bluuebunny/crossref_metadata_2025_split huggingface dataset:
Supplying the trip to antibody production—nutrients, signaling, and the programming of cellular metabolism in the mature B lineage
Authors: Boothby Mark R. , Brookens Shawna K. , Raybuck Ariel L. , Cho Sung Hoon 
Published: November 2021

AbstractThe COVID pandemic has refreshed and expanded recognition of the vital role that sustained antibody (Ab) secretion plays in our immune defenses against microbes and of the importance of vaccines that elicit Ab protection against infection. With this backdrop, it is especially timely to review aspects of the molecular programming that govern how the cells that secrete Abs arise, persist, and meet the challenge of secreting vast amounts of these glycoproteins. Whereas plasmablasts and plasma cells (PCs) are the primary sources of secreted Abs, the process leading to the existence of these cell types starts with naive B lymphocytes that proliferate and differentiate toward several potential fates. At each step, cells reside in specific microenvironments in which they not only receive signals from cytokines and other cell surface receptors but also draw on the interstitium for nutrients. Nutrients in turn influence flux through intermediary metabolism and sensor enzymes that regulate gene transcription, translation, and metabolism. This review will focus on nutrient supply and how sensor mechanisms influence distinct cellular stages that lead to PCs and their adaptations as factories dedicated to Ab secretion. Salient findings of this group and others, sometimes exhibiting differences, will be summarized with regard to the journey to a distinctive metabolic program in PCs.
Homeoprotein SIX1 compromises antitumor immunity through TGF-β-mediated regulation of collagens
Authors: Liu Wancheng , Gao Meiling , Li Lili , Chen Yu , Fan Huimin , Cai Qiaomei , Shi Yueyue , Pan Chaohu , Liu Junxiao , Cheng Lucy S. , Yang Heng , Cheng Genhong 
Published: November 2021

AbstractThe tumor microenvironment (TME), including infiltrated immune cells, is known to play an important role in tumor growth; however, the mechanisms underlying tumor immunogenicity have not been fully elucidated. Here, we discovered an unexpected role for the transcription factor SIX1 in regulating the tumor immune microenvironment. Based on analyses of patient datasets, we found that SIX1 was upregulated in human tumor tissues and that its expression levels were negatively correlated with immune cell infiltration in the TME and the overall survival rates of cancer patients. Deletion of Six1 in cancer cells significantly reduced tumor growth in an immune-dependent manner with enhanced antitumor immunity in the TME. Mechanistically, SIX1 was required for the expression of multiple collagen genes via the TGFBR2-dependent Smad2/3 activation pathway, and collagen deposition in the TME hampered immune cell infiltration and activation. Thus, our study uncovers a crucial role for SIX1 in modulating tumor immunogenicity and provides proof-of-concept evidence for targeting SIX1 in cancer immunotherapy.
Combined administration of laminin-221 and prostacyclin agonist enhances endogenous cardiac repair in an acute infarct rat heart
Authors: Sougawa Nagako , Miyagawa Shigeru , Kawamura Takuji , Matsuura Ryohei , Harada Akima , Sakai Yoshiki , Mochizuki-Oda Noriko , Sato-Nishiuchi Ryoko , Sekiguchi Kiyotoshi , Sawa Yoshiki 
Published: November 2021

AbstractAlthough endogenous cardiac repair by recruitment of stem cells may serve as a therapeutic approach to healing a damaged heart, how to effectively enhance the migration of stem cells to the damaged heart is unclear. Here, we examined whether the combined administration of prostacyclin agonist (ONO1301), a multiple-cytokine inducer, and stem cell niche laminin-221 (LM221), enhances regeneration through endogenous cardiac repair. We administered ONO1301- and LM221-immersed sheets, LM221-immersed sheets, ONO1301-immersed sheets, and PBS-immersed sheets (control) to an acute infarction rat model. Four weeks later, cardiac function, histology, and cytokine expression were analysed. The combined administration of LM221 and ONO1301 upregulated angiogenic and chemotactic factors in the myocardium after 4 weeks and enhanced the accumulation of ILB4 positive cells, SMA positive cells, and platelet-derived growth factor receptor alpha (PDGFRα) and CD90 double-positive cells, leading to the generation of mature microvascular networks. Interstitial fibrosis reduced and functional recovery was prominent in LM221- and ONO1301-administrated hearts as compared with those in ONO1301-administrated or control hearts. LM221 and ONO1301 combination enhanced recruitment of PDGFRα and CD90 double-positive cells, maturation of vessels, and functional recovery in rat acute myocardial infarction hearts, highlighting a new promising acellular approach for the failed heart.
Study the plasmonic property of gold nanorods highly above damage threshold via single-pulse spectral hole-burning experiments
Authors: Wang Zibo , Kan Zhe , Shen Mengyan 
Published: November 2021

