bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting the latent human cytomegalovirus reservoir for T-cell-mediated killing with virus-specific nanobodies
Authors: De Groof Timo W. M. , Elder Elizabeth G. , Lim Eleanor Y. , Heukers Raimond , Bergkamp Nick D. , Groves Ian J. , Wills Mark , Sinclair John H. , Smit Martine J. 
Published: July 2021

AbstractLatent human cytomegalovirus (HCMV) infection is characterized by limited gene expression, making latent HCMV infections refractory to current treatments targeting viral replication. However, reactivation of latent HCMV in immunosuppressed solid organ and stem cell transplant patients often results in morbidity. Here, we report the killing of latently infected cells via a virus-specific nanobody (VUN100bv) that partially inhibits signaling of the viral receptor US28. VUN100bv reactivates immediate early gene expression in latently infected cells without inducing virus production. This allows recognition and killing of latently infected monocytes by autologous cytotoxic T lymphocytes from HCMV-seropositive individuals, which could serve as a therapy to reduce the HCMV latent reservoir of transplant patients.
Continuous-wave upconversion lasing with a sub-10 W cm−2 threshold enabled by atomic disorder in the host matrix
Authors: Moon Byeong-Seok , Lee Tae Kyung , Jeon Woo Cheol , Kwak Sang Kyu , Kim Young-Jin , Kim Dong-Hwan 
Published: July 2021

AbstractMicroscale lasers efficiently deliver coherent photons into small volumes for intracellular biosensors and all-photonic microprocessors. Such technologies have given rise to a compelling pursuit of ever-smaller and ever-more-efficient microlasers. Upconversion microlasers have great potential owing to their large anti-Stokes shifts but have lagged behind other microlasers due to their high pump power requirement for population inversion of multiphoton-excited states. Here, we demonstrate continuous-wave upconversion lasing at an ultralow lasing threshold (4.7 W cm−2) by adopting monolithic whispering-gallery-mode microspheres synthesized by laser-induced liquefaction of upconversion nanoparticles and subsequent rapid quenching (“liquid-quenching”). Liquid-quenching completely integrates upconversion nanoparticles to provide high pump-to-gain interaction with low intracavity losses for efficient lasing. Atomic-scale disorder in the liquid-quenched host matrix suppresses phonon-assisted energy back transfer to achieve efficient population inversion. Narrow laser lines were spectrally tuned by up to 3.56 nm by injection pump power and operation temperature adjustments. Our low-threshold, wavelength-tunable, and continuous-wave upconversion microlaser with a narrow linewidth represents the anti-Stokes-shift microlaser that is competitive against state-of-the-art Stokes-shift microlasers, which paves the way for high-resolution atomic spectroscopy, biomedical quantitative phase imaging, and high-speed optical communication via wavelength-division-multiplexing.
Machine learning approach for discrimination of genotypes based on bright-field cellular images
Authors: Suzuki Godai , Saito Yutaka , Seki Motoaki , Evans-Yamamoto Daniel , Negishi Mikiko , Kakoi Kentaro , Kawai Hiroki , Landry Christian R. , Yachie Nozomu , Mitsuyama Toutai 
Published: July 2021

AbstractMorphological profiling is a combination of established optical microscopes and cutting-edge machine vision technologies, which stacks up successful applications in high-throughput phenotyping. One major question is how much information can be extracted from an image to identify genetic differences between cells. While fluorescent microscopy images of specific organelles have been broadly used for single-cell profiling, the potential ability of bright-field (BF) microscopy images of label-free cells remains to be tested. Here, we examine whether single-gene perturbation can be discriminated based on BF images of label-free cells using a machine learning approach. We acquired hundreds of BF images of single-gene mutant cells, quantified single-cell profiles consisting of texture features of cellular regions, and constructed a machine learning model to discriminate mutant cells from wild-type cells. Interestingly, the mutants were successfully discriminated from the wild type (area under the receiver operating characteristic curve = 0.773). The features that contributed to the discrimination were identified, and they included those related to the morphology of structures that appeared within cellular regions. Furthermore, functionally close gene pairs showed similar feature profiles of the mutant cells. Our study reveals that single-gene mutant cells can be discriminated from wild-type cells based on BF images, suggesting the potential as a useful tool for mutant cell profiling.
Integrating ensemble systems biology feature selection and bimodal deep neural network for breast cancer prognosis prediction
Authors: Cheng Li-Hsin , Hsu Te-Cheng , Lin Che 
Published: July 2021

