOTA, 79.79% MOTSP, and 79.56% recall. For the overall system for multiple-object tracking and segmentation tasks, we achieved 77.00% MOTSA, 75.60% MOTSP, and 80.30% recall.
Safety and efficacy of N-acetylcysteine (NAC) as an adjunct to standard treatment in patients with acute ischemic stroke: a randomized controlled pilot trial (NACTLYS)
Authors: Komakula Snigdha , Bhatia Rohit , Sahib Akhil , Upadhyay Ashish , S Leve Joseph , Garg Ajay , Y Vishnu V , Pandit Awadh Kishor , Vibha Deepti , Singh Mamta Bhushan , Tripathi Manjari , Srivastava M. V. Padma 
Published: January 2024

AbstractThere is a pressing clinical need for thrombolytic agents that can effectively disaggregate arterial thrombi in acute ischemic stroke without significantly increasing the risk of bleeding. This pilot study aimed to investigate the safety and efficacy of N-acetylcysteine (NAC) as an adjunctive therapy to intravenous recombinant tissue plasminogen activator (rtPA or alteplase). A randomized, open-label, blinded assessor pilot study was conducted. Patients presenting with an acute ischemic stroke within 4.5 h from onset were randomized into two groups: intravenous NAC and rtPA or rtPA alone. Primary outcomes included intracerebral hemorrhage, symptomatic intracerebral hemorrhage, extracranial bleeding, and adverse reactions. Secondary outcomes comprised major neurological improvement assessed by (National Institute of Health Stroke Scale) NIHSS at 24 h, recanalization on first run of angiography in patients who underwent thrombectomy or on repeat vascular imaging at 24 h, modified Rankin scale, and three-month mortality. Forty patients were enrolled, with 21 receiving only rtPA and 19 receiving NAC with rtPA. Baseline characteristics were comparable among groups. No significant differences were observed in adverse events (p = 0.99), intracranial hemorrhage (p = 0.21), symptomatic intracerebral hemorrhage (p = 0.47), or extracranial bleeding (p = 0.21). Median NIHSS at 24 h was significantly lower in the intervention group (p = 0.03). Functional outcomes and three-month mortality were similar between groups (p = 0.85 and p = 0.99 respectively). The co-administration of N-acetylcysteine with alteplase did not significantly alter safety profiles, morbidity, or mortality at 3 months. While no substantial differences were noted, a slightly improved early neurological outcome was observed in the intervention arm. The study's findings were constrained by a small sample size, emphasizing the necessity for future large-scale trials to comprehensively evaluate the safety and efficacy of N-acetylcysteine as a thrombolytic agent in acute ischemic stroke.Trial Registration Clinical Trials Registry India—CTRI/2019/05/019305.
An exploratory metabolomic comparison of participants with fast or absent functional progression from 2CARE, a randomized, double-blind clinical trial in Huntington’s disease
Authors: McGarry Andrew , Hunter Krystal , Gaughan John , Auinger Peggy , Ferraro Thomas N. , Pradhan Basant , Ferrucci Luigi , Egan Josephine M. , Moaddel Ruin 
Published: January 2024

AbstractHuntington’s disease (HD) is increasingly recognized for diverse pathology outside of the nervous system. To describe the biology of HD in relation to functional progression, we previously analyzed the plasma and CSF metabolome in a cross-sectional study of participants who had various degrees of functional impairment. Here, we carried out an exploratory study in plasma from HD individuals over a 3-year time frame to assess whether differences exist between those with fast or absent clinical progression. There were more differences in circulating metabolite levels for fast progressors compared to absent progressors (111 vs 20, nominal p < 0.05). All metabolite changes in faster progressors were decreases, whereas some metabolite concentrations increased in absent progressors. Many of the metabolite levels that decreased in the fast progressors were higher at Screening compared to absent progressors but ended up lower by Year 3. Changes in faster progression suggest greater oxidative stress and inflammation (kynurenine, diacylglycerides, cysteine), disturbances in nitric oxide and urea metabolism (arginine, citrulline, ornithine, GABR), lower polyamines (putrescine and spermine), elevated glucose, and deficient AMPK signaling. Metabolomic differences between fast and absent progressors suggest the possibility of predicting functional decline in HD, and possibly delaying it with interventions to augment arginine, polyamines, and glucose regulation.
Endometrial biopsy performed before the first in vitro fertilization does not impact the early pregnancy rate
Authors: Cellier Mathilde , Werlen Sophie , Lionel Mery , Genod Anne , Felloni Bertrand , Semay Tiphaine , Trombert Béatrice , Chauleur Céline , Raia-Barjat Tiphaine 
Published: January 2024

AbstractEndometrial biopsy (EB) has been showed to increase the rate of clinical pregnancy in patients who underwent in vitro fertilization (IVF) failures. The purpose of this work was to assess the impact of an EB performed before the first in IVF on the early pregnancy rate. Be One study is a prospective, single-centre, randomized, open-label study. In this parallel study, patients were evenly split into two groups. In one group, patients underwent an EB between days 17 and 22 of the menstrual cycle that precedes the ovarian stimulation. In the other group (control), no EB was performed. The hCG-positive rate (early pregnancy rate) was evaluated on day 14 after the ovarian puncture. In total, 157 patients were randomized in the EB group and 154 patients were in the control group. The early pregnancy rate was 33.1% (52/157) in the EB group and 29.9% (46/154) in the control group (p = 0.54). Other parameters, including perforation, endometritis, or pain level were reassuring. An EB performed during the luteal phase of the menstrual cycle preceding the stimulation of the first IVF did not increase early pregnancy rate.
Partisan styles of self-presentation in U.S. Twitter bios
Authors: Essig Liam , DellaPosta Daniel 
Published: January 2024

