bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Atmospheric Refractivity Estimation Methods and Their Influence on Radar Propagation Predictions
Authors: Pastore Douglas M. , Greenway Daniel P. , Stanek Mathew J. , Wessinger Sarah E. , Haack Tracy , Wang Qing , Hackett Erin E. 
Published: September 2021

AbstractEnvironmental predictions in the marine atmospheric surface layer (MASL) are imperative to optimize X‐band radar system performance in marine environments. Evaporation ducts (ED) lead to anomalous propagation where characterization of EDs in the MASL occurs primarily through two methods: in‐situ measurements and numerical modeling. This study investigates the differences in co‐located and synchronous refractivity estimations from the CASPER‐East campaign. Propagation predictions are generated for refractive profiles from in‐situ measurements, Monin‐Obukov boundary layer similarity theory, and numerical weather prediction forecasts. Variations in evaporation duct height (EDH) are found to be a primary driver of differences in propagation between the estimated refractivity profiles, where location of the EDH relative to the transmitter changes the sensitivity of propagation predictions to EDH estimates. Differences in propagation are large when EDH estimates span the transmitter height and the lowest EDH across the methods is small, regardless of how much variation there is in EDH estimates. When the lowest EDH is small and EDH estimates span the transmitter height there are differences in physical regimes causing large propagation discrepancies–for example, leakage into versus trapping within the duct. Variation in EDH between the methods is greatest in stable environments. M‐deficit and curvature of the refractive profiles also influence propagation specifically in scenarios when EDH spans the transmitter. When all EDHs are below the transmitter, EDH variance is the primary contributor to propagation variance, but M‐deficit and profile curvature variance play a secondary role. M‐deficits and curvature between the methods agree most often during periods of atmospheric stability.
Compaction of the Groningen Gas Reservoir Sandstone: Discrete Element Modeling Using Microphysically Based Grain‐Scale Interaction Laws
Authors: Mehranpour M. H. , Hangx S. J. T. , Spiers C. J. 
Published: September 2021

AbstractReservoir compaction, surface subsidence, and induced seismicity are often associated with prolonged hydrocarbon production. Recent experiments conducted on the Groningen gas field's Slochteren sandstone reservoir rock, at in‐situ conditions, have shown that compaction involves both poroelastic strain and time independent, permanent strain, caused by consolidation and shear of clay films coating the sandstone grains, with grain failure occurring at higher stresses. To model compaction of the reservoir in space and time, numerical approaches, such as the Discrete Element Method (DEM), populated with realistic grain‐scale mechanisms are needed. We developed a new particle‐interaction law (contact model) for classic DEM to explicitly account for the experimentally observed mechanisms of nonlinear elasticity, intergranular clay film deformation, and grain breakage. It was calibrated against both hydrostatic and conventional triaxial compression experiments and validated against an independent set of pore pressure depletion experiments conducted under uniaxial strain conditions, using a range of sample porosities, grain size distributions, and clay contents. The model obtained was used to predict compaction of the Groningen reservoir. These results were compared with field measurements of in‐situ compaction and matched favorably, within field measurement uncertainties. The new model allows systematic investigation of the effects of mineralogy, microstructure, boundary conditions, and loading path on compaction behavior of the reservoir. It also offers a means of generating a data bank suitable for developing generalized constitutive models and for predicting reservoir response to different scenarios of gas extraction, or of fluid injection for stabilization or storage purposes.
Activation of septal OXTr neurons induces anxiety- but not depressive-like behaviors
Authors: Huang Tuanjie , Guan Fangxia , Licinio Julio , Wong Ma-Li , Yang Yunlei 
Published: September 2021