AbstractIntense femtosecond laser irradiation reshapes gold nanorods, resulting in a persistent hole in the optical absorption spectrum of the nanorods at the wavelength of the laser. Single-pulse hole-burning experiments were performed in a mixture of nanorods with a broad absorption around 800 nm with a 35-fs laser with 800 nm wavelength and 6 mJ/pulse. A significant increase in hole burning width at an average fluence of 106 J/m2 has been found, suggesting a tripled damping coefficient of plasmon. This shows that the surface plasmonic effect still occurs at extremely high femtosecond laser fluences just before the nanorods are damaged and the remaining 10% plasmonic enhancement of light is at the fluence of 106 J/m2, which is several orders of magnitude higher than the damage threshold of the gold nanorods. Plasmon–photon interactions may also cause an increase in the damping coefficient.
Identification of ASCL1 as a determinant for human iPSC-derived dopaminergic neurons
Authors: Earley Aaron M. , Burbulla Lena F. , Krainc Dimitri , Awatramani Rajeshwar 
Published: November 2021

AbstractDuring cellular specification, transcription factors orchestrate cellular decisions through gene regulation. By hijacking these transcriptional networks, human pluripotent stem cells (hPSCs) can be specialized into neurons with different molecular identities for the purposes of regenerative medicine and disease modeling. However, molecular fine tuning cell types to match their in vivo counterparts remains a challenge. Directing cell fates often result in blended or incomplete neuron identities. A better understanding of hPSC to neuron gene regulation is needed. Here, we used single cell RNA sequencing to resolve some of these graded molecular identities during human neurogenesis from hPSCs. Differentiation platforms were established to model neural induction from stem cells, and we characterized these differentiated cell types by 10x single cell RNA sequencing. Using single cell trajectory and co-expression analyses, we identified a co-regulated transcription factor module expressing achaete-scute family basic helix-loop-helix transcription factor 1 (ASCL1) and neuronal differentiation 1 (NEUROD1). We then tested the function of these transcription factors in neuron subtype differentiation by gene knockout in a novel human system that reports the expression of tyrosine hydroxylase (TH), the rate limiting enzyme in dopamine synthesis. ASCL1 was identified as a necessary transcription factor for regulating dopaminergic neurotransmitter selection.
Machine learning models for screening carotid atherosclerosis in asymptomatic adults
Authors: Yu Jian , Zhou Yan , Yang Qiong , Liu Xiaoling , Huang Lili , Yu Ping , Chu Shuyuan 
Published: November 2021

AbstractCarotid atherosclerosis (CAS) is a risk factor for cardiovascular and cerebrovascular events, but duplex ultrasonography isn’t recommended in routine screening for asymptomatic populations according to medical guidelines. We aim to develop machine learning models to screen CAS in asymptomatic adults. A total of 2732 asymptomatic subjects for routine physical examination in our hospital were included in the study. We developed machine learning models to classify subjects with or without CAS using decision tree, random forest (RF), extreme gradient boosting (XGBoost), support vector machine (SVM) and multilayer perceptron (MLP) with 17 candidate features. The performance of models was assessed on the testing dataset. The model using MLP achieved the highest accuracy (0.748), positive predictive value (0.743), F1 score (0.742), area under receiver operating characteristic curve (AUC) (0.766) and Kappa score (0.445) among all classifiers. It’s followed by models using XGBoost and SVM. In conclusion, the model using MLP is the best one to screen CAS in asymptomatic adults based on the results from routine physical examination, followed by using XGBoost and SVM. Those models may provide an effective and applicable method for physician and primary care doctors to screen asymptomatic CAS without risk factors in general population, and improve risk predictions and preventions of cardiovascular and cerebrovascular events in asymptomatic adults.
Development of FRET-based indicators for visualizing homophilic trans interaction of a clustered protocadherin
Authors: Kanadome Takashi , Hoshino Natsumi , Nagai Takeharu , Matsuda Tomoki , Yagi Takeshi 
Published: November 2021

