bluuebunny/crossref_metadata_2025_split huggingface dataset:
An instructive role for Interleukin-7 receptor α in the development of human B-cell precursor leukemia
Authors: Geron Ifat , Savino Angela Maria , Fishman Hila , Tal Noa , Brown John , Turati Virginia A. , James Chela , Sarno Jolanda , Hameiri-Grossman Michal , Lee Yu Nee , Rein Avigail , Maniriho Hillary , Birger Yehudit , Zemlyansky Anna , Muler Inna , Davis Kara L. , Marcu-Malina Victoria , Mattson Nicole , Parnas Oren , Wagener Rabea , Fischer Ute , Barata João T. , Jamieson Catriona H. M. , Müschen Markus , Chen Chun-Wei , Borkhardt Arndt , Kirsch Ilan Richard , Nagler Arnon , Enver Tariq , Izraeli Shai 
Published: February 2022

AbstractKinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis “ph-like” BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rγnullmice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2 A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing ofCDKN2Ain primary human CD34+cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.
Cooling low-dimensional electron systems into the microkelvin regime
Authors: Levitin Lev V. , van der Vliet Harriet , Theisen Terje , Dimitriadis Stefanos , Lucas Marijn , Corcoles Antonio D. , Nyéki Ján , Casey Andrew J. , Creeth Graham , Farrer Ian , Ritchie David A. , Nicholls James T. , Saunders John 
Published: February 2022

AbstractTwo-dimensional electron gases (2DEGs) with high mobility, engineered in semiconductor heterostructures host a variety of ordered phases arising from strong correlations, which emerge at sufficiently low temperatures. The 2DEG can be further controlled by surface gates to create quasi-one dimensional systems, with potential spintronic applications. Here we address the long-standing challenge of cooling such electrons to below 1 mK, potentially important for identification of topological phases and spin correlated states. The 2DEG device was immersed in liquid 3He, cooled by the nuclear adiabatic demagnetization of copper. The temperature of the 2D electrons was inferred from the electronic noise in a gold wire, connected to the 2DEG by a metallic ohmic contact. With effective screening and filtering, we demonstrate a temperature of 0.9 ± 0.1 mK, with scope for significant further improvement. This platform is a key technological step, paving the way to observing new quantum phenomena, and developing new generations of nanoelectronic devices exploiting correlated electron states.
Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater
Authors: Smyth Davida S. , Trujillo Monica , Gregory Devon A. , Cheung Kristen , Gao Anna , Graham Maddie , Guan Yue , Guldenpfennig Caitlyn , Hoxie Irene , Kannoly Sherin , Kubota Nanami , Lyddon Terri D. , Markman Michelle , Rushford Clayton , San Kaung Myat , Sompanya Geena , Spagnolo Fabrizio , Suarez Reinier , Teixeiro Emma , Daniels Mark , Johnson Marc C. , Dennehy John J. 
Published: February 2022

AbstractTracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
TAZ links exercise to mitochondrial biogenesis via mitochondrial transcription factor A
Authors: Hwang Jun-Ha , Kim Kyung Min , Oh Ho Taek , Yoo Gi Don , Jeong Mi Gyeong , Lee Hyun , Park Joori , Jeong Kwon , Kim Yoon Ki , Ko Young-Gyu , Hwang Eun Sook , Hong Jeong-Ho 
Published: February 2022

AbstractMitochondria are energy-generating organelles and mitochondrial biogenesis is stimulated to meet energy requirements in response to extracellular stimuli, including exercise. However, the mechanisms underlying mitochondrial biogenesis remain unknown. Here, we demonstrate that transcriptional coactivator with PDZ-binding motif (TAZ) stimulates mitochondrial biogenesis in skeletal muscle. In muscle-specific TAZ-knockout (mKO) mice, mitochondrial biogenesis, respiratory metabolism, and exercise ability were decreased compared to wild-type mice. Mechanistically, TAZ stimulates the translation of mitochondrial transcription factor A via Ras homolog enriched in brain (Rheb)/Rheb like 1 (Rhebl1)-mTOR axis. TAZ stimulates Rhebl1 expression via TEA domain family transcription factor. Rhebl1 introduction by adeno-associated virus or mTOR activation recovered mitochondrial biogenesis in mKO muscle. Physiologically, mKO mice did not stimulate exercise-induced mitochondrial biogenesis. Collectively, our results suggested that TAZ is a novel stimulator for mitochondrial biogenesis and exercise-induced muscle adaptation.
Temporal dynamics of the neural representation of hue and luminance polarity
Authors: Hermann Katherine L. , Singh Shridhar R. , Rosenthal Isabelle A. , Pantazis Dimitrios , Conway Bevil R. 
Published: February 2022

