Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated chronostratigraphy of Proterozoic–Cambrian boundary beds in the western Anabar region, northern Siberia

Abstract Carbonate-rich sedimentary rocks of the western Anabar region, northern Siberia, preserve an exceptional record of evolutionary and biogeochemical events near the Proterozoic/Cambrian boundary. Sedimentologically, the boundary succession can be divided into three sequences representing successive episodes of late transgressive to early highstand deposition; four parasequences are recognized in the sequence corresponding lithostratigraphically to the Manykai Formation. Small shelly fossils are abundant and include many taxa that also occur in standard sections of southeastern Siberia. Despite this coincidence of faunal elements, biostratigraphic correlations between the two regions have been controversial because numerous species that first appear at or immediately above the basal Tommotian boundary in southeastern sections have first appearances scattered through more than thirty metres of section in the western Anabar. Carbon- and Sr-isotopic data on petrographically and geochemically screened samples collected at one- to two-metre intervals in a section along the Kotuikan River, favour correlation of the Staraya Reckha Formation and most of the overlying Manykai Formation with sub-Tommotian carbonates in southeastern Siberia. In contrast, isotopic data suggest that the uppermost Manykai Formation and the basal 26 m of the unconformably overlying Medvezhya Formation may have no equivalent in the southeast; they appear to provide a sedimentary and palaeontological record of an evolutionarily significant time interval represented in southeastern Siberia only by the sub-Tommotian unconformity. Correlations with radiometrically dated horizons in the Olenek and Kharaulakh regions of northern Siberia suggest that this interval lasted approximately three to six million years, during which essentially all 'basal Tommotian' small shelly fossils evolved.
Conjunction and Modal Assessment in Genre Classification : A Corpus-Based Study of Historical and Experimental Science Writing

We use textual features motivated by systemic functional linguistic theory for genre-based text categorization. We have developed feature sets representing different types of conjunctions and modal assessment, which together indicate (partially) how different genres structure texts and express attitudes towards propositions in the text. Using such features enables analysis of large-scale rhetorical differences between genres by examining which features are important for classification. The specific domain studied comprises scientific articles in historical and experimental sciences (paleontology and physical chemistry respectively). The SMO learning algorithm with our feature set achieved over 83% accuracy for classifying articles according to field, though no field-specific terms were used as features. The most highly-weighted features were consistent with hypothesized methodological differences between historical and experimental sciences, thus lending empirical evidence to the notion of multiple scientific methods.
Characterisation of Cdc25B localisation and nuclear export during the cell cycle and in response to stress

Cdc25 phosphatases are essential regulators of the cell cycle. In mammalian cells, the Cdc25B isoform activates cyclin A- and cyclin B1-containing complexes and is necessary for entry into mitosis. In this report, we characterise the subcellular localisation of Cdc25B by immunofluorescence in combination with RNA interference to identify specific antibody staining. We find that endogenous Cdc25B is mainly nuclear, but a fraction resides in the cytoplasm during the G2 phase of the cell cycle. Cdc25B starts to appear in S-phase cells and accumulates until prophase, after which the protein disappears. We characterise a nuclear export sequence in the N-terminus of Cdc25B (amino acids 54-67) that, when mutated, greatly reduces the ability of Cdc25B to shuttle in a fluorescence loss in photobleaching assay. Mutation of the nuclear export sequence makes Cdc25B less efficient in inducing mitosis, suggesting that an important mitotic function of Cdc25B occurs in the cytoplasm. Furthermore, we find that when cells are exposed to cycloheximide or ultraviolet irradiation, Cdc25B partially translocates to the cytoplasm. The dependence of this translocation event on a functional nuclear export sequence, an intact serine 323 residue (a 14-3-3 binding site) and p38 mitogen-activated protein kinase activity indicates that the p38 pathway regulates Cdc25B localisation in different situations of cellular stress.
Effective compiler generation by architecture description