AbstractBreast cancer is a heterogeneous disease. To guide proper treatment decisions for each patient, robust prognostic biomarkers, which allow reliable prognosis prediction, are necessary. Gene feature selection based on microarray data is an approach to discover potential biomarkers systematically. However, standard pure-statistical feature selection approaches often fail to incorporate prior biological knowledge and select genes that lack biological insights. Besides, due to the high dimensionality and low sample size properties of microarray data, selecting robust gene features is an intrinsically challenging problem. We hence combined systems biology feature selection with ensemble learning in this study, aiming to select genes with biological insights and robust prognostic predictive power. Moreover, to capture breast cancer's complex molecular processes, we adopted a multi-gene approach to predict the prognosis status using deep learning classifiers. We found that all ensemble approaches could improve feature selection robustness, wherein the hybrid ensemble approach led to the most robust result. Among all prognosis prediction models, the bimodal deep neural network (DNN) achieved the highest test performance, further verified by survival analysis. In summary, this study demonstrated the potential of combining ensemble learning and bimodal DNN in guiding precision medicine.
Associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following 28Si ion irradiation
Authors: Minnier Jessica , Emmett Mark R. , Perez Ruby , Ding Liang-Hao , Barnette Brooke L. , Larios Rianna E. , Hong Changjin , Hwang Tae Hyun , Yu Yongjia , Fallgren Christina M. , Story Michael D. , Weil Michael M. , Raber Jacob 
Published: July 2021

AbstractThe space radiation environment consists of multiple species of charged particles, including28Si ions, that may impact brain function during and following missions. To develop biomarkers of the space radiation response, BALB/c and C3H female and male mice and their F2 hybrid progeny were irradiated with28Si ions (350 MeV/n, 0.2 Gy) and tested for behavioral and cognitive performance 1, 6, and 12 months following irradiation. The plasma of the mice was collected for analysis of miRNA levels. Select pertinent brain regions were dissected for lipidomic analyses and analyses of levels of select biomarkers shown to be sensitive to effects of space radiation in previous studies. There were associations between lipids in select brain regions, plasma miRNA, and cognitive measures and behavioral following28Si ion irradiation. Different but overlapping sets of miRNAs in plasma were found to be associated with cognitive measures and behavioral in sham and irradiated mice at the three time points. The radiation condition revealed pathways involved in neurodegenerative conditions and cancers. Levels of the dendritic marker MAP2 in the cortex were higher in irradiated than sham-irradiated mice at middle age, which might be part of a compensatory response. Relationships were also revealed with CD68 in miRNAs in an anatomical distinct fashion, suggesting that distinct miRNAs modulate neuroinflammation in different brain regions. The associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following28Si ion irradiation could be used for the development of biomarker of the space radiation response.
PAX8 lineage-driven T cell engaging antibody for the treatment of high-grade serous ovarian cancer
Authors: Lee Emily , Szvetecz Sarah , Polli Ryan , Grauel Angelo , Chen Jayson , Judge Joyce , Jaiswal Smita , Maeda Rie , Schwartz Stephanie , Voedisch Bernd , Piksa Mateusz , Japutra Chietara , Sadhasivam Lingheswar , Wang Yiqin , Carrion Ana , Isim Sinan , Liang Jinsheng , Nicholson Thomas , Lei Hong , Fang Qing , Steinkrauss Michelle , Walker Dana , Wagner Joel , Cremasco Viviana , Wang Hui Qin , Galli Giorgio G. , Granda Brian , Mansfield Keith , Simmons Quincey , Nguyen Andrew Anh , Vincent Jordan Nicole 
Published: July 2021

