bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing
Authors: Allahyar Amin , Pieterse Mark , Swennenhuis Joost , Los-de Vries G. Tjitske , Yilmaz Mehmet , Leguit Roos , Meijers Ruud W. J. , van der Geize Robert , Vermaat Joost , Cleven Arjen , van Wezel Tom , Diepstra Arjan , van Kempen Léon C. , Hijmering Nathalie J. , Stathi Phylicia , Sharma Milan , Melquiond Adrien S. J. , de Vree Paula J. P. , Verstegen Marjon J. A. M. , Krijger Peter H. L. , Hajo Karima , Simonis Marieke , Rakszewska Agata , van Min Max , de Jong Daphne , Ylstra Bauke , Feitsma Harma , Splinter Erik , de Laat Wouter 
Published: June 2021

AbstractIn routine diagnostic pathology, cancer biopsies are preserved by formalin-fixed, paraffin-embedding (FFPE) procedures for examination of (intra-) cellular morphology. Such procedures inadvertently induce DNA fragmentation, which compromises sequencing-based analyses of chromosomal rearrangements. Yet, rearrangements drive many types of hematolymphoid malignancies and solid tumors, and their manifestation is instructive for diagnosis, prognosis, and treatment. Here, we present FFPE-targeted locus capture (FFPE-TLC) for targeted sequencing of proximity-ligation products formed in FFPE tissue blocks, and PLIER, a computational framework that allows automated identification and characterization of rearrangements involving selected, clinically relevant, loci. FFPE-TLC, blindly applied to 149 lymphoma and control FFPE samples, identifies the known and previously uncharacterized rearrangement partners. It outperforms fluorescence in situ hybridization (FISH) in sensitivity and specificity, and shows clear advantages over standard capture-NGS methods, finding rearrangements involving repetitive sequences which they typically miss. FFPE-TLC is therefore a powerful clinical diagnostics tool for accurate targeted rearrangement detection in FFPE specimens.
Gold-in-copper at low *CO coverage enables efficient electromethanation of CO2
Authors: Wang Xue , Ou Pengfei , Wicks Joshua , Xie Yi , Wang Ying , Li Jun , Tam Jason , Ren Dan , Howe Jane Y. , Wang Ziyun , Ozden Adnan , Finfrock Y. Zou , Xu Yi , Li Yuhang , Rasouli Armin Sedighian , Bertens Koen , Ip Alexander H. , Graetzel Michael , Sinton David , Sargent Edward H. 
Published: June 2021

AbstractThe renewable-electricity-powered CO2 electroreduction reaction provides a promising means to store intermittent renewable energy in the form of valuable chemicals and dispatchable fuels. Renewable methane produced using CO2 electroreduction attracts interest due to the established global distribution network; however, present-day efficiencies and activities remain below those required for practical application. Here we exploit the fact that the suppression of *CO dimerization and hydrogen evolution promotes methane selectivity: we reason that the introduction of Au in Cu favors *CO protonation vs. C−C coupling under low *CO coverage and weakens the *H adsorption energy of the surface, leading to a reduction in hydrogen evolution. We construct experimentally a suite of Au-Cu catalysts and control *CO availability by regulating CO2 concentration and reaction rate. This strategy leads to a 1.6× improvement in the methane:H2 selectivity ratio compared to the best prior reports operating above 100 mA cm−2. We as a result achieve a CO2-to-methane Faradaic efficiency (FE) of (56 ± 2)% at a production rate of (112 ± 4) mA cm−2.
Full-frame and high-contrast smart windows from halide-exchanged perovskites
Authors: Liu You , Wang Jungan , Wang Fangfang , Cheng Zhengchun , Fang Yinyu , Chang Qing , Zhu Jixin , Wang Lin , Wang Jianpu , Huang Wei , Qin Tianshi 
Published: June 2021