Embedded systems have an extremely short time to market and therefore require easily retargetable compilers. Architecture description languages (ADLs) provide a single concise architecture specification for the generation of hardware, instruction set simulators and compilers. In this article, we present an ADL for compiler generation. From a specification, we can derive an optimized tree pattern matching instruction selector, a register allocator and an instruction scheduler. Compared to a hand-crafted back end, the generated compiler produces smaller and faster code.The ADL is rich enough that other tools, such as assemblers, linkers, simulators and documentation, can all be obtained from a single specification.
A multi‐institutional comparison of outcomes of immunosuppressed and immunocompetent patients treated with surgery and radiation therapy for cutaneous squamous cell carcinoma of the head and neck

Patients who are chronically immunosuppressed have higher rates of cutaneous squamous cell carcinoma of the head and neck (cSCC‐HN). This is the largest multi‐institutional study to date investigating the effect of immune status on disease outcomes in patients with cSCC‐HN who underwent surgery and received postoperative radiation therapy (RT).
’ s repository of research publications and other research outputs Controls on the spatial distribution of oceanic 13 C

We describe the design and evaluation of a large ensemble of coupled climate–carbon cycle simulations with the Earth system model of intermediate complexity GENIE. This ensemble has been designed for application to a range of carbon cycle questions, including the causes of lateQuaternary fluctuations in atmospheric CO 2. Here we evaluate the ensemble by applying it to a transient experiment over the recent industrial era (1858 to 2008 AD). We employ singular vector decomposition and principal component emulation to investigate the spatial modes of ensemble variability of oceanic dissolved inorganic carbon (DIC) δ13C, considering both the spun-up pre-industrial state and the transient change. These analyses allow us to separate the natural (preindustrial) and anthropogenic controls on the δCDIC distribution. We apply the same dimensionally-reduced emulation techniques to consider the drivers of the spatial uncertainty in anthropogenic DIC. We show that the sources of uncertainty related to the uptake of anthropogenic δCDIC and DIC are quite distinct. Uncertainty in anthropogenic δ13C uptake is controlled by air–sea gas exchange, which explains 63 % of modelled variance. This mode of variability is largely absent from the ensemble variability in CO 2 uptake, which is rather driven by uncertainties in thermocline ventilation rates. Although the need to account for air–sea gas exchange is well known, these results suggest that, to leading order, uncertainties in the ocean uptake of anthropogenic 13C and CO2 are governed by very different processes. This illustrates the difficulties in reconstructing one from the other, and furthermore highlights the need for careful targeting of both δCDIC and DIC observations to better constrain the ocean sink of anthropogenic CO 2.
Multiscale kinetic Monte Carlo algorithm for simulating epitaxial growth

We present a fast Monte-Carlo algorithm for simulating epitaxial surface growth, based on the continuous-time Monte-Carlo algorithm of Bortz, Kalos and Lebowitz. When simulating realistic growth regimes, much computational time is consumed by the relatively fast dynamics of the adatoms. Continuum and continuum-discrete hybrid methods have been developed to approach this issue; however in many situations, the density of adatoms is too low to efficiently and accurately simulate as a continuum. To solve the problem of fast adatom dynamics, we allow adatoms to take larger steps, effectively reducing the number of transitions required. We achieve nearly a factor of ten speed up, for growth at moderate temperatures and large D/F.
Surgery for knee osteoarthritis in younger patients

