bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining clinical course of diffuse large B-cell lymphoma using targeted transcriptome and machine learning algorithms
Authors: Albitar Maher , Zhang Hong , Goy Andre , Xu-Monette Zijun Y. , Bhagat Govind , Visco Carlo , Tzankov Alexandar , Fang Xiaosheng , Zhu Feng , Dybkaer Karen , Chiu April , Tam Wayne , Zu Youli , Hsi Eric D. , Hagemeister Fredrick B. , Huh Jooryung , Ponzoni Maurilio , Ferreri Andrés J. M. , Møller Michael B. , Parsons Benjamin M. , van Krieken J. Han , Piris Miguel A. , Winter Jane N. , Li Yong , Xu Bing , Young Ken H. 
Published: February 2022

AbstractMultiple studies have demonstrated that diffuse large B-cell lymphoma (DLBCL) can be divided into subgroups based on their biology; however, these biological subgroups overlap clinically. Using machine learning, we developed an approach to stratify patients with DLBCL into four subgroups based on survival characteristics. This approach uses data from the targeted transcriptome to predict these survival subgroups. Using the expression levels of 180 genes, our model reliably predicted the four survival subgroups and was validated using independent groups of patients. Multivariate analysis showed that this patient stratification strategy encompasses various biological characteristics of DLBCL, and only TP53 mutations remained an independent prognostic biomarker. This novel approach for stratifying patients with DLBCL, based on the clinical outcome of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone therapy, can be used to identify patients who may not respond well to these types of therapy, but would otherwise benefit from alternative therapy and clinical trials.
Myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T): Mayo-Moffitt collaborative study of 158 patients
Authors: Mangaonkar Abhishek A. , Lasho Terra L. , Ketterling Rhett P. , Reichard Kaaren K. , Gangat Naseema , Al-Kali Aref , Begna Kebede H. , Pardanani Animesh , Al Ali Najla H. , Talati Chetasi , Sallman David , Padron Eric , Patnaik Mrinal M. , Tefferi Ayalew , Komrokji Rami 
Published: February 2022

AbstractThe current World Health Organization (WHO) classification of myeloid malignancies includes myelodysplastic/myeloproliferative neoplasms with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T) as a distinct entity. Previous literature on predictors of survival was based on the provisional category of refractory anemia with ring sideroblast and thrombocytosis (RARS-T), which was not subject to MDS/MPN-RS-T exclusionary criteria such as PB blast% ≥1, BM blast% ≥5 or cytogenetic abnormalities such as t(3;3)(q21.2;q26.2), inv(3)(q21.23q26.2) or isolated del(5q). We examined overall (OS) and leukemia-free (LFS) survival and its predictors, among 158 patients with WHO-defined MDS/MPN-RS-T. In univariate analysis, age ≥70 years (P = 0.006), hemoglobin (Hb) ≤10 g/dL (P = 0.03) and abnormal karyotype (excluding -Y, P = 0.008) were associated with shortened OS, which was otherwise not affected by either ASXL1 (P = 0.7), SF3B1 (P = 0.4) or JAK2 V617F (P = 0.7) mutations; in multivariable analysis, Hb ≤ 10 g/dL (P = 0.03) and abnormal karyotype (P = 0.001) remained significant, and thus allowed the development of an operational survival model with low (0 risk factors, median OS 10.5 years), intermediate (1 risk factor, median OS 4.8 years) and high risk (2 risk factors, median OS 1.4 years) categories (P = 0.0009). Comparison of MDS/MPN-RS-T (n = 158) and MDS/MPN-U with BM RS ≥ 15% (MDS/MPN-U-RS; n = 25) did not reveal significant differences in frequency of thrombosis, OS, or LFS, although SF3B1 mutation frequency was higher in the former (93% versus 59%; P = 0.0005). These data suggest limited survival impact for molecular abnormalities and the morphological distinction between MDS/MPN-RS-T and MDS/MPN-U-RS.
Cross-species metabolomic analysis identifies uridine as a potent regeneration promoting factor
Authors: Liu Zunpeng , Li Wei , Geng Lingling , Sun Liang , Wang Qiaoran , Yu Yang , Yan Pengze , Liang Chuqian , Ren Jie , Song Moshi , Zhao Qian , Lei Jinghui , Cai Yusheng , Li Jiaming , Yan Kaowen , Wu Zeming , Chu Qun , Li Jingyi , Wang Si , Li Chunyi , Han Jing-Dong J. , Hernandez-Benitez Reyna , Shyh-Chang Ng , Belmonte Juan Carlos Izpisua , Zhang Weiqi , Qu Jing , Liu Guang-Hui 
Published: February 2022