AbstractPolitical polarization in the United States goes beyond divided opinions on key political issues, extending to realms of culture, lifestyle, and social identity once thought to be apolitical. Using a sample of 1 million Twitter bios, this study investigates how users’ partisan self-presentation on social media tends to include cultural as well as political markers. Representing the text in Twitter bios as semantic networks, the study reveals clear partisan differences in how users describe themselves, even on topics that seem apolitical. Consequently, active Twitter users’ political alignments can be statistically inferred from the non-political references in their bios, even in the absence of explicitly partisan language. These findings offer further evidence of partisan polarization that is aligned with lifestyle preferences. Further research is needed to determine if users are aware of that alignment, which might indicate the politicization of lifestyle preferences. The findings also suggest an under-recognized way social media can promote polarization, not through political discourse or argument, but simply in how users present cultural and lifestyle preferences on those platforms.
Machine learning assisted exploration of the influential parameters on the PLGA nanoparticles
Authors: Rezvantalab Sima , Mihandoost Sara , Rezaiee Masoumeh 
Published: January 2024

AbstractPoly (lactic-co-glycolic acid) (PLGA)-based nanoparticles (NPs) are widely investigated as drug delivery systems. However, despite the numerous reviews and research papers discussing various physicochemical and technical properties that affect NP size and drug loading characteristics, predicting the influential features remains difficult. In the present study, we employed four different machine learning (ML) techniques to create ML models using effective parameters related to NP size, encapsulation efficiency (E.E.%), and drug loading (D.L.%). These parameters were extracted from the different literature. Least Absolute Shrinkage and Selection Operator was used to investigate the input parameters and identify the most influential features (descriptors). Initially, ML models were trained and validated using tenfold validation methods, and subsequently, next their performances were evaluated and compared in terms of absolute error, mean absolute, error and R-square. After comparing the performance of different ML models, we decided to use support vector regression for predicting the size and E.E.% and random forest for predicting the D.L.% of PLGA-based NPs. Furthermore, we investigated the interactions between these target variables using ML methods and found that size and E.E.% are interrelated, while D.L.% shows no significant relationship with the other targets. Among these variables, E.E.% was identified as the most influential parameter affecting the NPs' size. Additionally, we found that certain physicochemical properties of PLGA, including molecular weight (Mw) and the lactide-to-glycolide (LA/GA) ratio, are the most determining features for E.E.% and D.L.% of the final NPs, respectively.
Conjunctival ultraviolet autofluorescence as a biomarker of outdoor exposure in myopia: a systematic review and meta-analysis
Authors: Rodriguez Natali Gutierrez , Claici Aura Ortega , Ramos-Castaneda Jorge A. , González-Zamora Jorge , Bilbao-Malavé Valentina , de la Puente Miriam , Fernandez-Robredo Patricia , Garzón-Parra Sandra Johanna , Garza-Leon Manuel , Recalde Sergio 
Published: January 2024

AbstractOutdoor exposure is considered the primary modifiable risk factor in preventing the development of myopia. This effect is thought to be attributed to the light-induced synthesis and release of dopamine in the retina. However, until recent years, there was no objective quantifiable method available to measure the association between time spent outdoors and myopia. It is only recently that the conjunctival ultraviolet autofluorescence (CUVAF) area, serving as a biomarker for sun exposure, has begun to be utilized in numerous studies. To provide a comprehensive summary of the relevant evidence pertaining to the association between the CUVAF area and myopia across different geographic regions and age groups, a systematic review and meta-analysis were conducted. The search encompassed multiple databases, including MEDLINE, SCIENCE DIRECT, GOOGLE SCHOLAR, WEB OF SCIENCE, and SCOPUS, and utilized specific search terms such as "conjunctival ultraviolet autofluorescence", "CUVAF", "UVAF", "objective marker of ocular sun exposure", "myopia", "degenerative myopia", and "high myopia". The bibliographic research included papers published between the years 2006 and 2022. A total of 4051 records were initially identified, and after duplicates were removed, 49 articles underwent full-text review. Nine articles were included in the systematic review. These studies covered myopia and outdoor exposure across different regions (Australia, Europe and India) with a total population of 3615 individuals. They found that myopes generally had smaller CUVAF areas compared to non-myopes. The meta-analysis confirmed this, revealing statistically smaller CUVAF areas in myopic patients, with a mean difference of − 3.30 mm2 (95% CI − 5.53; − 1.06). Additionally, some studies showed a positive correlation between more outdoor exposure and larger CUVAF areas. In terms of outdoor exposure time, myopic patients reported less time outdoors than non-myopic individuals, with a mean difference of − 3.38 h/week (95% CI − 4.66; − 2.09). Overall, these findings highlight the connection between outdoor exposure, CUVAF area and myopia, with regional variations playing a significant role. The results of this meta-analysis validate CUVAF as a quantitative method to objectively measure outdoor exposure in relation with myopia development.