AbstractHigh-grade serous ovarian cancers (HGSOC) represent the most common subtype of ovarian malignancies. Due to the frequency of late-stage diagnosis and high rates of recurrence following standard of care treatments, novel therapies are needed to promote durable responses. We investigated the anti-tumor activity of CD3 T cell engaging bispecific antibodies (TCBs) directed against the PAX8 lineage-driven HGSOC tumor antigen LYPD1 and demonstrated that anti-LYPD1 TCBs induce T cell activation and promote in vivo tumor growth inhibition in LYPD1-expressing HGSOC. To selectively target LYPD1-expressing tumor cells with high expression while sparing cells with low expression, we coupled bivalent low-affinity anti-LYPD1 antigen-binding fragments (Fabs) with the anti-CD3 scFv. In contrast to the monovalent anti-LYPD1 high-affinity TCB (VHP354), the bivalent low-affinity anti-LYPD1 TCB (QZC131) demonstrated antigen density-dependent selectivity and showed tolerability in cynomolgus monkeys at the maximum dose tested of 3 mg/kg. Collectively, these data demonstrate that bivalent TCBs directed against LYPD1 have compelling efficacy and safety profiles to support its use as a treatment for high-grade serous ovarian cancers.
Lipid bilayer degradation induced by SARS-CoV-2 spike protein as revealed by neutron reflectometry
Authors: Luchini Alessandra , Micciulla Samantha , Corucci Giacomo , Batchu Krishna Chaithanya , Santamaria Andreas , Laux Valerie , Darwish Tamim , Russell Robert A. , Thepaut Michel , Bally Isabelle , Fieschi Franck , Fragneto Giovanna 
Published: July 2021

AbstractSARS-CoV-2 spike proteins are responsible for the membrane fusion event, which allows the virus to enter the host cell and cause infection. This process starts with the binding of the spike extramembrane domain to the angiotensin-converting enzyme 2 (ACE2), a membrane receptor highly abundant in the lungs. In this study, the extramembrane domain of SARS-CoV-2 Spike (sSpike) was injected on model membranes formed by supported lipid bilayers in presence and absence of the soluble part of receptor ACE2 (sACE2), and the structural features were studied at sub-nanometer level by neutron reflection. In all cases the presence of the protein produced a remarkable degradation of the lipid bilayer. Indeed, both for membranes from synthetic and natural lipids, a significant reduction of the surface coverage was observed. Quartz crystal microbalance measurements showed that lipid extraction starts immediately after sSpike protein injection. All measurements indicate that the presence of proteins induces the removal of membrane lipids, both in the presence and in the absence of ACE2, suggesting that sSpike molecules strongly associate with lipids, and strip them away from the bilayer, via a non-specific interaction. A cooperative effect of sACE2 and sSpike on lipid extraction was also observed.
Trichoderma reesei fungal degradation boosted the potentiality of date pit extract in fighting scopolamine-induced neurotoxicity in male rats
Authors: Saleh Samar R. , Masry Asmaa M. , Ghareeb Doaa A. , Newairy Al-Sayeda A. , Sheta Eman , Maher Adham M. 
Published: July 2021

