Miracle-dz/UniFAR-FTUs huggingface dataset:
The glacial/deglacial history of sedimentation in Bear Lake, Utah and Idaho

Bear Lake, in northeastern Utah and southern Idaho, lies in a large valley formed by an active half-graben. Bear River, the largest river in the Great Basin, enters Bear Lake Valley ~15 km north of the lake. Two 4-m-long cores provide a lake sediment record extending back ~26 cal k.y. The penetrated section can be divided into a lower unit composed of quartz-rich clastic sediments and an upper unit composed largely of endogenic carbonate. Data from modern fl uvial sediments provide the basis for interpreting changes in provenance of detrital material in the lake cores. Sediments from small streams draining elevated topography on the east and west sides of the lake are characterized by abundant dolomite, high magnetic susceptibility (MS) related to eolian magnetite, and low values of hard isothermal remanent magnetization (HIRM, indicative of hematite content). In contrast, sediments from the headwaters of the Bear River in the Uinta Mountains lack carbonate and have high HIRM and low MS. Sediments from lower reaches of the Bear River contain calcite but little dolomite and have low values of MS and HIRM. These contrasts in catchment properties allow interpretation of the following sequence from variations in properties of the lake sediment: (1) ca. 26 cal ka—onset of glaciation; (2) ca. 26–20 cal ka— quasicyclical, millennial-scale variations in the concentrations of hematite-rich glacial fl our derived from the Uinta Mountains, and dolomiteand magnetite-rich material derived from the local Bear Lake catchment (refl ecting variations in glacial extent); (3) ca. 20–19 cal ka—maximum content of glacial fl our; (4) ca. 19–17 cal ka—constant content of Bear River sediment but declining content of glacial fl our from the Uinta Mountains; (5) ca. 17–15.5 cal ka—decline in Bear River sediment and increase in content of sediment from the local catchment; and (6) ca. 15.5–14.5 cal ka—increase in content of endogenic calcite at the expense of detrital material. The onset of glaciation indicated in the Bear Lake record postdates the initial rise of Lake Bonneville and roughly corresponds to the Stansbury shoreline. The lake record indicates that maximum glaciation occurred as Lake Bonneville reached its maximum extent ca. 20 cal ka and that deglaciation was under way while Lake Bonneville remained at its Rosenbaum, J.G. , and Heil, C.W. , Jr., 2009, The glacial/deglacial history of sedimentation in Bear Lake, Utah and Idaho, in Rosenbaum, J.G. , and Kaufman, D.S. , eds., Paleoenvironments of Bear Lake, Utah and Idaho, and its catchment: Geological Society of America Special Paper 450, p. 247–261, doi: 10.1130/2009.2450(11). For permission to copy, contact editing@geosociety.org. ©2009 The Geological Society of America. All rights reserved. 248 Rosenbaum and Heil
Prevalence, patterns, and predictors of patient-reported non-motor outcomes at 30 days after acute stroke: Prospective observational hospital cohort study

Background: Adverse non-motor outcomes are common after acute stroke and likely to substantially affect quality of life, yet few studies have comprehensively assessed their prevalence, patterns, and predictors across multiple health domains. Aims: We aimed to identify the prevalence, patterns, and the factors associated with non-motor outcomes 30 days after stroke. Methods: This prospective observational hospital cohort study—Stroke Investigation in North and Central London (SIGNAL)—identified patients with acute ischemic stroke or intracerebral hemorrhage (ICH) admitted to the Hyperacute Stroke Unit (HASU) at University College Hospital (UCH), London, between August 1, 2018 and August 31, 2019. We assessed non-motor outcomes (anxiety, depression, fatigue, sleep, participation in social roles and activities, pain, bowel function, and bladder function) at 30-day follow-up using the Patient-Reported Outcome Measurement Information System-Version 29 (PROMIS-29) scale and Barthel Index scale. Results: We obtained follow-up data for 605/719 (84.1%) eligible patients (mean age 72.0 years; 48.3% female; 521 with ischemic stroke, 84 with ICH). Anxiety (57.0%), fatigue (52.7%), bladder dysfunction (50.2%), reduced social participation (49.2%), and pain (47.9%) were the commonest adverse non-motor outcomes. The rates of adverse non-motor outcomes in ⩾ 1, ⩾ 2 and ⩾ 3 domains were 89%, 66.3%, and 45.8%, respectively; in adjusted analyses, stroke due to ICH (compared to ischemic stroke) and admission stroke severity were the strongest and most consistent predictors. There were significant correlations between bowel dysfunction and bladder dysfunction (κ = 0.908); reduced social participation and bladder dysfunction (κ = 0.844); and anxiety and fatigue (κ = 0.613). We did not identify correlations for other pairs of non-motor domains. Conclusion: Adverse non-motor outcomes were very common at 30 days after stroke, affecting nearly 90% of evaluated patients in at least one health domain, about two-thirds in two or more domains, and almost 50% in three or more domains. Stroke due to ICH and admission stroke severity were the strongest and most consistent predictors. Adverse outcomes occurred in pairs of domains, such as with anxiety and fatigue. Our findings emphasize the importance of a multi-domain approach to effectively identify adverse non-motor outcomes after stroke to inform the development of more holistic patient care pathways after stroke.
Evaluation of Vascular Endothelial Growth Factor Gene Expression in Recellularized Liver Tissue by Mouse Embryo Fibroblast