AbstractThe neuropeptide oxytocin (OXT) is well recognized for eliciting anxiolytic effects and promoting social reward. However, emerging evidence shows that OXT increases aversive events. These seemingly inconsistent results may be attributable to the broad OXT receptor (OXTr) expression in the central nervous system. This study selectively activated septal neurons expressing OXTr using chemogenetics. We found that chemogenetic activation of septal OXTr neurons induced anxiety- but not depressive-like behavior. In addition, septal OXTr neurons projected dense fibers to the horizontal diagonal band of Broca (HDB), and selective stimulation of those HDB projections also elicited anxiety-like behaviors. We also found that septal OXTr neurons express the vesicular GABA transporter (vGAT) protein and optogenetic stimulation of septal OXTr projections to the HDB inactivated HDB neurons. Our data collectively reveal that septal OXTr neurons increase anxiety by projecting inhibitory GABAergic inputs to the HDB.
The role of reciprocal fusions in MLL-r acute leukemia: studying the chromosomal translocation t(4;11)
Authors: Wilhelm Alexander , Marschalek Rolf 
Published: September 2021

AbstractLeukemia patients bearing the t(4;11)(q21;q23) translocations can be divided into two subgroups: those expressing both reciprocal fusion genes, and those that have only the MLL-AF4 fusion gene. Moreover, a recent study has demonstrated that patients expressing both fusion genes have a better outcome than patients that are expressing the MLL-AF4 fusion protein alone. All this may point to a clonal process where the reciprocal fusion gene AF4-MLL could be lost during disease progression, as this loss may select for a more aggressive type of leukemia. Therefore, we were interested in unraveling the decisive role of the AF4-MLL fusion protein at an early timepoint of disease development. We designed an experimental model system where the MLL-AF4 fusion protein was constitutively expressed, while an inducible AF4-MLL fusion gene was induced for only 48 h. Subsequently, we investigated genome-wide changes by RNA- and ATAC-Seq experiments at distinct timepoints. These analyses revealed that the expression of AF4-MLL for only 48 h was sufficient to significantly change the genomic landscape (transcription and chromatin) even on a longer time scale. Thus, we have to conclude that the AF4-MLL fusion protein works through a hit-and-run mechanism, probably necessary to set up pre-leukemic conditions, but being dispensable for later disease progression.
Large cell neuroendocrine lung carcinoma: consensus statement from The British Thoracic Oncology Group and the Association of Pulmonary Pathologists
Authors: Lindsay Colin R. , Shaw Emily C. , Moore David A. , Rassl Doris , Jamal-Hanjani Mariam , Steele Nicola , Naheed Salma , Dick Craig , Taylor Fiona , Adderley Helen , Black Fiona , Summers Yvonne , Evans Matt , Rice Alexandra , Fabre Aurelie , Wallace William A. , Nicholson Siobhan , Haragan Alex , Taniere Phillipe , Nicholson Andrew G. , Laing Gavin , Cave Judith , Forster Martin D. , Blackhall Fiona , Gosney John , Popat Sanjay , Kerr Keith M. 
Published: September 2021

AbstractOver the past 10 years, lung cancer clinical and translational research has been characterised by exponential progress, exemplified by the introduction of molecularly targeted therapies, immunotherapy and chemo-immunotherapy combinations to stage III and IV non-small cell lung cancer. Along with squamous and small cell lung cancers, large cell neuroendocrine carcinoma (LCNEC) now represents an area of unmet need, particularly hampered by the lack of an encompassing pathological definition that can facilitate real-world and clinical trial progress. The steps we have proposed in this article represent an iterative and rational path forward towards clinical breakthroughs that can be modelled on success in other lung cancer pathologies.
Characterisation and outcomes of patients referred to a regional cancer of unknown primary team: a 10-year analysis
Authors: Stares Mark , Purshouse Karin , Knowles Gillian , Haigh Rachel , Irvine Jenny , Gatenby Aoife , Patton Rebekah , McGinty Jo , Christie Alan , MacLennan Marjory , Barrie Colin , Clive Sally 
Published: September 2021

Abstract
Background
In the United Kingdom, national guidance published in 2010 recommended the establishment of specialist teams to improve clinical pathways for patients presenting with malignancies of undefined primary origin (MUO) and cancer of unknown primary (CUP). This study sought to define outcomes of patients referred to a regional MUO/CUP service.