AbstractDate pits are nutritious by-products, containing high levels of indigestible carbohydrates and polyphenols. To maximize the biological effects of the active ingredients, the hard shell of the polysaccharide must be degraded. Therefore, the current study aimed to assess the protective potentials of date pits extract (DP) and fungal degraded date pits extract (FDDP) against scopolamine (SCO)-induced neurodegeneration in male rats. Date pits were subjected to fungal degradation and extraction, followed by the measurement of phytochemicals and free radical scavenging activities. Forty-two adult Sprague–Dawley male rats were divided into seven groups: three control groups administered with either saline, DP or FDDP; four groups with neurodegeneration receiving SCO (ip 2 mg/kg/day, SCO group) with no treatment, SCO with DP (oral 100 mg/kg/day, DP + SCO group), SCO with FDDP (oral, 100 mg/kg/day, FDDP + SCO group), and SCO with donepezil (DON, oral, 2.25 mg/kg/day, DON + SCO group). The treatment duration was 28 days, and in the last 14 days, SCO was administered daily. Morris water maze test, acetylcholine esterase activity, oxidative stress, markers of inflammation and amyloidogenesis, and brain histopathology were assessed.
Changes in peanut canopy structure and photosynthetic characteristics induced by an arbuscular mycorrhizal fungus in a nutrient-poor environment
Authors: Bi Yinli , Zhou Huili 
Published: July 2021

AbstractA well-developed canopy structure can increase the biomass accumulation and yield of crops. Peanut seeds were sown in a soil inoculated with an arbuscular mycorrhizal fungus (AMF) and uninoculated controls were also sown. Canopy structure was monitored using a 3-D laser scanner and photosynthetic characteristics with an LI-6400 XT photosynthesis system after 30, 45 and 70 days of growth to explore the effects of the AMF on growth, canopy structure and photosynthetic characteristics and yield. The AMF colonized the roots and AMF inoculation significantly increased the height, canopy width and total leaf area of the host plants and improved canopy structure. AMF reduced the tiller angle of the upper and middle canopy layers, increased that of the lower layer, reduced the leaf inclination of the upper, middle and lower layers, and increased the average leaf area and leaf area index after 45 days of growth, producing a well-developed and hierarchical canopy. Moreover, AMF inoculation increased the net photosynthetic rate in the upper, middle and lower layers. Plant height, canopy width, and total leaf area were positively correlated with net photosynthetic rate, and the inclination angle and tiller angle of the upper leaves were negatively correlated with net photosynthetic rate. Overall, the results demonstrate the effects of AMF inoculation on plant canopy structure and net photosynthetic rate.
Identification of Bacillus anthracis, Brucella spp., and Coxiella burnetii DNA signatures from bushmeat
Authors: Katani Robab , Schilling Megan A. , Lyimo Beatus , Eblate Ernest , Martin Andimile , Tonui Triza , Cattadori Isabella M. , Francesconi Stephen C. , Estes Anna B. , Rentsch Dennis , Srinivasan Sreenidhi , Lyimo Samson , Munuo Lidia , Tiambo Christian K. , Stomeo Francesca , Gwakisa Paul , Mosha Fausta , Hudson Peter J. , Buza Joram J. , Kapur Vivek 
Published: July 2021

AbstractMeat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.
Variable rather than extreme slow reaction times distinguish brain states during sustained attention
Authors: Yamashita Ayumu , Rothlein David , Kucyi Aaron , Valera Eve M. , Germine Laura , Wilmer Jeremy , DeGutis Joseph , Esterman Michael 
Published: July 2021

AbstractA common behavioral marker of optimal attention focus is faster responses or reduced response variability. Our previous study found two dominant brain states during sustained attention, and these states differed in their behavioral accuracy and reaction time (RT) variability. However, RT distributions are often positively skewed with a long tail (i.e., reflecting occasional slow responses). Therefore, a larger RT variance could also be explained by this long tail rather than the variance around an assumed normal distribution (i.e., reflecting pervasive response instability based on both faster and slower responses). Resolving this ambiguity is important for better understanding mechanisms of sustained attention. Here, using a large dataset of over 20,000 participants who performed a sustained attention task, we first demonstrated the utility of the exGuassian distribution that can decompose RTs into a strategy factor, a variance factor, and a long tail factor. We then investigated which factor(s) differed between the two brain states using fMRI. Across two independent datasets, results indicate unambiguously that the variance factor differs between the two dominant brain states. These findings indicate that ‘suboptimal’ is different from ‘slow’ at the behavior and neural level, and have implications for theoretically and methodologically guiding future sustained attention research.
Immune system challenge improves recognition memory and reverses malaria-induced cognitive impairment in mice
Authors: de Sousa Luciana Pereira , Ribeiro-Gomes Flávia Lima , de Almeida Roberto Farina , Souza Tadeu Mello e , Werneck Guilherme Loureiro , Souza Diogo Onofre , Daniel-Ribeiro Cláudio Tadeu 
Published: July 2021