AbstractClustered protocadherins (Pcdhs), which are cell adhesion molecules, play a fundamental role in self-recognition and non-self-discrimination by conferring diversity on the cell surface. Although systematic cell-based aggregation assays provide information regarding the binding properties of Pcdhs, direct visualization of Pcdh trans interactions across cells remains challenging. Here, we present Förster resonance energy transfer (FRET)-based indicators for directly visualizing Pcdh trans interactions. We developed the indicators by individually inserting FRET donor and acceptor fluorescent proteins (FPs) into the ectodomain of Pcdh molecules. They enabled successful visualization of specific trans interactions of Pcdh and revealed that the Pcdh trans interaction is highly sensitive to changes in extracellular Ca2+ levels. We expect that FRET-based indicators for visualizing Pcdh trans interactions will provide a new approach for investigating the roles of Pcdh in self-recognition and non-self-discrimination processes.
Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production
Authors: Sudasinghe Thanuja D. , Banco Michael T. , Ronning Donald R. 
Published: November 2021

AbstractErgothioneine (EGT) is a low molecular weight histidine betaine essential in all domains of life but only synthesized by selected few organisms. Synthesis of EGT by Mycobacterium tuberculosis (M. tb) is critical for maintaining bioenergetic homeostasis and protecting the bacterium from alkylating agents, oxidative stress, and anti-tubercular drugs. EgtD, an S-adenosylmethionine-dependent methyltransferase (AdoMet), catalyzes the trimethylation of L-Histidine to initiate EGT biosynthesis and this reaction has been shown to be essential for EGT production in mycobacteria and for long-term infection of murine macrophages by M. tb. In this work, library screening and structure-guided strategies identified multiple classes of M. tb EgtD inhibitors that bind in various regions of the enzyme active site. X-ray crystal structures of EgtD-inhibitor complexes confirm that L-Histidine analogs bind solely to the L-Histidine binding site while drug-like inhibitors, such as TGX-221, and S-Glycyl-H-1152 span both the L-Histidine and AdoMet binding sites. These enzyme-inhibitor complexes provide detailed structural information of compound scaffolds useful for developing more potent inhibitors that could shorten Tuberculosis treatment regimens by weakening important bacterial defenses.
Synergetic effect of the surface ligand and SiO2 driven photoluminescence stabilization of the CH3NH3PbBr3 perovskite magic-sized clusters
Authors: Permatasari Fitri Aulia , Masitoh Hilma Eka , Mahen Ea Cahya Septia , Nuryadin Bebeh Wahid , Aimon Akfiny Hasdi , Syah Yana Maolana , Iskandar Ferry 
Published: November 2021

AbstractZero-dimensional Perovskite Magic-size Clusters play crucial roles in understanding and controlling nucleation and growth of semiconductor nanoparticles. However, their metastability behavior is a critical hindrance for reliable characterizations. Here, we report the first demonstration of using an excess amount of surface ligand and SiO2 as novel passivation for synthesizing the magic-sized clusters (MSCs) by the Ligand-assisted reprecipitation method. A synergetic effect between an excessed surface ligand and SiO2 inhibits the protonation and deprotonation reaction between amine-based and acid-based ligand, leading to enhanced PL stability. The obtained CH3NH3PbBr3 PMSCs/SiO2 retain 70% of its initial emission intensity in ambient conditions for 20 days. This passivation approach opens an entirely new avenue for the reliable characterizations of CH3NH3PbBr3 PMSCs, which will significantly broaden their application for understanding and controlling nucleation and growth of semiconductor nanoparticles.
Preferences regarding emerging HIV prevention technologies among Toronto men who have sex with men: a discrete choice experiment
Authors: Tan Darrell H. S. , Rana Jayoti , Tengra Zavare , Hart Trevor A. , Wilton James , Bayoumi Ahmed M. 
Published: November 2021