AbstractHue and luminance contrast are basic visual features. Here we use multivariate analyses of magnetoencephalography data to investigate the timing of the neural computations that extract them, and whether they depend on common neural circuits. We show that hue and luminance-contrast polarity can be decoded from MEG data and, with lower accuracy, both features can be decoded across changes in the other feature. These results are consistent with the existence of both common and separable neural mechanisms. The decoding time course is earlier and more temporally precise for luminance polarity than hue, a result that does not depend on task, suggesting that luminance contrast is an updating signal that separates visual events. Meanwhile, cross-temporal generalization is slightly greater for representations of hue compared to luminance polarity, providing a neural correlate of the preeminence of hue in perceptual grouping and memory. Finally, decoding of luminance polarity varies depending on the hues used to obtain training and testing data. The pattern of results is consistent with observations that luminance contrast is mediated by both L-M and S cone sub-cortical mechanisms.
Cyclin B/CDK1 and Cyclin A/CDK2 phosphorylate DENR to promote mitotic protein translation and faithful cell division
Authors: Clemm von Hohenberg Katharina , Müller Sandra , Schleich Sibylle , Meister Matthias , Bohlen Jonathan , Hofmann Thomas G. , Teleman Aurelio A. 
Published: February 2022

AbstractDENR and MCTS1 have been identified as oncogenes in several different tumor entities. The heterodimeric DENR·MCTS1 protein complex promotes translation of mRNAs containing upstream Open Reading Frames (uORFs). We show here that DENR is phosphorylated on Serine 73 by Cyclin B/CDK1 and Cyclin A/CDK2 at the onset of mitosis, and then dephosphorylated as cells exit mitosis. Phosphorylation of Ser73 promotes mitotic stability of DENR protein and prevents its cleavage at Asp26. This leads to enhanced translation of mRNAs involved in mitosis. Indeed, we find that roughly 40% of all mRNAs with elevated translation in mitosis are DENR targets. In the absence of DENR or of Ser73 phosphorylation, cells display elevated levels of aberrant mitoses and cell death. This provides a mechanism how the cell cycle regulates translation of a subset of mitotically relevant mRNAs during mitosis.
Deep phenotyping of Alzheimer’s disease leveraging electronic medical records identifies sex-specific clinical associations
Authors: Tang Alice S. , Oskotsky Tomiko , Havaldar Shreyas , Mantyh William G. , Bicak Mesude , Solsberg Caroline Warly , Woldemariam Sarah , Zeng Billy , Hu Zicheng , Oskotsky Boris , Dubal Dena , Allen Isabel E. , Glicksberg Benjamin S. , Sirota Marina 
Published: February 2022

AbstractAlzheimer’s Disease (AD) is a neurodegenerative disorder that is still not fully understood. Sex modifies AD vulnerability, but the reasons for this are largely unknown. We utilize two independent electronic medical record (EMR) systems across 44,288 patients to perform deep clinical phenotyping and network analysis to gain insight into clinical characteristics and sex-specific clinical associations in AD. Embeddings and network representation of patient diagnoses demonstrate greater comorbidity interactions in AD in comparison to matched controls. Enrichment analysis identifies multiple known and new diagnostic, medication, and lab result associations across the whole cohort and in a sex-stratified analysis. With this data-driven method of phenotyping, we can represent AD complexity and generate hypotheses of clinical factors that can be followed-up for further diagnostic and predictive analyses, mechanistic understanding, or drug repurposing and therapeutic approaches.
Stratification in planetary cores by liquid immiscibility in Fe-S-H
Authors: Yokoo Shunpei , Hirose Kei , Tagawa Shoh , Morard Guillaume , Ohishi Yasuo 
Published: February 2022

AbstractLiquid-liquid immiscibility has been widely observed in iron alloy systems at ambient pressure and is important for the structure and dynamics in iron cores of rocky planets. While such previously known liquid immiscibility has been demonstrated to disappear at relatively low pressures, here we report immiscible S(±Si,O)-rich liquid and H(±C)-rich liquid above ~20 GPa, corresponding to conditions of the Martian core. Mars’ cosmochemically estimated core composition is likely in the miscibility gap, and the separation of two immiscible liquids could have driven core convection and stable stratification, which explains the formation and termination of the Martian planetary magnetic field. In addition, we observed liquid immiscibility in Fe-S-H(±Si,O,C) at least to 118 GPa, suggesting that it can occur in the Earth’s topmost outer core and form a low-velocity layer below the core-mantle boundary.
A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis
Authors: Robertson Nic , Shchepachev Vadim , Wright David , Turowski Tomasz W. , Spanos Christos , Helwak Aleksandra , Zamoyska Rose , Tollervey David 
Published: February 2022