Methods
Data were collected prospectively on all patients (n = 1225) referred to a regional CUP team over a 10-year period. Patient demographics, clinical, pathological and outcome data were recorded and analysed.

Results
Confirmed CUP (cCUP) was diagnosed in 25% of patients. A primary metastatic cancer was identified in 36%, 5% were diagnosed with provisional CUP (pCUP), 27% retained the diagnosis of MUO and in 8% a non-cancer diagnosis was made. Median survival was low in all patients with a final malignant diagnosis: primary identified 9.0 months, cCUP 4.0 months, pCUP 1.5 months and MUO 1.5 months.

Conclusions
Patients presenting with MUO have poor outcomes irrespective of the final diagnosis. These patients need a patient-centred, streamlined, rapid diagnostic pathway. There are clear benefits to primary and secondary care teams having access to a dedicated, multidisciplinary MUO/CUP service, with clinical nurse specialists supporting the patients, to help facilitate this pathway and ensure early oncology review.
Differential programming enabled functional imaging with Lorentz transmission electron microscopy
Authors: Zhou Tao , Cherukara Mathew , Phatak Charudatta 
Published: September 2021

AbstractLorentz transmission electron microscopy is an advanced characterization technique that enables the simultaneous imaging of both the microstructure and functional properties of materials. Information such as magnetization and electric potentials is carried by the phase of the electron wave, and is lost during image acquisition. Various methods have been proposed to retrieve the phase of the electron wavefunction using intensities of the acquired images, most of which work only in the small defocus limit. Imaging at strong defoci not only carries more quantitative phase information, but is essential to the study of weak magnetic and electrostatic fields at the nanoscale. In this work we develop a method based on differentiable programming to solve the inverse problem of phase retrieval. We show that our method maintains a high spatial resolution and robustness against noise even at the upper defocus limit of the microscope. More importantly, our proposed method can go beyond recovering just the phase information. We demonstrate this by retrieving the electron-optical parameters of the contrast transfer function alongside the electron exit wavefunction.
Expansion of the high field-boosted superconductivity in UTe2 under pressure
Authors: Ran Sheng , Saha Shanta R. , Liu I-Lin , Graf David , Paglione Johnpierre , Butch Nicholas P. 
Published: September 2021

AbstractMagnetic field-induced superconductivity is a fascinating quantum phenomenon, whose origin is yet to be fully understood. The recently discovered spin-triplet superconductor, UTe2, exhibits two such superconducting phases, with the second one reentering in the magnetic field of 45 T and persisting up to 65 T. More surprisingly, in order to induce this superconducting phase, the magnetic field has to be applied in a special angle range, not along any high symmetry crystalline direction. Here we investigated the evolution of this high-field-induced superconducting phase under pressure. Two superconducting phases merge together under pressure, and the zero resistance persists up to 45 T, the field limit of the current study. We also reveal that the high-field-induced superconducting phase is completely decoupled from the first-order field-polarized phase transition, different from the previously known example of field-induced superconductivity in URhGe, indicating superconductivity boosted by a different paring mechanism.
Cyclic pulsation stress promotes bone formation of tissue engineered laminae through the F-actin/YAP-1/β-Catenin signaling axis
Authors: Li Linli , Li Hailong , He Yiqun , Tang Han , Dong Jian , Chen Xujun , Lyu Feizhou , Dong Youhai 
Published: September 2021