AbstractThe immune system plays a role in the maintenance of healthy neurocognitive function. Different patterns of immune response triggered by distinct stimuli may affect nervous functions through regulatory or deregulatory signals, depending on the properties of the exogenous immunogens. Here, we investigate the effect of immune stimulation on cognitive-behavioural parameters in healthy mice and its impact on cognitive sequelae resulting from non-severe experimental malaria. We show that immune modulation induced by a specific combination of immune stimuli that induce a type 2 immune response can enhance long-term recognition memory in healthy adult mice subjected to novel object recognition task (NORT) and reverse a lack of recognition ability in NORT and anxiety-like behaviour in a light/dark task that result from a single episode of mild Plasmodium berghei ANKA malaria. Our findings suggest a potential use of immunogens for boosting and recovering recognition memory that may be impaired by chronic and infectious diseases and by the effects of ageing.
Associations between smoking and blood-group, and the risk of dyslipidaemia amongst French women
Authors: MacDonald C. J. , Madika A. L. , Severi G. , Fournier A. , Boutron-Ruault M. C. 
Published: July 2021

AbstractDyslipidaemia is a major risk factor for cardio-vascular disease, as it promotes atherosclerosis. While cross-sectional studies have identified higher serum cholesterol amongst individuals with the A blood group, there is less evidence from prospective studies whether this translates into a higher risk of dyslipidaemia that requires treatment, nor if this genetic factor interacts with smoking status. This study aimed to prospectively determine potential associations between smoking, ABO blood groups, and risk of incident dyslipidaemia requiring treatment, and to assess associations over strata of blood ABO group. We assessed associations between blood ABO group, smoking and dyslipidaemia in 74,206 women participating in the E3N cohort. We included women who did not have cardiovascular disease at baseline. Logistic regression was used to determine associations between ABO group, smoking and prevalent dyslipidaemia at baseline. Cox proportional hazard models were then used to determine if blood ABO group and smoking were associated with the risk of incident dyslipidaemia, amongst women free of dyslipidaemia at baseline. At baseline 28,281 women with prevalent dyslipidaemia were identified. Compared to the O-blood group, the non-O blood group was associated higher odds of with prevalent dyslipidaemia (ORnon-O = 1.09 [1.06: 1.13]). Amongst the women free of dyslipidaemia at baseline, 6041 incident cases of treated dyslipidaemia were identified during 454,951 person-years of follow-up. The non-O blood groups were associated with an increased risk of dyslipidaemia when compared to the O-group (HRnon-O = 1.16 [1.11: 1.22]), specifically the A blood-group (HRA = 1.18 [1.12: 1.25]). Current smokers were associated with an increased risk of incident dyslipidaemia (HR smokers = 1.27 [1.16: 1.37]), compared to never-smokers. No evidence for effect modification between smoking and ABO blood group was observed (p-effect modification = 0.45), although the highest risk was observed among AB blood group women who smoked (HR = 1.76 [1.22: 2.55]). In conclusion, the non-O blood groups, specifically the A group were associated with an increased risk of dyslipidaemia. Current smokers were associated with a 30% increased risk of dyslipidaemia. These results could aid in personalised approaches to the prevention of cardiovascular risk-factors.