AbstractNew forms of HIV pre-exposure prophylaxis (PrEP) include long-acting injectables and topical microbicides, each with unique attributes that may appeal to distinct users. We used a discrete choice experiment to characterize preferences for new PrEP formulations among Toronto men who have sex with men. MSM undergoing anonymous HIV testing completed a discrete choice experiment with 12 choice sets by selecting their preferred option within each set. Each set included “usual methods to prevent HIV” (excluding PrEP) as one alternative and two hypothetical PrEP alternatives, which differed according formulation/dosing, side effects (none/mild), risk of drug resistance (none/low/moderate), and HIV prevention efficacy (50%, 65%, 80% or 99% risk reduction). We used mixed logistic regression to infer preferences for PrEP attributes and calculate the marginal rate of substitution between efficacy and other PrEP attributes. 306 men with median (interquartile range) age = 29 (25, 36) years participated, and reported 6 (3, 10) partners and 0 (0, 2) condomless receptive anal sex acts in the preceding six months. An on-demand pill was the most preferred formulation, followed by a monthly injection, daily pill, and on-demand rectal gel. Drug resistance was an important determinant of preferences if the risk was moderate, but not if it was low. The minimum efficacy required for an on-demand pill to be preferred over no PrEP was 32.6% (95%CI = 21.2–43.9%); for a daily pill, injections, and rectal gel, minimum efficacy was 57.9% (95%CI = 44.1–71.7%), 40.1% (27.0–53.2%), and 71.3% (60.5–82.1%), respectively. Attitudes towards PrEP formulations vary among men who have sex with men, with on-demand pills and monthly injections having the highest average preference scores. Understanding these preferences may help to predict uptake.
Safety and efficacy of 0.02% and 0.01% atropine on controlling myopia progression: a 2-year clinical trial
Authors: Cui Can , Li Xiujuan , Lyu Yong , Wei Li , Zhao Bingxin , Yu Shiao , Rong Junbo , Bai Yanhui , Fu Aicun 
Published: November 2021

AbstractFour hundred myopic children randomly received atropine 0.02% (n = 138) or 0.01% (n = 142) in both eyes once-nightly or only wore single-vision spectacles (control group) (n = 120) for 2 years. Spherical equivalent refractive error (SER), axial length (AL), pupil diameter (PD), and amplitude of accommodation (AMP) were measured every 4 months. After 2 years, the SER changes were − 0.80 (0.52) D, − 0.93 (0.59) D and − 1.33 (0.72) D and the AL changes were 0.62 (0.29) mm, 0.72 (0.31) mm and 0.88 (0.35) mm in the 0.02% and 0.01% atropine groups and control group, respectively. There were significant differences between changes in SER and AL in the three groups (all P < 0.001). The changes in SER and AL in the 2nd year were similar to the changes in the 1st year in the three groups (all P > 0.05). From baseline to 2 years, the overall decrease in AMP and increase in PD were not significantly different in the two atropine groups, whereas the AMP and PD in the control group remained stable (all P > 0.05). 0.02% atropine had a better effect on myopia control than 0.01% atropine, and its effects on PD and AMP were similar to 0.01% atropine. 0.02% or 0.01% atropine controlled myopia progression and AL elongation synchronously and had similar effects on myopia control each year.
SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument
Authors: Rosenstierne Maiken W. , Joshi Shreya , Danielsen E. Thomas , Webb Helen , Luong Dac Mui , Bjerring Julie , Hindkær Julie , Jørgensen Lærke , Blauenfeldt Julie , Bojesen Ask , Holck Flemming , Lau Johnny Weber , Bangsgaard Lars , Lind Jakob Broberg , Dragheim Mette Bjergaard , Jacobsen Mikkel Rohde , Elkjær Robert , Clauwaert Steven , Christensen Kristina , Polacek Charlotta , Fomsgaard Anders , Ojalehto Tuomas , Tullila Antti , Brummer Mirko , Jensen Claus Juel , Jensen Frederikke Holm , Schneider Uffe Vest , Lisby Jan Gorm , Jørgensen Rikke Lind , Warthoe Thomas , Finding Ebbe , Warthoe Peter 
Published: November 2021

AbstractRapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns. Here, we present a novel compact portable detection instrument (the Egoo Health System) for extraction-free detection of SARS-CoV-2 using isothermal reverse transcription strand invasion based amplification (RT-SIBA). The SARS-CoV-2 RT-SIBA assay can be performed directly on crude oropharyngeal swabs without nucleic acid extraction with a reaction time of 30 min. The Egoo Health system uses a capsule system, which is automatically sealed tight in the Egoo instrument after applying the sample, resulting in a closed system optimal for molecular isothermal amplification. The performance of the Egoo Health System is comparable to the PCR instrument with an analytical sensitivity of 25 viral RNA copies per SARS-CoV-2 RT-SIBA reaction and a clinical sensitivity and specificity between 87.0–98.4% and 96.6–98.2% respectively.
Quantum Fourier transform is the building block for creating entanglement
Authors: Mastriani Mario 
Published: November 2021