AbstractWindow glazing plays an essential role to modulate indoor light and heat transmission, which is a prospect to save the energy cost in buildings. The latest photovoltachromic technology has been regarded as one of the most ideal solutions, however, to achieve full-frame size (100% active area) and high-contrast ratio (>30% variable in visible wavelength) for smart window applicability is still a challenge. Here we report a photovoltachromic device combining full-transparent perovskite photovoltaic and ion-gel based electrochromic components in a vertical tandem architecture without any intermediated electrode. Most importantly, by accurately adjusting the halide-exchanging period, this photovoltachromic module can realize a high pristine transmittance up to 76%. Moreover, it possesses excellent colour-rendering index to 96, wide contrast ratio (>30%) on average visible transmittance (400-780 nm), and a self-adaptable transmittance adjustment and control indoor brightness and temperature automatically depending on different solar irradiances.
Spatial intimacy of binary active-sites for selective sequential hydrogenation-condensation of nitriles into secondary imines
Authors: Zhang Sai , Xia Zhaoming , Zou Yong , Zhang Mingkai , Qu Yongquan 
Published: June 2021

AbstractPrecisely controlling the spatial intimacy of multiple active sites at sub-nanoscale in heterogeneous catalysts can improve their selectivity and activity. Herein, we realize a highly selective nitrile-to-secondary imine transformation through a cascaded hydrogenation and condensation process by Pt1/CoBOx comprising the binary active sites of the single-dispersed Pt and interfacial Lewis acidic B. Atomic Pt sites with large inter-distances (>nanometers) only activate hydrogen for nitrile hydrogenation, but inhibit condensation. Both adjacent B…B on CoBOx and neighbouring Pt…B pairs with close intimacy of ~0.45 nm can satisfy the spatial prerequisites for condensation. Mechanism investigations demonstrate the energetically favorable pathway occurred on adjacent Lewis acidic B sites through the nitrile adsorption (acid-base interaction), hydrogenation via hydrogen spillover from Pt to B sites and sequential condensation. Strong intermolecular tension and steric hindrance of secondary imines on active sites lead to their effective desorption and thereby a high chemoselectivity of secondary imines.
Intratumoral synthesis of nano-metalchelate for tumor catalytic therapy by ligand field-enhanced coordination
Authors: Yang Bowen , Yao Heliang , Tian Han , Yu Zhiguo , Guo Yuedong , Wang Yuemei , Yang Jiacai , Chen Chang , Shi Jianlin 
Published: June 2021

AbstractThe iron gall ink-triggered chemical corrosion of hand-written documents is a big threat to Western cultural heritages, which was demonstrated to result from the iron gall (GA-Fe) chelate-promoted reactive oxygen species generation. Such a phenomenon has inspired us to apply the pro-oxidative mechanism of GA-Fe to anticancer therapy. In this work, we construct a composite cancer nanomedicine by loading gallate into a Fe-engineered mesoporous silica nanocarrier, which can degrade in acidic tumor to release the doped Fe3+and the loaded gallate, forming GA-Fe nanocomplex in situ. The nanocomplex with a highly reductive ligand field can promote oxygen reduction reactions generating hydrogen peroxide. Moreover, the resultant two-electron oxidation form of GA-Fe is an excellent Fenton-like agent that can catalyze hydrogen peroxide decomposition into hydroxyl radical, finally triggering severe oxidative damage to tumors. Such a therapeutic approach by intratumoral synthesis of GA-Fe nano-metalchelate may be instructive to future anticancer researches.
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
Authors: Wilhelm Mathias , Zolg Daniel P. , Graber Michael , Gessulat Siegfried , Schmidt Tobias , Schnatbaum Karsten , Schwencke-Westphal Celina , Seifert Philipp , de Andrade Krätzig Niklas , Zerweck Johannes , Knaute Tobias , Bräunlein Eva , Samaras Patroklos , Lautenbacher Ludwig , Klaeger Susan , Wenschuh Holger , Rad Roland , Delanghe Bernard , Huhmer Andreas , Carr Steven A. , Clauser Karl R. , Krackhardt Angela M. , Reimer Ulf , Kuster Bernhard 
Published: June 2021

AbstractCharacterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational challenges. To address these, we synthesized and analyzed >300,000 peptides by multi-modal LC-MS/MS within the ProteomeTools project representing HLA class I & II ligands and products of the proteases AspN and LysN. The resulting data enabled training of a single model using the deep learning framework Prosit, allowing the accurate prediction of fragment ion spectra for tryptic and non-tryptic peptides. Applying Prosit demonstrates that the identification of HLA peptides can be improved up to 7-fold, that 87% of the proposed proteasomally spliced HLA peptides may be incorrect and that dozens of additional immunogenic neo-epitopes can be identified from patient tumors in published data. Together, the provided peptides, spectra and computational tools substantially expand the analytical depth of immunopeptidomics workflows.
Topographic numerosity maps cover subitizing and estimation ranges
Authors: Cai Yuxuan , Hofstetter Shir , van Dijk Jelle , Zuiderbaan Wietske , van der Zwaag Wietske , Harvey Ben M. , Dumoulin Serge O. 
Published: June 2021

AbstractNumerosity, the set size of a group of items, helps guide behaviour and decisions. Non-symbolic numerosities are represented by the approximate number system. However, distinct behavioural performance suggests that small numerosities, i.e. subitizing range, are implemented differently in the brain than larger numerosities. Prior work has shown that neural populations selectively responding (i.e. hemodynamic responses) to small numerosities are organized into a network of topographical maps. Here, we investigate how neural populations respond to large numerosities, well into the ANS. Using 7 T fMRI and biologically-inspired analyses, we found a network of neural populations tuned to both small and large numerosities organized within the same topographic maps. These results demonstrate a continuum of numerosity preferences that progressively cover both the subitizing range and beyond within the same numerosity map, suggesting a single neural mechanism. We hypothesize that differences in map properties, such as cortical magnification and tuning width, underlie known differences in behaviour.
Lead halide perovskite for efficient optoacoustic conversion and application toward high-resolution ultrasound imaging
Authors: Du Xinyuan , Li Jiapu , Niu Guangda , Yuan Jun-Hui , Xue Kan-Hao , Xia Mengling , Pan Weicheng , Yang Xiaofei , Zhu Benpeng , Tang Jiang 
Published: June 2021

AbstractLead halide perovskites have exhibited excellent performance in solar cells, LEDs and detectors. Thermal properties of perovskites, such as heat capacity and thermal conductivity, have rarely been studied and corresponding devices have barely been explored. Considering the high absorption coefficient (104~105 cm−1), low specific heat capacity (296–326 J kg−1 K−1) and small thermal diffusion coefficient (0.145 mm2 s−1), herein we showcase the successful use of perovskite in optoacoustic transducers. The theoretically calculated phonon spectrum shows that the overlap of optical phonons and acoustic phonons leads to the up-conversion of acoustic phonons, and thus results in experimentally measured low thermal diffusion coefficient. The assembled device of PDMS/MAPbI3/PDMS simultaneously achieves broad bandwidths (−6 dB bandwidth: 40.8 MHz; central frequency: 29.2 MHz), and high conversion efficiency (2.97 × 10−2), while all these parameters are the record values for optoacoustic transducers. We also fabricate miniatured devices by assembling perovskite film onto fibers, and clearly resolve the fine structure of fisheyes, which demonstrates the strong competitiveness of perovskite based optoacoustic transducers for ultrasound imaging.
Autofluorescence as a noninvasive biomarker of senescence and advanced glycation end products in Caenorhabditis elegans
Authors: Komura Tomomi , Yamanaka Mikihiro , Nishimura Kohji , Hara Keita , Nishikawa Yoshikazu 
Published: June 2021