AbstractRMRP encodes a non-coding RNA forming the core of the RNase MRP ribonucleoprotein complex. Mutations cause Cartilage Hair Hypoplasia (CHH), characterized by skeletal abnormalities and impaired T cell activation. Yeast RNase MRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Patient-derived human fibroblasts with CHH-linked mutations showed similar pre-rRNA processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy.
Granular porous landslide tsunami modelling – the 2014 Lake Askja flank collapse
Authors: Rauter Matthias , Viroulet Sylvain , Gylfadóttir Sigríður Sif , Fellin Wolfgang , Løvholt Finn 
Published: February 2022

AbstractSubaerial landslides and volcano flank collapses can generate tsunamis with devastating consequences. The lack of comprehensive models incorporating both the landslide and the wave mechanics represents a gap in providing consistent predictions of real events. Here, we present a novel three-dimensional granular landslide and tsunami model and apply it to the 2014 Lake Askja landslide tsunami. For the first time, we consistently simulate small-scale laboratory experiments as well as full scale catastrophic events with the same model. The model captures the complete event chain from the landslide dynamics to the wave generation and inundation. Unique and complete field data, along with the limited geographic extent of Lake Askja enabled a rigorous validation. The model gives deep insights into the physical landslide processes and improves our understanding and prediction capabilities of frequent and catastrophic landslide tsunamis.
Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice
Authors: Kallergi Emmanouela , Daskalaki Akrivi-Dimitra , Kolaxi Angeliki , Camus Come , Ioannou Evangelia , Mercaldo Valentina , Haberkant Per , Stein Frank , Sidiropoulou Kyriaki , Dalezios Yannis , Savitski Mikhail M. , Bagni Claudia , Choquet Daniel , Hosy Eric , Nikoletopoulou Vassiliki 
Published: February 2022

AbstractThe pruning of dendritic spines during development requires autophagy. This process is facilitated by long-term depression (LTD)-like mechanisms, which has led to speculation that LTD, a fundamental form of synaptic plasticity, also requires autophagy. Here, we show that the induction of LTD via activation of NMDA receptors or metabotropic glutamate receptors initiates autophagy in the postsynaptic dendrites in mice. Dendritic autophagic vesicles (AVs) act in parallel with the endocytic machinery to remove AMPA receptor subunits from the membrane for degradation. During NMDAR-LTD, key postsynaptic proteins are sequestered for autophagic degradation, as revealed by quantitative proteomic profiling of purified AVs. Pharmacological inhibition of AV biogenesis, or conditional ablation of atg5 in pyramidal neurons abolishes LTD and triggers sustained potentiation in the hippocampus. These deficits in synaptic plasticity are recapitulated by knockdown of atg5 specifically in postsynaptic pyramidal neurons in the CA1 area. Conducive to the role of synaptic plasticity in behavioral flexibility, mice with autophagy deficiency in excitatory neurons exhibit altered response in reversal learning. Therefore, local assembly of the autophagic machinery in dendrites ensures the degradation of postsynaptic components and facilitates LTD expression.
Constructing neural network models from brain data reveals representational transformations linked to adaptive behavior
Authors: Ito Takuya , Yang Guangyu Robert , Laurent Patryk , Schultz Douglas H. , Cole Michael W. 
Published: February 2022

AbstractThe human ability to adaptively implement a wide variety of tasks is thought to emerge from the dynamic transformation of cognitive information. We hypothesized that these transformations are implemented via conjunctive activations in “conjunction hubs”—brain regions that selectively integrate sensory, cognitive, and motor activations. We used recent advances in using functional connectivity to map the flow of activity between brain regions to construct a task-performing neural network model from fMRI data during a cognitive control task. We verified the importance of conjunction hubs in cognitive computations by simulating neural activity flow over this empirically-estimated functional connectivity model. These empirically-specified simulations produced above-chance task performance (motor responses) by integrating sensory and task rule activations in conjunction hubs. These findings reveal the role of conjunction hubs in supporting flexible cognitive computations, while demonstrating the feasibility of using empirically-estimated neural network models to gain insight into cognitive computations in the human brain.
Pressure-induced concomitant topological and metal-insulator quantum phase transitions in Ce3Pd3Bi4
Authors: Xu Chenchao , Cao Chao , Zhu Jian-Xin 
Published: February 2022