AbstractRegenerative capacity declines throughout evolution and with age. In this study, we asked whether metabolic programs underlying regenerative capability might be conserved across species, and if so, whether such metabolic drivers might be harnessed to promote tissue repair. To this end, we conducted metabolomic analyses in two vertebrate organ regeneration models: the axolotl limb blastema and antler stem cells. To further reveal why young individuals have higher regenerative capacity than the elderly, we also constructed metabolic profiles for primate juvenile and aged tissues, as well as young and aged human stem cells. In joint analyses, we uncovered that active pyrimidine metabolism and fatty acid metabolism correlated with higher regenerative capacity. Furthermore, we identified a set of regeneration-related metabolite effectors conserved across species. One such metabolite is uridine, a pyrimidine nucleoside, which can rejuvenate aged human stem cells and promote regeneration of various tissues in vivo. These observations will open new avenues for metabolic intervention in tissue repair and regeneration.
CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity
Authors: Long Yiru , Sun Jianhua , Song Tian-Zhang , Liu Tingting , Tang Feng , Zhang Xinxin , Ding Longfei , Miao Yunqiu , Zhu Weiliang , Pan Xiaoyan , An Qi , Qin Mian , Tong Xiankun , Peng Xionghua , Yu Pan , Zhu Peng , Xu Jianqing , Zhang Xiaoyan , Zhang Yachun , Liu Datao , Chen Ben , Chen Huilin , Zhang Leike , Xiao Gengfu , Zuo Jianping , Tang Wei , Zhou Ji , Li Heng , Xu Zhijian , Zheng Hong-Yi , Long Xin-Yan , Qin Qiuping , Gan Yong , Ren Jin , Huang Wei , Zheng Yong-Tang , Jin Guangyi , Gong Likun 
Published: February 2022

AbstractSafe, effective, and economical vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and end the pandemic. We constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains immunodominant peptides screened from the receptor-binding domain (RBD) and is fully chemically synthesized. It has been formulated in an optimized nanoemulsion formulation and is stable at 40 °C for 1 month. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of protective neutralizing antibodies against multiple RBD mutations, SARS-CoV-2 original strain, and variants (B.1.1.7 and B.1.617.2). Specific peptides booster immunization against the B.1.351 variant has also been shown to be effective in improving protection against B.1.351. Meanwhile, CoVac501 elicited the increase of memory T cells, antigen-specific CD8+ T-cell responses, and Th1-biased CD4+ T-cell immune responses in NHPs. Notably, at an extremely high SARS-CoV-2 challenge dose of 1 × 107 TCID50, CoVac501 provided near-complete protection for the upper and lower respiratory tracts of cynomolgus macaques.
Robust induction of B cell and T cell responses by a third dose of inactivated SARS-CoV-2 vaccine
Authors: Liu Yihao , Zeng Qin , Deng Caiguanxi , Li Mengyuan , Li Liubing , Liu Dayue , Liu Ming , Ruan Xinyuan , Mei Jie , Mo Ruohui , Zhou Qian , Liu Min , Peng Sui , Wang Ji , Zhang Hui , Xiao Haipeng 
Published: February 2022