Background and purpose In Sweden, surgery for knee osteoarthritis (OA) in patients younger than 55 years of age has doubled during the last 10 years. We evaluated the use of 3 surgical alternatives: high tibial osteotomy (HTO), unicompartmental arthroplasty (UKA), and total knee arthroplasty (TKA). We also examined the outcome, expressed by rate of revision. Methods The numbers of all procedures during 1998–2007 were obtained from the Swedish Knee Arthroplasty Register (SKAR) (UKA < 55 years: n = 1,050; UKA ≥ 55 years: n = 7,743; TKA < 55 years: n = 2,832; TKA ≥ 55 years: n = 62,829) and the National Board of Health and Welfare (NHW) (HTO 25–55 years: n = 2,266). The revision rate (presented as life tables) was based on the SKAR material for arthroplasties. For HTOs, a single institutional series of 450 patients aged 30–64 years was used to calculate the revision rate and to compare it to that for UKAs (n = 4,799; age 30–64 years). Results During the 10 years, the use of TKA in patients younger than 55 years increased fivefold. While UKA increased threefold, its use diminished in the last 2 years. Although the use of HTO halved during the period, it is still used more often than UKA. The risk of revision increased in patients younger than 55 years and was lower for TKA (9%) than for UKA (24%). The revision rate was similar for HTO (17%) and for UKA (17%) in patients aged 30–64 years. Interpretation TKA is the preferred method for young OA patients in Sweden today. The use of HTO and UKA has diminished, and as the few operations are spread over many hospitals, there is a risk of gradual loss of experience with respect to patient selection and surgical routine—with a negative effect on outcome. Thus, there is a risk that these treatment alternatives for younger patients will eventually be abandoned.
Differentiation of Marrow Stromal Cells into Photoreceptors in the Rat Eye

Retinal degenerations and dystrophies are the major causes of genetically inherited blindness that are characterized by the apoptotic death of the photoreceptor cell layer of the retina. To date, no treatment exists for these diseases and only recently have they been considered as candidates for gene and stem cell therapies. Here we report the ability of adult CD90+ marrow stromal cells (MSCs) to be induced by activin A, taurine, and EGF into cells (20-32%) expressing photoreceptor-specific markers rhodopsin, opsin, and recoverin in vitro. CD90+ cells were either transduced with recombinant adeno-associated virus expressing green fluorescent protein (GFP) or bromodeoxyuridine (BrdU) labeled and then injected into the subretinal space of adult Royal College of Surgeons rats. Fundus photography and angiography showed no adverse effects of CD90+ MSC transplantation. GFP-expressing cells or BrdU-positive cells covered ∼30% of the entire retinal area. By 2 weeks after injection, CD90+ MSCs integrated into the host retina, forming structures similar to the photoreceptor layer and expressed a photoreceptor-specific marker. No teratoma formation was observed in the recipient retina. The subretinally delivered CD90+ MSCs did not stain for proliferating cell nuclear antigen, indicating that they primarily undergo differentiation rather than proliferation. In addition, we established that transplanted cells can attract synaptic vesicles and hence are potentially capable of signal transduction. This study demonstrates for the first time the partial differentiation of adult CD90+ MSCs into photoreceptors in vitro and in vivo. Our results establish a proof of concept for CD90+ MSC differentiation with autologous transplantation, which may provide a promising therapeutic strategy for the treatment of some forms of genetically inherited retinal degenerations.
Document clustering based on non-negative matrix factorization

In this paper, we propose a novel document clustering method based on the non-negative factorization of the term-document matrix of the given document corpus. In the latent semantic space derived by the non-negative matrix factorization (NMF), each axis captures the base topic of a particular document cluster, and each document is represented as an additive combination of the base topics. The cluster membership of each document can be easily determined by finding the base topic (the axis) with which the document has the largest projection value. Our experimental evaluations show that the proposed document clustering method surpasses the latent semantic indexing and the spectral clustering methods not only in the easy and reliable derivation of document clustering results, but also in document clustering accuracies.
Phenolic composition and antioxidant effect of aqueous extract of Arisaema cum Bile, the Oriental Herb Medicine, in human fibroblast cells

Phenolic composition and antioxidant activities of the aqueous extract of Arisaema cum Bile, which is widely used as a folk medicine in Korea, were determined. Phenolic composition profile revealed that the aqueous extract is rich in sinapic acid (13.14 mg/100 g extract), catechin (9.88 mg/100 g extract), neohesperidin (7.38 mg/100 g extract), and chlorogenic acid (3.64 mg/100 g extract). The aqueous extract effectively scavenged toward 2,2-diphenyl-1-picrylhydrazyl (90.63%), hydrogen peroxide (98.13%), and hydroxyl radical (59.62%) at 2.0 mg/mL, and also showed high reducing power. In cytotoxic evaluation, the aqueous extract exhibited no significant cytotoxicity in human fibroblast, and it also exhibited appreciable suppression of intracellular reactive oxygen species and inhibition of lipid peroxidation. In addition, the aqueous extract upregulated the level of glutathione in a dose-dependent manner. Taken together, the aqueous extract of Arisaema cum Bile could be considered as a potential natural source that may be useful for curing diseases arising from oxidative deterioration.
Organic Phototransistors With All-Polymer Bulk Heterojunction Layers of p-Type and n-Type Sulfur-Containing Conjugated Polymers