AbstractThe electronic property and magnetic susceptibility of Ce3Pd3Bi4 were systemically investigated from 18 to 290 K for varying values of cell volume using dynamic mean-field theory coupled with density functional theory. By extrapolating to zero temperature, the ground state of Ce3Pd3Bi4 at ambient pressure is found to be a correlated semimetal due to insufficient hybridization. Upon applying pressure, the hybridization strength increases and a crossover to the Kondo insulator is observed at finite temperatures. The characteristic temperature signaling the formation of Kondo singlet, as well as the characteristic temperature associated with f-electron delocalization–localization change, simultaneously vanishes around a critical volume of 0.992 V0, suggesting that such metal–insulator transition is possibly associated with a quantum critical point. Finally, Wilson’s loop calculations indicate that the Kondo insulating side is topologically trivial, thus a topological transition also occurs across the quantum critical point.
Threat by marine heatwaves to adaptive large marine ecosystems in an eddy-resolving model
Authors: Guo Xiuwen , Gao Yang , Zhang Shaoqing , Wu Lixin , Chang Ping , Cai Wenju , Zscheischler Jakob , Leung L. Ruby , Small Justin , Danabasoglu Gokhan , Thompson Luanne , Gao Huiwang 
Published: February 2022

AbstractMarine heatwaves (MHWs), episodic periods of abnormally high sea surface temperature, severely affect marine ecosystems. Large marine ecosystems (LMEs) cover ~22% of the global ocean but account for 95% of global fisheries catches. Yet how climate change affects MHWs over LMEs remains unknown because such LMEs are confined to the coast where low-resolution climate models are known to have biases. Here, using a high-resolution Earth system model and applying a ‘future threshold’ that considers MHWs as anomalous warming above the long-term mean warming of sea surface temperatures, we find that future intensity and annual days of MHWs over the majority of the LMEs remain higher than in the present-day climate. Better resolution of ocean mesoscale eddies enables simulation of more realistic MHWs than low-resolution models. These increases in MHWs under global warming pose a serious threat to LMEs, even if resident organisms could adapt fully to the long-term mean warming.
ResOpsUS, a dataset of historical reservoir operations in the contiguous United States
Authors: Steyaert Jennie C. , Condon Laura E. , W.D. Turner Sean , Voisin Nathalie 
Published: February 2022

AbstractThere are over 52,000 dams in the contiguous US ranging from 0.5 to 243 meters high that collectively hold 600,000 million cubic meters of water. These structures have dramatically affected the river dynamics of every major watershed in the country. While there are national datasets that document dam attributes, there is no national dataset of reservoir operations. Here we present a dataset of historical reservoir inflows, outflows and changes in storage for 679 major reservoirs across the US, called ResOpsUS. All of the data are provided at a daily temporal resolution. Temporal coverage varies by reservoir depending on construction date and digital data availability. Overall, the data spans from 1930 to 2020, although the best coverage is for the most recent years, particularly 1980 to 2020. The reservoirs included in our dataset cover more than half of the total storage of large reservoirs in the US (defined as reservoirs with storage greater 0.1 km3). We document the assembly process of this dataset as well as its contents. Historical operations are also compared to static reservoir attribute datasets for validation.
The case for altruism in institutional diagnostic testing
Authors: Specht Ivan , Sani Kian , Botti-Lodovico Yolanda , Hughes Michael , Heumann Kristin , Bronson Amy , Marshall John , Baron Emily , Parrie Eric , Glennon Olivia , Fry Ben , Colubri Andrés , Sabeti Pardis C. 
Published: February 2022

AbstractAmid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members’ close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18 to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.
Algorithm for sample availability prediction in a hospital-based epidemiological study spreadsheet-based sample availability calculator
Authors: Sudershan Amrit , Mahajan Kanak , Panjaliya Rakesh K. , Dhar Manoj K. , Kumar Parvinder 
Published: February 2022

AbstractLooking at the population’s behavior by taking samples is quite uncertain due to its big and dynamic structure and unimaginable variability. All quantitative sampling approaches aim to draw a representative sample from the population so that the results of the studying samples can then be generalized back to the population. The probability of detecting a true effect of a study largely depends on the sample size and if taking small samples will give lowers statistical power, higher risk of missing a meaningful underlying difference. The probability of rejecting the null hypothesis i.e., finding significant difference using the sample largely depends upon the statistical power. There are a lot of online tools used for calculating the sample size, but none tell us about the availability of samples from single site in a fixed span. This study aims to provide an efficient calculation method for the availability of samples during a specific period of a research study which is an important question to be answered during the research study design. So, we have designed a spreadsheet-based sample availability calculator tool implemented in MS-Excel 2007.