AbstractSARS-CoV-2 inactivated vaccines have shown remarkable efficacy in clinical trials, especially in reducing severe illness and casualty. However, the waning of humoral immunity over time has raised concern over the durability of immune memory following vaccination. Thus, we conducted a nonrandomized trial among the healthcare workers (HCWs) to investigate the long-term sustainability of SARS-CoV-2-specific B cells and T cells stimulated by inactivated vaccines and the potential need for a third booster dose. Although neutralizing antibodies elicited by the standard two-dose vaccination schedule dropped from a peak of 29.3 arbitrary units (AU)/mL to 8.8 AU/mL 5 months after the second vaccination, spike-specific memory B and T cells were still detectable, forming the basis for a quick recall response. As expected, the faded humoral immune response was vigorously elevated to 63.6 AU/mL by 7.2 folds 1 week after the third dose along with abundant spike-specific circulating follicular helper T cells in parallel. Meanwhile, spike-specific CD4+ and CD8+ T cells were also robustly elevated by 5.9 and 2.7 folds respectively. Robust expansion of memory pools by the third dose potentiated greater durability of protective immune responses. Another key finding in this trial was that HCWs with low serological response to two doses were not truly “non-responders” but fully equipped with immune memory that could be quickly recalled by a third dose even 5 months after the second vaccination. Collectively, these data provide insights into the generation of long-term immunological memory by the inactivated vaccine, which could be rapidly recalled and further boosted by a third dose.
Multiplexed nanomaterial-assisted laser desorption/ionization for pan-cancer diagnosis and classification
Authors: Zhang Hua , Zhao Lin , Jiang Jingjing , Zheng Jie , Yang Li , Li Yanyan , Zhou Jian , Liu Tianshu , Xu Jianmin , Lou Wenhui , Yang Weige , Tan Lijie , Liu Weiren , Yu Yiyi , Ji Meiling , Xu Yaolin , Lu Yan , Li Xiaomu , Liu Zhen , Tian Rong , Hu Cheng , Zhang Shumang , Hu Qinsheng , Deng Yangdong , Ying Hao , Zhong Sheng , Zhang Xingdong , Wang Yunbing , Wang Hua , Bai Jingwei , Li Xiaoying , Duan Xiangfeng 
Published: February 2022

AbstractAs cancer is increasingly considered a metabolic disorder, it is postulated that serum metabolite profiling can be a viable approach for detecting the presence of cancer. By multiplexing mass spectrometry fingerprints from two independent nanostructured matrixes through machine learning for highly sensitive detection and high throughput analysis, we report a laser desorption/ionization (LDI) mass spectrometry-based liquid biopsy for pan-cancer screening and classification. The Multiplexed Nanomaterial-Assisted LDI for Cancer Identification (MNALCI) is applied in 1,183 individuals that include 233 healthy controls and 950 patients with liver, lung, pancreatic, colorectal, gastric, thyroid cancers from two independent cohorts. MNALCI demonstrates 93% sensitivity at 91% specificity for distinguishing cancers from healthy controls in the internal validation cohort, and 84% sensitivity at 84% specificity in the external validation cohort, with up to eight metabolite biomarkers identified. In addition, across those six different cancers, the overall accuracy for identifying the tumor tissue of origin is 92% in the internal validation cohort and 85% in the external validation cohort. The excellent accuracy and minimum sample consumption make the high throughput assay a promising solution for non-invasive cancer diagnosis.
Orbital stability analysis and photometric characterization of the second Earth Trojan asteroid 2020 XL5
Authors: Santana-Ros T. , Micheli M. , Faggioli L. , Cennamo R. , Devogèle M. , Alvarez-Candal A. , Oszkiewicz D. , Ramírez O. , Liu P.-Y. , Benavidez P. G. , Campo Bagatin A. , Christensen E. J. , Wainscoat R. J. , Weryk R. , Fraga L. , Briceño C. , Conversi L. 
Published: February 2022