Background: The aim of the present study was to evaluate alterations in the vegf gene expression as an angiogenic factor in mouse embryo fibroblasts seeded on the decellularized liver fragments. Methods: Liver tissue samples (n = 10) collected from adult male mice were randomly divided into decellularized and native control groups. Tissues were decellularized by treating with 1% Triton X-100 and 0.1% SDS for 24 hours and assessed by H&E staining and SEM. Then DNA content analysis and toxicity tests were performed. By centrifugation, DiI-labeled mouse embryo fibroblasts were seeded on each scaffold and cultured for one week. The recellularized scaffolds were studied by H&E staining, SEM, and LSCM. After RNA extraction and cDNA synthesis, the expression of the vegf gene in these samples was investigated using real-time RT-PCR. Results: Our observations showed that the decellularized tissues had morphology and porous structure similar to the control group, and their DNA content significantly reduced (p < 0.05) and reached to 4.12% of the control group. The MTT test indicated no significant cellular toxicity for the decellularized scaffolds. Light microscopy, SEM, and LSCM observations confirmed the attachment and penetration of embryonic fibroblast cells on the surface and into different depths of the scaffolds. There was no statistically significant difference in terms of vegf gene expression in the cultured cells in the presence and absence of a scaffold. Conclusion: The reconstructed scaffold had no effect on vegf gene expression. Decellularized mouse liver tissue recellularized by embryonic fibroblasts could have an application in regenerative medicine.
Analysis on spatial structure characteristics in Xinjiang oases

Oasis is a special landscape that is setting in desert or semi desert. Far from 25 million years ago, the dry climate environment is gradually formed. Meanwhile, the earliest oases are appeared in Tianshan valley and Tarim Basin. From then on, rising of mountains and continuing of dry climate are provided basic conditions for oasis formation. Because of geomorphology pattern of three mountains surrounded two basins, a lot of coupling systems of mountain oasis desert are formed. Among them, the areas of mountain region and desert as well as oasis are account for 49.5%, 22.5% and 3.53% respectively. Depending on remote sensing technologies and methods of geographical related analysis and environmental base as well as landscape ecology, the characteristics of typical oases in Xinjiang are analyzed. The results show that oasis has high efficiency of substance and energy as well as information fusion. In addition, oasis landscape pattern is distinctness. Moreover, ecological environment of oasis is fragile, and so on. The formation and evolution of oases are resulted from natural and artificial elements. Hydrological condition determins landscape pattern and scale of oases. Geomorphology condition determins macro location of oases. Human activities determins evolution direction of oases. In order to sustain ecosafty and harmony of oases some measurements, such as building safeguard system, executing complex monitoring and management, and strengthening infrastructure should be taken.
Contact resonance atomic force microscopy using long elastic tips