AbstractMechanical loads are fundamental regulators of bone formation and remodeling. However, the molecular regulation of mechanotransduction during vertebral laminae regeneration remains poorly understood. Here, we found that cerebrospinal fluid pulsation (CSFP) stress—cyclic pulsation stress—could promote the osteogenic and angiogenic abilities of rat mesenchymal stromal cells (MSC), thereby promoting tissue-engineered laminae’s bone and blood vessel formation. In the process, F-actin relayed CSFP stress to promote the nuclear translocation of YAP1, which then decreased the degradation and promoted the nuclear translocation of β-Catenin. In turn, the nuclear translocation of β-Catenin promoted the osteogenic differentiation and angiogenic abilities of MSC, thereby promoting tissue-engineered laminae’s bone and blood vessel formation. Thus, we conclude that CSFP promotes the osteogenesis and angiogenesis of tissue-engineered laminae through the F-actin/YAP-1/β-Catenin signaling axis. This study advances our understanding of vertebral laminae regeneration and provides potential therapeutic approaches for spinal degeneration after spinal laminectomy.
Large-scale randomized experiments reveals that machine learning-based instruction helps people memorize more effectively
Authors: Upadhyay Utkarsh , Lancashire Graham , Moser Christoph , Gomez-Rodriguez Manuel 
Published: September 2021

AbstractWe perform a large-scale randomized controlled trial to evaluate the potential of machine learning-based instruction sequencing to improve memorization while allowing the learners the freedom to choose their review times. After controlling for the length and frequency of study, we find that learners for whom a machine learning algorithm determines which questions to include in their study sessions remember the content over ~69% longer. We also find that the sequencing algorithm has an effect on users’ engagement.
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Authors: Lohoff T. , Ghazanfar S. , Missarova A. , Koulena N. , Pierson N. , Griffiths J. A. , Bardot E. S. , Eng C.-H. L. , Tyser R. C. V. , Argelaguet R. , Guibentif C. , Srinivas S. , Briscoe J. , Simons B. D. , Hadjantonakis A.-K. , Göttgens B. , Reik W. , Nichols J. , Cai L. , Marioni J. C. 
Published: September 2021

AbstractMolecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8–12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain–hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal–ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae
Authors: Almutairi Hatim , Urbaniak Michael D. , Bates Michelle D. , Jariyapan Narissara , Kwakye-Nuako Godwin , Thomaz Soccol Vanete , Al-Salem Waleed S. , Dillon Rod J. , Bates Paul A. , Gatherer Derek 
Published: September 2021

AbstractWe provide the raw and processed data produced during the genome sequencing of isolates from six species of parasites from the sub-familyLeishmaniinae:Leishmania martiniquensis(Thailand),Leishmania orientalis(Thailand),Leishmania enriettii(Brazil),Leishmaniasp. Ghana,Leishmaniasp. Namibia andPorcisia hertigi(Panama).De novoassembly was performed using Nanopore long reads to construct chromosome backbone scaffolds. We then corrected erroneous base calling by mapping short Illumina paired-end reads onto the initial assembly. Data has been deposited at NCBI as follows: raw sequencing output in the Sequence Read Archive, finished genomes in GenBank, and ancillary data in BioSample and BioProject. Derived data such as quality scoring, SAM files, genome annotations and repeat sequence lists have been deposited in Lancaster University’s electronic data archive with DOIs provided for each item. Our coding workflow has been deposited in GitHub and Zenodo repositories. This data constitutes a resource for the comparative genomics of parasites and for further applications in general and clinical parasitology.
Prognostic factors in elderly patients with T1 glottic cancer treated with radiotherapy
Authors: Mucha-Małecka Anna , Małecki Krzysztof , Amrogowicz Natalia , Biesaga Beata , Modrzejewski Maciej 
Published: September 2021