AbstractTrojan asteroids are small bodies orbiting around the L4 or L5 Lagrangian points of a Sun-planet system. Due to their peculiar orbits, they provide key constraints to the Solar System evolution models. Despite numerous dedicated observational efforts in the last decade, asteroid 2010 TK7 has been the only known Earth Trojan thus far. Here we confirm that the recently discovered 2020 XL5 is the second transient Earth Trojan known. To study its orbit, we used archival data from 2012 to 2019 and observed the object in 2021 from three ground-based observatories. Our study of its orbital stability shows that 2020 XL5 will remain in L4 for at least 4 000 years. With a photometric analysis we estimate its absolute magnitude to be $${H}_{r}=18.5{8}_{-0.15}^{+0.16}$$

H

r

=
18.5

8

−
0.15

+
0.16

, and color indices suggestive of a C-complex taxonomy. Assuming an albedo of 0.06 ± 0.03, we obtain a diameter of 1.18 ± 0.08 km, larger than the first known Earth Trojan asteroid.
Downstream high-speed plasma jet generation as a direct consequence of shock reformation
Authors: Raptis Savvas , Karlsson Tomas , Vaivads Andris , Pollock Craig , Plaschke Ferdinand , Johlander Andreas , Trollvik Henriette , Lindqvist Per-Arne 
Published: February 2022

AbstractShocks are one of nature’s most powerful particle accelerators and have been connected to relativistic electron acceleration and cosmic rays. Upstream shock observations include wave generation, wave-particle interactions and magnetic compressive structures, while at the shock and downstream, particle acceleration, magnetic reconnection and plasma jets can be observed. Here, using Magnetospheric Multiscale (MMS) we show in-situ evidence of high-speed downstream flows (jets) generated at the Earth’s bow shock as a direct consequence of shock reformation. Jets are observed downstream due to a combined effect of upstream plasma wave evolution and an ongoing reformation cycle of the bow shock. This generation process can also be applicable to planetary and astrophysical plasmas where collisionless shocks are commonly found.
PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation
Authors: Khadka Prasidda , Reitman Zachary J. , Lu Sophie , Buchan Graham , Gionet Gabrielle , Dubois Frank , Carvalho Diana M. , Shih Juliann , Zhang Shu , Greenwald Noah F. , Zack Travis , Shapira Ofer , Pelton Kristine , Hartley Rachel , Bear Heather , Georgis Yohanna , Jarmale Spandana , Melanson Randy , Bonanno Kevin , Schoolcraft Kathleen , Miller Peter G. , Condurat Alexandra L. , Gonzalez Elizabeth M. , Qian Kenin , Morin Eric , Langhnoja Jaldeep , Lupien Leslie E. , Rendo Veronica , Digiacomo Jeromy , Wang Dayle , Zhou Kevin , Kumbhani Rushil , Guerra Garcia Maria E. , Sinai Claire E. , Becker Sarah , Schneider Rachel , Vogelzang Jayne , Krug Karsten , Goodale Amy , Abid Tanaz , Kalani Zohra , Piccioni Federica , Beroukhim Rameen , Persky Nicole S. , Root David E. , Carcaboso Angel M. , Ebert Benjamin L. , Fuller Christine , Babur Ozgun , Kieran Mark W. , Jones Chris , Keshishian Hasmik , Ligon Keith L. , Carr Steven A. , Phoenix Timothy N. , Bandopadhayay Pratiti 
Published: February 2022

AbstractThe role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of Diffuse Midline Gliomas (DMGs) and are enriched in primary pontine tumors. Through the development of DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D phosphatase activity is required for in vivo oncogenesis. Finally, we apply integrative phosphoproteomic and functional genomics assays and find that oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition.
Colossal and reversible barocaloric effect in liquid-solid-transition materials n-alkanes
Authors: Lin Jianchao , Tong Peng , Zhang Kai , Tao Kun , Lu Wenjian , Wang Xianlong , Zhang Xuekai , Song Wenhai , Sun Yuping 
Published: February 2022