In this work, a new theoretical model for contact resonance atomic force microscopy, which incorporates the elastic dynamics of a long sensing tip is presented. The model is based on the Euler–Bernoulli beam theory and includes coupling effects from the two-beam structure, also known as an ‘L-shaped’ beam in the literature. Here, high-accuracy prediction of the sample stiffness, using several vibration modes with a relative error smaller than 10% for practical working ranges, is demonstrated. A discussion on the model’s capability to predict the dynamic phenomena of eigenmode veering and crossing, as the force applied to the sample increases, is presented. The L-shaped beam model presented here is also applicable for structural applications such as: micro-electro-mechanical systems, energy harvesting, and unmanned aerial vehicle landing gear.
New Specimens of Protoceratops (Dinosauria: Neoceratopsia) from the Upper Cretaceous in Udyn Sayr, Southern Gobi Area, Mongolia

Abstract. Four skull specimens (MPC-D 100/537,100/538,100/539 and100/540) of Protoceratopsidae from the Upper Cretaceous in Udyn Sayr, Mongolia are described, and their ontogenetic stage and expression of sexual dimorphism are estimated. These specimens are identified as Protoceratops andrewsi (MPC-D 100/537, 100/539), P. cf. andrewsi (MPC-D 100/538), and Protoceratops sp. (MPC-D 100/540), respectively. MPC-D 100/537 and 100/539 are attributed to subadult “female” and MPC-D 100/538 to subadult “male”. MPC-D 100/540 is adult with unknown sex. Based on the frill morphologies, the Udyn Sayr specimens are classified into three types: type 1 (MPC-D 100/539), well developed ridge on the lateral surface of the squamosal; posteriorly projected posterior margin of the squamosal; type 2 (MPC-D 100/537), posteriorly rounded posterior margin of the squamosal; developed ridge on the posterior margin of the parietal; and type 3 (MPC-D 100/540), large size; posteriorly curved posterior margin of the squamosal; the rugose surface texture on the dorsal side of parietal. MPC-D 100/538 could not be categorized because the specimen's frill is not preserved. These frill morphologies differ from those of Protoceratops from the Djadokhta Formation in the adjacent dinosaur locality Tugrikin Shire. The morphological differences among the Udyn Sayr specimens may indicate intraspecific variation of Protoceratops.
Granule cells perform frequency‐dependent pattern separation in a computational model of the dentate gyrus

Mnemonic discrimination (MD) may be dependent on oscillatory perforant path input frequencies to the hippocampus in a “U”‐shaped fashion, where some studies show that slow and fast input frequencies support MD, while other studies show that intermediate frequencies disrupt MD. We hypothesize that pattern separation (PS) underlies frequency‐dependent MD performance. We aim to study, in a computational model of the hippocampal dentate gyrus (DG), the network and cellular mechanisms governing this putative “U”‐shaped PS relationship. We implemented a biophysical model of the DG that produces the hypothesized “U”‐shaped input frequency–PS relationship, and its associated oscillatory electrophysiological signatures. We subsequently evaluated the network's PS ability using an adapted spatiotemporal task. We undertook systematic lesion studies to identify the network‐level mechanisms driving the “U”‐shaped input frequency‐PS relationship. A minimal circuit of a single granule cell (GC) stimulated with oscillatory inputs was also used to study potential cellular‐level mechanisms. Lesioning synapses onto GCs did not impact the “U”‐shaped input frequency–PS relationship. Furthermore, GC inhibition limits PS performance for fast frequency inputs, while enhancing PS for slow frequency inputs. GC interspike interval was found to be input frequency dependent in a “U”‐shaped fashion, paralleling frequency‐dependent PS observed at the network level. Additionally, GCs showed an attenuated firing response for fast frequency inputs. We conclude that independent of network‐level inhibition, GCs may intrinsically be capable of producing a “U”‐shaped input frequency‐PS relationship. GCs may preferentially decorrelate slow and fast inputs via spike timing reorganization and high frequency filtering.
Exploring multisite heterogeneity of human basal cell carcinoma proteome and transcriptome

Basal cell carcinoma (BCC) is the most common type of skin cancer. Due to multiple, potential underlying molecular tumor aberrations, clinical treatment protocols are not well-defined. This study presents multisite molecular heterogeneity profiles of human BCC based on RNA and proteome profiling. Three areas from lesions excised from 9 patients were analyzed. The focus was gene expression profiles based on proteome and RNA measurements of intra-tumor heterogeneity from the same patient and inter-tumor heterogeneity in nodular, infiltrative, and superficial BCC tumor subtypes from different patients. We observed significant overlap in intra- and inter-tumor variability of proteome and RNA expression profiles, showing significant multisite heterogeneity of protein expression in the BCC tumors. Inter-subtype analysis has also identified unique proteins for each BCC subtype. This profiling leads to a deeper understanding of BCC molecular heterogeneity and potentially contributes to developing new sampling tools for personalized diagnostics therapeutic approaches to BCC.
Almost free of calibration for SSVEP-based brain-computer interfaces

