Miracle-dz/UniFAR-FTUs huggingface dataset:
Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences.
Wave Climate Analysis for a Wave Energy Conversion Application in Brazil

A variety of ocean wave energy conversion devices have been proposed worldwide considering different technology and energy extraction methods. In order to support full-scale prototype design and performance assessments of a conversion scheme to be deployed on the northern coast of Brazil, a long-term wave climate analysis is under development. A 5-year pitch-roll buoy data series has been investigated through an adaptive technique to enhance spatial resolution and allow for accurate wave directionality evaluation. Device design most influential variables such as extreme significant wave height, peak period and directionality were considered. Temporal variability in wave energy levels was particularly investigated for energy resource assessment. The major findings of this work include the narrow directional amplitude of the incident wave and higher significant wave heights of locally generated waves. The estimated energy resource levels agreed well with literature, also showing little annual fluctuation. The wave climate demonstrated to be in full agreement with the large-scale Equatorial Atlantic atmospheric variability, dominated by either local wind waves or by distant storm swells. © 2007 ASME
An evaluation of nutrient nonpoint offset trading in Virginia: A role for agricultural nonpoint sources?

Many advocates of water quality trading in the United States frequently assume that agricultural nonpoint sources will be the primary trading partner for regulated point sources. Virginia requires regulated point sources to offset new nutrient discharges. Nutrient offsets generated by agricultural nonpoint source reductions are compared against urban nonpoint source and nutrient assimilation offsets. Evidence suggests that agricultural nonpoint source offsets may not be a technically feasible or particularly cost effective compliance option for regulated point sources.
Prehabilitation to Improve Outcomes of Patients with Gynaecological Cancer: A New Window of Opportunity?

Simple Summary Surgery is an important mainstay in the treatment of gynaecological cancers but is associated with operative complications, especially for those with poor physical and mental health. Prehabilitation is a new and upcoming strategy to optimise patients’ functional capacity, nutritional status and psychosocial wellbeing in order to reduce complications and enhance recovery. In this review, we assessed the evidence on prehabilitation programmes for patients with gynaecological cancer. The limited evidence shows that prehabilitation may reduce length of hospital stay for ovarian cancer patients, and may result in significant weight loss in patients with endometrial and cervical cancer. Comparative prospective studies are required to determine the effectiveness of prehabilitation on reducing operative complications and improving quality of life, and to further specify the content of such a programme for patients with gynaecological cancer. Abstract The literature evaluating the effect of prehabilitation programmes on postoperative outcomes and quality of life of patients with gynaecological cancer undergoing surgery was reviewed. Databases including Pubmed, Medline, EMBASE (Ovid) and PsycINFO were systematically searched to identify studies evaluating the effect of prehabilitation programmes on patients with gynaecological cancer. Both unimodal and multimodal prehabilitation programmes were included encompassing physical exercise and nutritional and psychological support. Primary outcomes were surgical complications and quality of life. Secondary outcomes were anthropometric changes and adherence to the prehabilitation programme. Seven studies fulfilled the inclusion criteria, comprising 580 patients. Included studies were nonrandomised prospective studies (n = 4), retrospective studies (n = 2) and one case report. Unimodal programmes and multimodal programmes were included. In patients with ovarian cancer, multimodal prehabilitation resulted in significantly reduced hospital stay and time to chemotherapy. In patients with endometrial and cervical cancer, prehabilitation was associated with significant weight loss, but had no significant effects on surgical complications or mortality. No adverse events of the programmes were reported. Evidence on the effect of prehabilitation for patients with gynaecological cancer is limited. Future studies are needed to determine the effects on postoperative complications and quality of life.
Evaluation of PCR inhibitory effect of enrichment broths and comparison of DNA extraction methods for detection of Salmonella Enteritidis using real-time PCR assay

The best enrichment broth and DNA extraction scheme was determined for rapid and sensitive detection of Salmonella Enteritidis in steamed pork using real-time PCR. The inhibitory effect of commonly used Salmonella enrichment broths, Rappaport-Vassiliadis (RV) and Muller-Kauffmann tetrathionate with novobiocin (MKTTn), on real-time PCR was confirmed. The inhibition of PCR was statistically significant (p < 0.05) in RV and MKTTn, as compared with buffered peptone water (BPW) or phosphate-buffered saline. The inhibitory effect of the selective enrichment media was successfully removed by using a modified DNA extraction, PrepMan Ultra Reagent with an additional washing step or the DNeasy Tissue Kit. In three experiments, when applied to detection of Salmonella Enteritidis in steamed pork, the real-time PCR coupled with single 24 h enrichment with BPW performed better than double 48 h enrichment with BPW plus RV or MKTTn. The simple real-time PCR assay using BPW proved to be a rapid and sensitive test for detection of low concentrations of Salmonella Enteritidis in steamed pork samples as compared with the conventional culture method.
Surface uplift, uplift of rocks, and exhumation of rocks