AbstractEmerging caloric cooling technology provides a green alternative to conventional vapor-compression technology which brings about serious environmental problems. However, the reported caloric materials are much inferior to their traditional counterparts in cooling capability. Here we report the barocaloric (BC) effect associated with the liquid-solid-transition (L-S-T) in n-alkanes. A low-pressure of ~50 MPa reversibly triggers an entropy change of ~700 J kg−1 K−1, comparable to those of the commercial refrigerants in vapor-based compression systems. The Raman study and theoretical calculations reveal that applying pressure to the liquid state suppresses the twisting and random thermal motions of molecular chains, resulting in a lower configurational entropy. When the pressure is strong enough to drive the L-S-T, the configurational entropy will be fully suppressed and induce the colossal BC effect. This work could open a new avenue for exploring the colossal BC effect by evoking L-S-T materials.
Cost-effectiveness of routine adolescent vaccination with an M72/AS01E-like tuberculosis vaccine in South Africa and India
Authors: Harris Rebecca C. , Quaife Matthew , Weerasuriya Chathika , Gomez Gabriela B. , Sumner Tom , Bozzani Fiammetta , White Richard G. 
Published: February 2022

AbstractThe M72/AS01E tuberculosis vaccine showed 50% (95%CI: 2–74%) efficacy in a phase 2B trial in preventing active pulmonary tuberculosis disease, but potential cost-effectiveness of adolescent immunisation is unknown. We estimated the impact and cost-effectiveness of six scenarios of routine adolescent M72/AS01E-like vaccination in South Africa and India. All scenarios suggested an M72/AS01E-like vaccine would be highly (94–100%) cost-effective in South Africa compared to a cost-effectiveness threshold of $2480/disability-adjusted life-year (DALY) averted. For India, a prevention of disease vaccine, effective irrespective of recipient’s M. tuberculosis infection status at time of administration, was also highly likely (92–100%) cost-effective at a threshold of $264/DALY averted; however, a prevention of disease vaccine, effective only if the recipient was already infected, had 0–6% probability of cost-effectiveness. In both settings, vaccinating 50% of 18 year-olds was similarly cost-effective to vaccinating 80% of 15 year-olds, and more cost-effective than vaccinating 80% of 10 year-olds. Vaccine trials should include adolescents to ensure vaccines can be delivered to this efficient-to-target population.
Electrode reconstruction strategy for oxygen evolution reaction: maintaining Fe-CoOOH phase with intermediate-spin state during electrolysis
Authors: Lee Woong Hee , Han Man Ho , Ko Young-Jin , Min Byoung Koun , Chae Keun Hwa , Oh Hyung-Suk 
Published: February 2022

AbstractComputational calculations and experimental studies reveal that the CoOOH phase and the intermediate-spin (IS) state are the key factors for realizing efficient Co-based electrocatalysts for the oxygen evolution reaction (OER). However, according to thermodynamics, general cobalt oxide converts to the CoO2 phase under OER condition, retarding the OER kinetics. Herein, we demonstrate a simple and scalable strategy to fabricate electrodes with maintaining Fe-CoOOH phase and an IS state under the OER. The changes of phase and spin states were uncovered by combining in-situ/operando X-ray based absorption spectroscopy and Raman spectroscopy. Electrochemical reconstruction of chalcogenide treated Co foam affords a highly enlarged active surface that conferred excellent catalytic activity and stability in a large-scale water electrolyzer. Our findings are meaningful in that the calculated results were experimentally verified through the operando analyses. It also proposes a new strategy for electrode fabrication and confirms the importance of real active phases and spin states under a particular reaction condition.
Matrix condition mediates the effects of habitat fragmentation on species extinction risk
Authors: Ramírez-Delgado Juan Pablo , Di Marco Moreno , Watson James E. M. , Johnson Chris J. , Rondinini Carlo , Corredor Llano Xavier , Arias Miguel , Venter Oscar 
Published: February 2022