Objective. Steady-state visual evoked potential (SSVEP)-based brain-computer interface (BCI) is a promising technology that can achieve high information transfer rate (ITR) with supervised algorithms such as ensemble task-related component analysis (eTRCA) and task-discriminant component analysis (TDCA). However, training individual models requires a tedious and time-consuming calibration process, which hinders the real-life use of SSVEP-BCIs. A recent data augmentation method, called source aliasing matrix estimation (SAME), can generate new EEG samples from a few calibration trials. But SAME does not exploit the information across stimuli as well as only reduces the number of calibration trials per command, so it still has some limitations. Approach. This study proposes an extended version of SAME, called multi-stimulus SAME (msSAME), which exploits the similarity of the aliasing matrix across frequencies to enhance the performance of SSVEP-BCI with insufficient calibration trials. We also propose a semi-supervised approach based on msSAME that can further reduce the number of SSVEP frequencies needed for calibration. We evaluate our method on two public datasets, Benchmark and BETA, and an online experiment. Main results. The results show that msSAME outperforms SAME for both eTRCA and TDCA on the public datasets. Moreover, the semi-supervised msSAME-based method achieves comparable performance to the fully calibrated methods and outperforms the conventional free-calibrated methods. Remarkably, our method only needs 24 s to calibrate 40 targets in the online experiment and achieves an average ITR of 213.8 bits min−1 with a peak of 242.6 bits min−1. Significance. This study significantly reduces the calibration effort for individual SSVEP-BCIs, which is beneficial for developing practical plug-and-play SSVEP-BCIs.
Face Age is Mapped Into Three-Dimensional Space

People can represent temporal stimuli (e.g., pictures depicting past and future events) as spatially connoted dimensions arranged along the three main axes (horizontal, sagittal, and vertical). For example, past and future events are generally represented, from the perspective of the individuals, as being placed behind and in front of them, respectively. Here, we report that such a 3D representation can also emerge for facial stimuli of different ages. In three experiments, participants classified a central target face, representing an individual at different age stages, as younger or older than the reference face of 40 years. Manual responses were provided with two keys placed along the horizontal axis (Experiment 1), the sagittal axis (Experiment 2), and the vertical axis (Experiment 3). The results indicated that the younger faces were represented on the left/back/top side of the space, whereas the older faces were represented on the right/forward/bottom side of the space. Furthermore, in all experiments, the latencies decreased with the absolute difference between the age of the target face and that of the reference face (i.e., a distance effect). Overall, this work suggests that the spatial representation of time includes social features of the human face.
PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences

Abstract Summary In recent years, phased small interfering RNA has been found to play crucial roles in many biological processes in plants. However, efficiently predicting phasiRNA regulatory cascades with computational methods is still challenging. Here, we introduce PhasiHunter, a phasiRNA regulatory network prediction tool that has several distinctive features compared to existing tools: (i) PhasiHunter employs two major phasiRNA prediction algorithms, namely phase score and hypergeometric distribution-based methods, to ensure the integrity and accuracy of prediction; (ii) PhasiHunter can identify phasiRNAs and their regulatory networks based on multiple reference sequences and the predicted results can be automatically integrated; (iii) PhasiHunter can efficiently identify the phasiRNAs generated through alternative splicing events; and (iv) the excellent data structure and parallel computing architecture allow PhasiHunter to predict phasiRNAs and their regulatory pathways with high efficiency. Availability and implementation PhasiHunter is an open-source tool that is available at https://github.com/HuangLab-CBI/PhasiHunter.
Estrogen inhibits colonic smooth muscle contractions by regulating BKβ1 signaling