AbstractTo assess the utility of autofluorescence as a noninvasive biomarker of senescence in Caenorhabditis elegans, we measured the autofluorescence of individual nematodes using spectrofluorometry. The fluorescence of each worm increased with age. Animals with lower fluorescence intensity exhibited longer life expectancy. When proteins extracted from worms were incubated with sugars, the fluorescence intensity and the concentration of advanced glycation end products (AGEs) increased over time. Ribose enhanced these changes not only in vitro but also in vivo. The glycation blocker rifampicin suppressed this rise in fluorescence. High-resolution mass spectrometry revealed that vitellogenins accumulated in old worms, and glycated vitellogenins emitted six-fold higher fluorescence than naive vitellogenins. The increase in fluorescence with ageing originates from glycated substances, and therefore could serve as a useful noninvasive biomarker of AGEs. C. elegans can serve as a new model to look for anti-AGE factors and to study the relationship between AGEs and senescence.
Multiomic analysis of stretched osteocytes reveals processes and signalling linked to bone regeneration and cancer
Authors: Santos Lívia , Ugun-Klusek Aslihan , Coveney Clare , Boocock David J. 
Published: June 2021

AbstractExercise is a non-pharmacological intervention that can enhance bone regeneration and improve the management of bone conditions like osteoporosis or metastatic bone cancer. Therefore, it is gaining increasing importance in an emerging area of regenerative medicine—regenerative rehabilitation (RR). Osteocytes are mechanosensitive and secretory bone cells that orchestrate bone anabolism and hence postulated to be an attractive target of regenerative exercise interventions. However, the human osteocyte signalling pathways and processes evoked upon exercise remain to be fully identified. Making use of a computer-controlled bioreactor that mimics exercise and the latest omics approaches, RNA sequencing (RNA-seq) and tandem liquid chromatography-mass spectrometry (LC-MS), we mapped the transcriptome and secretome of mechanically stretched human osteocytic cells. We discovered that a single bout of cyclic stretch activated network processes and signalling pathways likely to modulate bone regeneration and cancer. Furthermore, a comparison between the transcriptome and secretome of stretched human and mouse osteocytic cells revealed dissimilar results, despite both species sharing evolutionarily conserved signalling pathways. These findings suggest that osteocytes can be targeted by exercise-driven RR protocols aiming to modulate bone regeneration or metastatic bone cancer.
Novel recombinant keratin degrading subtilisin like serine alkaline protease from Bacillus cereus isolated from marine hydrothermal vent crabs
Authors: Gurunathan Revathi , Huang Bin , Ponnusamy Vinoth Kumar , Hwang Jiang-Shiou , Dahms Hans-Uwe 
Published: June 2021

AbstractMicrobial secondary metabolites from extreme environments like hydrothermal vents are a promising source for industrial applications. In our study the protease gene from Bacillus cereus obtained from shallow marine hydrothermal vents in the East China Sea was cloned, expressed and purified. The protein sequence of 38 kDa protease SLSP-k was retrieved from mass spectrometry and identified as a subtilisin serine proteinase. The novel SLSP-k is a monomeric protein with 38 amino acid signal peptides being active over wide pH (7–11) and temperature (40–80 °C) ranges, with maximal hydrolytic activities at pH 10 and at 50 °C temperature. The hydrolytic activity is stimulated by Ca2+, Co2+, Mn2+, and DTT. It is inhibited by Fe2+, Cd2+, Cu2+, EDTA, and PMSF. The SLSP-k is stable in anionic, non-anionic detergents, and solvents. The ability to degrade keratin in chicken feather and hair indicates that this enzyme is suitable for the degradation of poultry waste without the loss of nutritionally essential amino acids which otherwise are lost in hydrothermal processing. Therefore, the proteinase is efficient in environmental friendly bioconversion of animal waste into fertilizers or value added products such as secondary animal feedstuffs.
Prognostic influences of BCL1 and BCL2 expression on disease-free survival in breast cancer
Authors: Hwang Ki-Tae , Kim Young A. , Kim Jongjin , Oh Hyeon Jeong , Park Jeong Hwan , Choi In Sil , Park Jin Hyun , Oh Sohee , Chu Ajung , Lee Jong Yoon , Hwang Kyu Ri 
Published: June 2021