Uplift of the surface of mountain belts requires forces that are comparable in magnitude to those associated with plate motion, and therefore determination of rates of surface uplift could provide important information on the dynamics of mountain ranges. Rates of uplift of the surfaces of mountain ranges have not, however, been quantified sufficiently well that they provide useful constraints on those processes. Many reports off surface uplift in mountain ranges are based on mistaking exhumation of rocks or uplift of rocks for surface uplift, and provide no information whatsoever on the rates of surface uplift.
On the initiation of subduction

Estimates of shear resistance associated with lithospheric thrusting and convergence represent lower bounds on the force necessary to promote trench formation. Three environments proposed as preferential sites of incipient subduction are investigated: passive continental margins, transform faults/fracture zones, and extinct ridges. None of these are predicted to convert into subduction zones simply by the accumulation of local gravitational stresses. Subduction cannot initiate through the foundering of dense oceanic lithosphere immediately adjacent to passive continental margins. The attempted subduction of buoyant material at a mature trench can result in large compressional forces in both subducting and overriding plates. This is the only tectonic force sufficient to trigger the nucleation of a new subduction zone. The ubiquitous distribution of transform faults and fracture zones, combined with the common proximity of these features to mature subduction complexes, suggests that they may represent the most likely sites of trench formation if they are even marginally weaker than normal oceanic lithosphere.
U–Pb zircon geochronology of plagiogranites from the Lough Nafooey (= Midland Valley) arc in western Ireland: constraints on the onset of the Grampian orogeny

The timing of peak Grampian metamorphism is well constrained from the detrital record of the adjacent fore-arc basin fill and geochronology of synorogenic intrusive rocks, but the onset of collision is less certain. Proximal Silurian conglomerates contain plagiogranite boulders unequivocally derived from the Lough Nafooey arc, two of which yield U–Pb secondary ionization mass spectrometry zircon ages of 489.9 ± 3.1 Ma and 487.8 ± 2.3 Ma. Nd isotopic evidence (ϵNd(490) c. 0) demonstrates that the plagiogranites assimilated significant amounts of old continental crust. This provides an absolute age constraint on a previously poorly constrained and inferred event, demonstrating that the arc had encountered subducting Laurentian margin sediments by 490 Ma.
Structure of the human volume regulated anion channel

SWELL1 (LRRC8A) is the only essential subunit of the Volume Regulated Anion Channel (VRAC), which regulates cellular volume homeostasis and is activated by hypotonic solutions. SWELL1, together with four other LRRC8 family members, forms a vastly heterogeneous cohort of VRAC channels with different properties; however, SWELL1 alone is also functional. Here, we report a high-resolution cryo-electron microscopy structure of full-length human homo-hexameric SWELL1. The structure reveals a trimer of dimers assembly with symmetry mismatch between the pore-forming domain and the cytosolic leucine-rich repeat (LRR) domains. Importantly, mutational analysis demonstrates that a charged residue at the narrowest constriction of the homomeric channel is an important pore determinant of heteromeric VRAC. This structure provides a scaffold for further dissecting the heterogeneity and mechanism of activation of VRAC.
A Case Report and Review of the Literature

Electroconvulsive therapy (ECT) is a safe and effective treatment for major depressive disorder, but cerebrovascular and cardiovascular complications, although rare, remain the most concerning. This is particularly notable in those with preexisting cerebrovascular disease, which impacts dynamic cerebral autoregulation. In these patients, the increased blood flow to the seizing portions of the brain induced by ECT potentially can reduce cerebral blood flow to ischemic areas, possibly causing adverse neurological events. The authors describe a patient with chronic cerebral ischemic disease, chronic anemia, and major depressive disorder undergoing ECT to achieve remission. The patient developed recurrent focal neurological deficits after each ECT procedure, with neurological recovery within 48 hours post-ECT. Clinical guidelines may need to be updated for the management of ECT patients with cerebrovascular disease who may be at an increased risk of intraictal and possibly postictal regional ischemia, especially in areas already compromised by a prior stroke and/or by reduced cerebral oxygenation caused by symptomatic anemia at risk of ischemia. Research is needed to assess changes in regional cerebral blood flow during and after ECT in patients with cerebrovascular disease, including small-vessel cerebral ischemia, and to evaluate these changes in relation to the location, intensity, and duration of induced seizure.
A study of the leakage of the Antarctic polar vortex in late austral winter and spring using isentropic and 3-D trajectories