All-polymer phototransistors were fabricated using both glass and flexible plastic film substrates by employing bulk heterojunction channel layers of p-type polymer (P3HT) and n-type polymer (THBT-ht). The devices could detect the entire visible light because the n-type polymer could sense photons in the deep red parts (>650 nm). The responsivity of devices was higher at the lower light intensity, while it could be controlled by varying the gate and/or drain voltages. Similar performances were measured for flexible all-polymer phototransistors with a bottom-source/drain and top-gate electrode configuration.
Short‐Term and Long‐Term Fracture Prediction by Bone Mass Measurements: A Prospective Study

Prospective and cross‐sectional studies have demonstrated that bone mass predicts fracture risk. However, most prospective studies have been limited to a few years of follow‐up. We investigated the long‐term associations of bone mass with vertebral fractures using longitudinal data collected from more than 500 postmenopausal Japanese‐American women in the Hawaii Osteoporosis Study. New vertebral fractures were identified during an average of 2.7 years between 1992 and 1995. Short‐term fracture prediction was evaluated using bone mass (spine, calcaneus, distal radius, and proximal radius) measured at the beginning of follow‐up. Long‐term prediction was evaluated using bone mass measured before the follow‐up period (11 years earlier for nonspine bone mass and 8 years earlier for spine). All four bone mass measurements were significant predictors of vertebral fractures identified during the subsequent 2.7 years (short‐term prediction), with odds ratios (ORs) ranging from 1.5 to 1.9. The ORs for long‐term prediction were slightly lower in magnitude, but the confidence intervals overlapped the short‐term ORs considerably, suggesting that both long‐term and short‐term associations are similar in magnitude. Furthermore, cross‐sectional analyses based on bone mass measurements performed at the end of follow‐up (after fractures had occurred) yielded results similar to those based on prospective data (bone mass measured prior to fractures), suggesting that the relatively quick and inexpensive cross‐sectional studies are useful for preliminary evaluations of new bone mass measurement techniques. The results suggest that bone mass measurements made up to 11 years earlier can predict vertebral fractures almost as well as measurements made more recently.
Construction and decoding of a class of algebraic geometry codes

A class of codes derived from algebraic plane curves is constructed. The concepts and results from algebraic geometry that were used are explained in detail; no further knowledge of algebraic geometry is needed. Parameters, generator and parity-check matrices are given. The main result is a decoding algorithm which turns out to be a generalization of the Peterson algorithm for decoding BCH decoder codes. >
The Context-Tree Weighting Method : Extensions

First we modify the basic (binary) context-tree weighting method such that the past symbols x/sub 1-D/, x/sub 2-D/, . , x/sub 0/ are not needed by the encoder and the decoder. Then we describe how to make the context-tree depth D infinite, which results in optimal redundancy behavior for all tree sources, while the number of records in the context tree is not larger than 2T-1. Here T is the length of the source sequence. For this extended context-tree weighting algorithm we show that with probability one the compression ratio is not larger than the source entropy for source sequence length T/spl rarr//spl infin/ for stationary and ergodic sources.
Towards Fingerpointing in the Emulab Dynamic Distributed System

In the large-scale Emulab distributed system, the many failure reports make skilled operator time a scarce and costly resource, as shown by statistics on failure frequency and root cause. We describe the lessons learned with error reporting in Emulab, along with the design, initial implementation, and results of a new local error-analysis approach that is running in production. Through structured error reporting, association of context with each error-type, and propagation of both error-type and context, our new local analysis locates the most prominent failure at the procedure, script, or session level. Evaluation of this local analysis for a targeted set of common Emulab failures suggests that this approach is generally accurate and will facilitate global fingerpointing, which will aim for reliable suggestions as to the root-cause of the failure at the system level.
Expression and Transport Activity of Breast Cancer Resistance Protein (Bcrp/Abcg2) in Dually Perfused Rat Placenta and HRP-1 Cell Line