The estrogen inhibits colonic smooth muscle contractions, which may lead to constipation. However, the mechanisms of inhibition are poorly understood. Therefore, the present study examined the effect of estrogen on rat colonic smooth muscle contractions and its potential association with the large-conductance Ca2+-activated K+ channels β1 (BKβ1) subunit. Twenty-four female Sprague Dawley rats were randomly assigned to 4 groups. After 2 weeks of intervention, the contraction activity of isolated colonic smooth muscle and the expression of BKβ1 in colonic smooth muscle of rats were detected. Additionally, in order to investigate the effects of estrogen on BKβ1 expression and calcium mobilization, in vitro experiments were conducted using rat and human colonic smooth muscle cells (SMCs). BKβ1 shRNA was used to investigate whether calcium mobilization is affected by BKβ1 in colonic SMCs. To explore the relationship between ERβ and BKβ1, serial deletions, site-directed mutagenesis, a dual-luciferase reporter assay, and chromatin immunoprecipitation assays were employed. In response to E2, colonic smooth muscle strips showed a decrease in tension, while IBTX exposure transiently increased tension. Furthermore, in these muscle tissues, BKβ1 and α-SMA were found to be co-expressed. The E2 group showed significantly higher BKβ1 expression. In cultured colonic SMCs, the expression of BKβ1 was found to increase in the presence of E2 or DPN. E2 treatment reduced Ca2+ concentrations, while BKβ1 shRNA treatment increased Ca2+ concentrations relative to the control. ERβ-initiated BKβ1 expression appears to occur via binding to the BKβ1 promoter. These results indicated that E2 may upregulate BKβ1 expression via ERβ and inhibit colonic smooth muscle contraction through ERβ by directly targeting BKβ1.
Dry Drainage Culvert Use and Design Considerations for Small- and Medium-Sized Mammal Movement Across a Major Transportation Corridor

Drainage culverts are ubiquitous features in road and rail corridors. Yet practically nothing is known about the effectiveness of culverts for increasing road permeability and habitat connectivity for small- and medium-sized mammals. The authors quantified mammal use of dry drainage culverts to cross a major transportation corridor. The authors used a null model to evaluate whether culverts serve all species equally or whether some culverts limit habitat connectivity across roads in species-specific ways. The authors also modeled species response to structural, landscape, and road-related attributes and identified which are most important in explaining animal passage rates and culvert effectiveness. Species performance ratios (i.e., observed passage frequency / expected passage frequency) were evaluated for eight small- and medium-sized mammal taxa to 24 culverts along the Trans-Canada highway in Banff National Park, Alberta. Observed passage frequencies were collected from three winter months of culvert monitoring. Carnivores (weasels Mustela sp., martens Martes americana) used more culverts and used them more frequently than small mammals (hares Lepus americanus, red squirrels Tamiasciurus hudsonicus, mice, shrews Sorex sp.). Small mammals were most prevalent on transects outside the culverts. The null model showed that species responded to culverts differently. The authors found that passage use was positively correlated with traffic density, road width, road clearance and culvert length. All species except coyotes ( Canis latrans) and shrews preferred small culverts with low openness ratios. Weasels and shrews preferred culverts with cover nearby. The authors results indicate that drainage culverts can mitigate harmful effects of a high-speed motorway. To maximize road permeability for small fauna, the authors recommend frequently spaced culverts (150-300 m) of varying sizes situated in close proximity to shrub or tree cover.
Long-term consequences of osteoporosis therapy with bisphosphonates

ABSTRACT Bisphosphonates (BPs) are medications widely used in clinical practice to treat osteoporosis and reduce fragility fractures. Its beneficial effects on bone tissue have been consolidated in the literature for the last decades. They have a high affinity for bone hydroxyapatite crystals, and most bisphosphonates remain on the bone surface for a long period of time. Benefits of long-term use of BPs: Large and important trials (Fracture Intervention Trial Long-term Extension and Health Outcomes and Reduced Incidence with Zoledronic acid Once Yearly-Pivotal Fracture Trial) with extended use of alendronate (up to 10 years) and zoledronate (up to 6 years) evidenced significant gain of bone mineral density (BMD) and vertebral fracture risk reduction. Risks of long-term use of BPs: The extended use of antiresorptive therapy has drawn attention to two extremely rare, although severe, adverse events. That is, atypical femoral fracture and medication-related osteonecrosis of the jaw are more common in patients with high cumulative doses and longer duration of therapy. BPs have demonstrated safety and effectiveness throughout the years and evidenced increased BMD and reduced fracture risks, resulting in reduced morbimortality, and improved quality of life. These benefits overweight the risks of rare adverse events.