AbstractThe aim of the study was the evaluation of the effectiveness of radiotherapy in elderly T1 glottic cancer patients and prognostic factors with particular focus on comorbidities. Five-year overall survival, disease-specific survival, and local control rates were 63%, 92%, and 93%, respectively. Multivariate analysis showed that the following factors had statistically significant impact on local relapse risk and cancer death risk: diabetes, underweight, and fraction dose of 2 Gy. High number of comorbidities, high CCI, and underweight negatively influenced overall survival. A retrospective analysis was performed in a group of 131 T1N0M0 glottic cancer patients aged 70 and above treated with irradiation at the National Institute of Oncology in Cracow between 1977 and 2007. In the analyzed group men prevailed (92%) of mean age of 74 years. Each patient was diagnosed with at least one comorbidity with the following comorbid conditions being most frequent: hypertension, ischemic heart disease, and chronic obstructive pulmonary disease. In the studied group, the effect of comorbidities on overall survival was evaluated using Charlson Comorbidity Index (CCI). Twenty five (19%) patients showed underweight. All patients were irradiated once daily, 5 days a week, to a total dose of 60–70 Gy with a fraction dose of 2 or 2.5 Gy. Radiotherapy is an effective treatment modality in elderly T1 glottic cancer patients. Diabetes as comorbidity, underweight, and conventional dose fractionation decrease the probability of curative effect of radiotherapy in this group of patients, while high number of comorbidities diminishes the probability of long-term survival.
Leptin sensitizing effect of 1,3-butanediol and its potential mechanism
Authors: Isoda Masayo , Ebihara Ken , Sawayama Nagisa , Murakami Akiko , Ebihara Chihiro , Shibuya Koji , Takei Akihito , Takei Shoko , Wakabayashi Tetsuji , Yamamuro Daisuke , Takahashi Manabu , Nagashima Shuichi , Ishibashi Shun 
Published: September 2021

AbstractLeptin is an adipocyte-derived hormone that regulates appetite and energy expenditure via the hypothalamus. Since the majority of obese subjects are leptin resistant, leptin sensitizers, rather than leptin itself, are expected to be anti-obesity drugs. Endoplasmic reticulum (ER) stress in the hypothalamus plays a key role in the pathogenesis of leptin resistance. ATP-deficient cells are vulnerable to ER stress and ATP treatment protects cells against ER stress. Thus, we investigated the therapeutic effects of oral 1,3-butanediol (BD) administration, which increases plasma β-hydroxybutyrate and hypothalamic ATP concentrations, in diet induced obese (DIO) mice with leptin resistance. BD treatment effectively decreased food intake and body weight in DIO mice. In contrast, BD treatment had no effect in leptin deficient ob/ob mice. Co-administration experiment demonstrated that BD treatment sensitizes leptin action in both DIO and ob/ob mice. We also demonstrated that BD treatment attenuates ER stress and leptin resistance at the hypothalamus level. This is the first report to confirm the leptin sensitizing effect of BD treatment in leptin resistant DIO mice. The present study provides collateral evidence suggesting that the effect of BD treatment is mediated by the elevation of hypothalamic ATP concentration. Ketone bodies and hypothalamic ATP are the potential target for the treatment of obesity and its complications.
Essential tremor amplitude modulation by median nerve stimulation
Authors: Reis Carolina , Arruda Beatriz S. , Pogosyan Alek , Brown Peter , Cagnan Hayriye 
Published: September 2021

AbstractEssential tremor is a common neurological disorder, characterised by involuntary shaking of a limb. Patients are usually treated using medications which have limited effects on tremor and may cause side-effects. Surgical therapies are effective in reducing essential tremor, however, the invasive nature of these therapies together with the high cost, greatly limit the number of patients benefiting from them. Non-invasive therapies have gained increasing traction to meet this clinical need. Here, we test a non-invasive and closed-loop electrical stimulation paradigm which tracks peripheral tremor and targets thalamic afferents to modulate the central oscillators underlying tremor. To this end, 9 patients had electrical stimulation delivered to the median nerve locked to different phases of tremor. Peripheral stimulation induced a subtle but significant modulation in five out of nine patients—this modulation consisted mainly of amplification rather than suppression of tremor amplitude. Modulatory effects of stimulation were more pronounced when patient’s tremor was spontaneously weaker at stimulation onset, when significant modulation became more frequent amongst subjects. This data suggests that for selected individuals, a more sophisticated control policy entailing an online estimate of both tremor phase and amplitude, should be considered in further explorations of the treatment potential of tremor phase-locked peripheral stimulation.