Breast cancer resistance protein (BCRP/ABCG2) is a member of the ATP-binding cassette transporter family that recognizes a variety of chemically unrelated compounds. Its expression has been revealed in many mammal tissues, including placenta. The purpose of this study was to describe its role in transplacental pharmacokinetics using rat placental HRP-1 cell line and dually perfused rat placenta. In HRP-1 cells, expression of Bcrp, but not P-glycoprotein, was revealed at mRNA and protein levels. Cell accumulation studies confirmed Bcrp-dependent uptake of BODIPY FL prazosin. In the placental perfusion studies, a pharmacokinetic model was applied to distinguish between passive and Bcrp-mediated transplacental passage of cimetidine as a model substrate. Bcrp was shown to act in a concentration-dependent manner and to hinder maternal-to-fetal transport of the drug. Fetal-to-maternal clearance of cimetidine was found to be 25 times higher than that in the opposite direction; this asymmetry was partly eliminated by BCRP inhibitors fumitremorgin C (2 μM) or N-(4-[2-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-isoquinolinyl)ethyl]-phenyl)-9,10-dihydro-5-methoxy-9-oxo-4-acridine carboxamide (GF120918; 2 μM) and abolished at high cimetidine concentrations (1000 μM). When fetal perfusate was recirculated, Bcrp was found to actively remove cimetidine from the fetal compartment to the maternal compartment even against a concentration gradient and to establish a 2-fold maternal-to-fetal concentration ratio. Based on our results, we propose a two-level defensive role of Bcrp in the rat placenta in which the transporter 1) reduces passage of its substrates from mother to fetus but also 2) removes the drug already present in the fetal circulation.
Sodium and Potassium Currents Influence Wallerian Degeneration of Injured Drosophila Axons

Axons degenerate after injury and in neuropathies and disease via a self-destruction program whose mechanism is poorly understood. Axons that have lost connection to their cell bodies have altered electrical and synaptic activities, but whether such changes play a role in the axonal degeneration process is not clear. We have used a Drosophila model to study the Wallerian degeneration of motoneuron axons and their neuromuscular junction synapses. We found that degeneration of the distal nerve stump after a nerve crush is greatly delayed when there is increased potassium channel activity (by overexpression of two different potassium channels, Kir2.1 and dORKΔ-C) or decreased voltage-gated sodium channel activity (using mutations in the para sodium channel). Conversely, degeneration is accelerated when potassium channel activity is decreased (by expressing a dominant-negative mutation of Shaker). Despite the effect of altering voltage-gated sodium and potassium channel activity, recordings made after nerve crush demonstrated that the distal stump does not fire action potentials. Rather, a variety of lines of evidence suggest that the sodium and potassium channels manifest their effects upon degeneration through changes in the resting membrane potential, which in turn regulates the level of intracellular free calcium within the isolated distal axon.
Distant Supervision for Relation Extraction with Matrix Completion

The essence of distantly supervised relation extraction is that it is an incomplete multi-label classification problem with sparse and noisy features. To tackle the sparsity and noise challenges, we propose solving the classification problem using matrix completion on factorized matrix of minimized rank. We formulate relation classification as completing the unknown labels of testing items (entity pairs) in a sparse matrix that concatenates training and testing textual features with training labels. Our algorithmic framework is based on the assumption that the rank of item-byfeature and item-by-label joint matrix is low. We apply two optimization models to recover the underlying low-rank matrix leveraging the sparsity of feature-label matrix. The matrix completion problem is then solved by the fixed point continuation (FPC) algorithm, which can find the global optimum. Experiments on two widely used datasets with different dimensions of textual features demonstrate that our low-rank matrix completion approach significantly outperforms the baseline and the state-of-the-art methods.