AbstractWe investigated the prognostic influences of BCL1 and BCL2 expression on disease-free survival in breast cancer patients. BCL1 and BCL2 expression statuses were assessed by immunohistochemistry using tissue microarrays from 393 breast cancer patients. The Kaplan–Meier estimator and log-rank test were used for survival analyses. The Cox proportional hazards model was used to calculate hazard ratio (HR) and the 95% confidence interval (CI) of survival analyses. BCL1 expression revealed no impact on survival. The high BCL2 group showed superior disease-free survival compared with the low BCL2 group (p = 0.002), especially regarding local recurrence-free survival (p = 0.045) and systemic recurrence-free survival (p = 0.002). BCL2 expression was a significant prognostic factor by univariable analysis (HR, 0.528; 95% CI, 0.353–0.790; p = 0.002) and by multivariable analysis (HR, 0.547; 95% CI, 0.362–0.826; p = 0.004). High BCL2 expression was associated with higher disease-free survival in the hormone receptor (HRc)-positive and human epidermal growth factor receptor 2 (HER2)-negative (HRc(+)/HER2(−)) subtype only (p = 0.002). The high BCL2 group was associated with positive estrogen receptor (ER), positive progesterone receptor (PR), low histologic grade, and age ≤ 50 years. BCL1 expression had no prognostic impact, but BCL2 expression was a significant independent prognostic factor. High BCL2 expression was associated with higher disease-free survival, especially regarding local recurrence and systemic recurrence. The prognostic effect of BCL2 expression was effective only in the HRc(+)/HER2(−) subtype. Favorable clinicopathologic features and a strong association with the ER/PR status could partly explain the superior prognosis of the high BCL2 group. BCL2 expression could be utilized to assess the prognosis of breast cancer patients in clinical settings.
ALDH1 expression predicts progression of premalignant lesions to cancer in Type I endometrial carcinomas
Authors: Mah Vei , Elshimali Yahya , Chu Alison , Moatamed Neda A. , Uzzell Jamar P. , Tsui Jessica , Schettler Stephen , Shakeri Hania , Wadehra Madhuri 
Published: June 2021

AbstractIn type 1 endometrial cancer, unopposed estrogen stimulation is thought to lead to endometrial hyperplasia which precedes malignant progression. Recent data from our group and others suggest that ALDH activity mediates stemness in endometrial cancer, but while aldehyde dehydrogenase 1 (ALDH1) has been suggested as a putative cancer stem cell marker in several cancer types, its clinical and prognostic value in endometrial cancer remains debated. The aim of this study was to investigate the clinical value of ALDH1 expression in endometrial hyperplasia and to determine its ability to predict progression to endometrial cancer. Interrogation of the TCGA database revealed upregulation of several isoforms in endometrial cancer, of which the ALDH1 isoforms collectively constituted the largest group. To translate its expression, a tissue microarray was previously constructed which contained a wide sampling of benign and malignant endometrial samples. The array contained a metachronous cohort of samples from individuals who either developed or did not develop endometrial cancer. Immunohistochemical staining was used to determine the intensity and frequency of ALDH1 expression. While benign proliferative and secretory endometrium showed very low levels of ALDH1, slightly higher expression was observed within the stratum basalis. In disease progression, cytoplasmic ALDH1 expression showed a step-wise increase between endometrial hyperplasia, atypical hyperplasia, and endometrial cancer. ALDH1 was also shown to be an early predictor of EC development, suggesting that it can serve as an independent prognostic indicator of patients with endometrial hyperplasia with or without atypia who would progress to cancer (p = 0.012).
Identification of Nrf2-responsive microRNA networks as putative mediators of myocardial reductive stress
Authors: Quiles Justin M. , Pepin Mark E. , Sunny Sini , Shelar Sandeep B. , Challa Anil K. , Dalley Brian , Hoidal John R. , Pogwizd Steven M. , Wende Adam R. , Rajasekaran Namakkal S. 
Published: June 2021