AbstractThis study demonstrates entanglement can be exclusively constituted by quantum Fourier transform (QFT) blocks. A bridge between entanglement and QFT will allow incorporating a spectral analysis to the already traditional temporal approach of entanglement, which will result in the development of new more performant, and fault-tolerant protocols to be used in quantum computing as well as quantum communication, with particular emphasis in the future quantum Internet.
Estimating LOCP cancer mortality rates in small domains in Spain using its relationship with lung cancer
Authors: Retegui Garazi , Etxeberria Jaione , Ugarte María Dolores 
Published: November 2021

AbstractThe distribution of lip, oral cavity, and pharynx (LOCP) cancer mortality rates in small domains (defined as the combination of province, age group, and gender) remains unknown in Spain. As many of the LOCP risk factors are preventable, specific prevention programmes could be implemented but this requires a clear specification of the target population. This paper provides an in-depth description of LOCP mortality rates by province, age group and gender, giving a complete overview of the disease. This study also presents a methodological challenge. As the number of LOCP cancer cases in small domains (province, age groups and gender) is scarce, univariate spatial models do not provide reliable results or are even impossible to fit. In view of the close link between LOCP and lung cancer, we consider analyzing them jointly by using shared component models. These models allow information-borrowing among diseases, ultimately providing the analysis of cancer sites with few cases at a very disaggregated level. Results show that males have higher mortality rates than females and these rates increase with age. Regions located in the north of Spain show the highest LOCP cancer mortality rates.
Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle
Authors: Deviatiiarov Ruslan , Ishikawa Kiyomi , Gazizova Guzel , Abe Takaya , Kiyonari Hiroshi , Takahashi Masayo , Gusev Oleg , Sunagawa Genshiro A. 
Published: November 2021

AbstractMice enter an active hypometabolic state, called daily torpor when they experience a lowered caloric intake under cold ambient temperature. During torpor, the oxygen consumption rate in some animals drops to less than 30% of the normal rate without harming the body. This safe but severe reduction in metabolism is attractive for various clinical applications; however, the mechanism and molecules involved are unclear. Therefore, here we systematically analyzed the gene expression landscape on the level of the RNA transcription start sites in mouse skeletal muscles under various metabolic states to identify torpor-specific transcribed regulatory patterns. We analyzed the soleus muscles from 38 mice in torpid and non-torpid conditions and identified 287 torpor-specific promoters out of 12,862 detected promoters. Furthermore, we found that the transcription factor ATF3 is highly expressed during torpor deprivation and its binding motif is enriched in torpor-specific promoters. Atf3 was also highly expressed in the heart and brown adipose tissue during torpor and systemically knocking out Atf3 affected the torpor phenotype. Our results demonstrate that mouse torpor combined with powerful genetic tools is useful for studying active hypometabolism.
Sterilization effects of UV laser irradiation onBacillus atrophaeusspore viability, structure, and proteins
Authors: Nguyen My-Chi Thi , Nguyen Huu-Quang , Jang Hanbyeol , Noh Sojung , Lee Seong-Yeon , Jang Kyoung-Soon , Lee Jaebeom , Sohn Youngku , Yee Kiju , Jung Heesoo , Kim Jeongkwon 
Published: November 2021

A UV-C laser is capable of sterilizing Bacillus atrophaeus spores.
Transition-metal catalyzed oxidative spirocyclization of N-aryl alkynamides with methylarenes under microwave irradiation
Authors: Yuan Jin-Wei , Mou Chen-Xu , Zhang Yang , Hu Wen-Yu , Yang Liang-Ru , Xiao Yong-Mei , Mao Pu , Zhang Shou-Ren , Qu Ling-Bo 
Published: November 2021

A variety of 3-benzyl spiro[4,5]trienones were synthesized via Cu/Ag-catalyzed ipso-annulation of alkynes with methylarenes using TBPB as an oxidant under microwave irradiation.
Batch quadratic programming network with maximum entropy constraint for anomaly detection
Authors: Zhou Di , Chen Weigang , Guo Chunsheng , Zhang Mark 
Published: November 2021

AbstractThe difficulty of anomaly detection lies in balancing the impact of noise on the network (noise suppression) and distinguishing the real anomaly from the noise (abnormal exposure). So, a deep anomaly detector Batch Quadratic Programming (BQP) network with Maximum Entropy Constraint is proposed. It imposes quadratic programming constraints on Support Vector Data Description through the BQP output layer to achieve noise suppression. In BQP network processes’ batch data, Maximum Entropy Constraint is used to balance abnormal samples and noise. The experiment compared the shallow method with the currently popular deep method on MNIST and CIFAR‐10 data sets and proved that the BQP network with Maximum Entropy Constraint has excellent performance.