AbstractHabitat loss is the leading cause of the global decline in biodiversity, but the influence of human pressure within the matrix surrounding habitat fragments remains poorly understood. Here, we measure the relationship between fragmentation (the degree of fragmentation and the degree of patch isolation), matrix condition (measured as the extent of high human footprint levels), and the change in extinction risk of 4,426 terrestrial mammals. We find that the degree of fragmentation is strongly associated with changes in extinction risk, with higher predictive importance than life-history traits and human pressure variables. Importantly, we discover that fragmentation and the matrix condition are stronger predictors of risk than habitat loss and habitat amount. Moreover, the importance of fragmentation increases with an increasing deterioration of the matrix condition. These findings suggest that restoration of the habitat matrix may be an important conservation action for mitigating the negative effects of fragmentation on biodiversity.
Pharmacologic IRE1/XBP1s activation promotes systemic adaptive remodeling in obesity
Authors: Madhavan Aparajita , Kok Bernard P. , Rius Bibiana , Grandjean Julia M. D. , Alabi Adekunle , Albert Verena , Sukiasyan Ara , Powers Evan T. , Galmozzi Andrea , Saez Enrique , Wiseman R. Luke 
Published: February 2022

AbstractIn obesity, signaling through the IRE1 arm of the unfolded protein response exerts both protective and harmful effects. Overexpression of the IRE1-regulated transcription factor XBP1s in liver or fat protects against obesity-linked metabolic deterioration. However, hyperactivation of IRE1 engages regulated IRE1-dependent decay (RIDD) and TRAF2/JNK pro-inflammatory signaling, which accelerate metabolic dysfunction. These pathologic IRE1-regulated processes have hindered efforts to pharmacologically harness the protective benefits of IRE1/XBP1s signaling in obesity-linked conditions. Here, we report the effects of a XBP1s-selective pharmacological IRE1 activator, IXA4, in diet-induced obese (DIO) mice. IXA4 transiently activates protective IRE1/XBP1s signaling in liver without inducing RIDD or TRAF2/JNK signaling. IXA4 treatment improves systemic glucose metabolism and liver insulin action through IRE1-dependent remodeling of the hepatic transcriptome that reduces glucose production and steatosis. IXA4-stimulated IRE1 activation also enhances pancreatic function. Our findings indicate that systemic, transient activation of IRE1/XBP1s signaling engenders multi-tissue benefits that integrate to mitigate obesity-driven metabolic dysfunction.
Vegetation-based climate mitigation in a warmer and greener World
Authors: Alkama Ramdane , Forzieri Giovanni , Duveiller Gregory , Grassi Giacomo , Liang Shunlin , Cescatti Alessandro 
Published: February 2022

AbstractThe mitigation potential of vegetation-driven biophysical effects is strongly influenced by the background climate and will therefore be influenced by global warming. Based on an ensemble of remote sensing datasets, here we first estimate the temperature sensitivities to changes in leaf area over the period 2003–2014 as a function of key environmental drivers. These sensitivities are then used to predict temperature changes induced by future leaf area dynamics under four scenarios. Results show that by 2100, under high-emission scenario, greening will likely mitigate land warming by 0.71 ± 0.40 °C, and 83% of such effect (0.59 ± 0.41 °C) is driven by the increase in plant carbon sequestration, while the remaining cooling (0.12 ± 0.05 °C) is due to biophysical land-atmosphere interactions. In addition, our results show a large potential of vegetation to reduce future land warming in the very-stringent scenario (35 ± 20% of the overall warming signal), whereas this effect is limited to 11 ± 6% under the high-emission scenario.