AbstractAlthough recent advances in the treatment of acute coronary heart disease have reduced mortality rates, few therapeutic strategies exist to mitigate the progressive loss of cardiac function that manifests as heart failure. Nuclear factor, erythroid 2 like 2 (Nfe2l2, Nrf2) is a transcriptional regulator that is known to confer transient myocardial cytoprotection following acute ischemic insult; however, its sustained activation paradoxically causes a reductive environment characterized by excessive antioxidant activity. We previously identified a subset of 16 microRNAs (miRNA) significantly diminished in Nrf2-ablated (Nrf2−/−) mouse hearts, leading to the hypothesis that increasing levels of Nrf2 activation augments miRNA induction and post-transcriptional dysregulation. Here, we report the identification of distinct miRNA signatures (i.e. “reductomiRs”) associated with Nrf2 overexpression in a cardiac-specific and constitutively active Nrf2 transgenic (caNrf2-Tg) mice expressing low (TgL) and high (TgH) levels. We also found several Nrf2 dose-responsive miRNAs harboring proximal antioxidant response elements (AREs), implicating these “reductomiRs” as putative meditators of Nrf2-dependent post-transcriptional regulation. Analysis of mRNA-sequencing identified a complex network of miRNAs and effector mRNAs encoding known pathological hallmarks of cardiac stress-response. Altogether, these data support Nrf2 as a putative regulator of cardiac miRNA expression and provide novel candidates for future mechanistic investigation to understand the relationship between myocardial reductive stress and cardiac pathophysiology.
Colossal barocaloric effects in the complex hydride Li$$_{2}$$B$$_{12}$$H$$_{12}$$
Authors: Sau Kartik , Ikeshoji Tamio , Takagi Shigeyuki , Orimo Shin-ichi , Errandonea Daniel , Chu Dewei , Cazorla Claudio 
Published: June 2021

AbstractTraditional refrigeration technologies based on compression cycles of greenhouse gases pose serious threats to the environment and cannot be downscaled to electronic device dimensions. Solid-state cooling exploits the thermal response of caloric materials to changes in the applied external fields (i.e., magnetic, electric and/or mechanical stress) and represents a promising alternative to current refrigeration methods. However, most of the caloric materials known to date present relatively small adiabatic temperature changes ($$|\Delta T| \sim 1$$

|
Δ
T
|
∼
1

to 10 K) and/or limiting irreversibility issues resulting from significant phase-transition hysteresis. Here, we predict by using molecular dynamics simulations the existence of colossal barocaloric effects induced by pressure (isothermal entropy changes of $$|\Delta S| \sim 100$$

|
Δ
S
|
∼
100

J K$$^{-1}$$

-
1

kg$$^{-1}$$

-
1

) in the energy material Li$$_{2}$$

2

B$$_{12}$$

12

H$$_{12}$$

12

. Specifically, we estimate $$|\Delta S| = 367$$

|
Δ
S
|
=
367

J K$$^{-1}$$

-
1

kg$$^{-1}$$

-
1

and $$|\Delta T| = 43$$

|
Δ
T
|
=
43

K for a small pressure shift of P = 0.1 GPa at $$T = 480$$

T
=
480

K. The disclosed colossal barocaloric effects are originated by a fairly reversible order–disorder phase transformation involving coexistence of Li$$^{+}$$

+

diffusion and (BH)$$_{12}^{-2}$$

12

-
2

reorientational motion at high temperatures.