[1] The permeability of the Antarctic polar vortex is investigated in late austral winter and spring by comparing isentropic and three-dimensional (3-D) trajectories. Trajectory computations were performed with the help of the Royal Dutch Meteorological Institute (KNMI) trajectory model, using data from the European Centre for Medium-Range Weather Forecasts (ECMWF) from August to November 1998. Large numbers of air parcels were initially released inside and outside the polar vortex on the 350, 450, and 550 K isentropic surfaces. They were integrated 4 months forward in time in an isentropic mode, as well as in a 3-D mode that uses all three wind components from the ECMWF and takes into account diabatic heating and cooling effects. For the isentropic trajectory calculations, very little transport (0.37%/week) was found for August and September, while October and November gave somewhat higher transport rates (1.95%/week). The 3-D trajectory calculations for October gave much more exchange between the vortex and midlatitudes than the isentropic ones owing to a significant number of parcels that descended inside the vortex. Descent rates were calculated for 350 K (October), 450 K (August–October) and 550 K (October). Overall, the results show that 3-D trajectories will provide more accurate leakage rates than the isentropic ones. Also, despite the large-scale mixing in the polar vortex or in midlatitudes, little ozone-depleted air leaks from the ozone hole into the midlatitude stratosphere.
Comparison of surface temperature minimum and maximum and satellite measured cloudiness and radiation budget

Mean surface temperature extremes over land areas during 1983 to 1990 are discussed in terms of satellite-measured cloud and radiation parameters. These show that cloud fluctuations induce changes in the temperatures with the decrease of temperature maximum stronger than the increase of temperature minimum because clouds cause changes in incident shortwave surface flux as well as downward long-wave radiation. Sensitivity to top of the atmosphere radiation is complicated by the intervening clouds and atmosphere. A comparison is also made to a sample general circulation model simulation showing the same effects.
Geothermal investigations in Idaho. Part 5. Geochemistry and geologic setting of the thermal waters of the northern Cache Valley area, Franklin County, Idaho

The thermal waters of the north-south trending graben structure known as northern Cache Valley in southeastern Idaho were sampled during the summer and fall of 1973. Geologic and gravity data for the area indicate fault control for nearly all thermal water occurrences. Thermal-water discharges are generally restricted to the course of the Bear River with few known in areas away from the river. Spring deposits in the form of travertine may not be indications of low temperature thermal waters because abundant limestone and dolomite make up the geologic framework. Much gas, believed to consist mostly of carbon dioxide, is being evolved from many of the springs. The hottest water is found near Battle Creek and Squaw hot springs approximately 4 kilometers northwest of the town of Preston. Metoric waters descend along fault planes, fractures, and fissures to depths at which they are heated by increasing rock temperatures (geothermal gradient of 5/sup 0/C per 100 meters). Due to decreased density, the heated waters rise along the same or adjacent fault planes to the surface. The quartz equilibrium geochemical thermometer applied to the thermal water discharges indicates temperatures approaching 150/sup 0/C may be encountered by deep drilling. Mixing models, based on quartzmore » solubility, indicate higher aquifer temperatures than the quartz equilibrium thermometer, but chloride concentration vs. temperature plots are not linear. The sodium-potassium-calcium geochemical thermometer indicates higher temperatures than quartz equilibrium and mixing models. The thermal waters are higher in total dissolved solids (12,000 to 13,000 milligrams per liter) than are known elsewhere in Idaho and represent potential pollution hazards should large scale withdrawal be attempted. « less
Evaluation of Complication Rates after Breast Surgery Using Acellular Dermal Matrix: Median Follow-Up of Three Years

Introduction Acellular dermal matrices (ADMs) are now commonly used for breast reconstruction surgery. There are various products available: ADMs derived from human (HADM), porcine (PADM), or bovine (BADM) sources. Detailed long-term follow-up studies are necessary to detect differences in complication rates between these products. Material and Methods From 2010 to 2015, forty-one patients underwent 52 ADM-breast reconstructions in our clinic, including oncologic breast reconstructions and breast augmentation revisions (n = 52). 15x HADMs (Epiflex®/DIZG), 21x PADMs (Strattice®/LifeCell), and 16x BADMs (Tutomesh®/RTI Surgical) were implanted. Retrospective data collection with median follow-up of 36 months (range: 12–54 months) was performed. Results Overall complication rate was 17% after ADM implantation (HADM: 7%; PADM: 14%; BADM: 31%). In a composite endpoint of complications and Red Breast Syndrome, a lower event probability was observed between BADMs, PADMs, and HADMs (44%, 19%, and 7%, resp.; p = 0.01 for the trend). Furthermore, capsular contracture occurred in 6%, more frequently as compared to the current literature. Conclusions When ADM-based reconstruction is indicated, the authors suggest primarily the use of HADMs and secondary the use of PADMs. It is shown that BADMs have the highest complication probability within our patient cohort; nevertheless, BADMs convey physical advantages in terms of flexibility and better aesthetic outcomes. The indication for the use of ADMs should be filled for each case individually.
Data fusion of high-resolution satellite images and airborne laser scanning data for building detection in an urban environment

High-resolution satellite imagery has become widely available recently and it enables urban remote sensing to not only classify land-use, but also map the details in urban environment. However, due to high object density and scene complexity, normally it is extremely difficult to automatically extract urban objects solely based on images. This paper describes our approach to detect buildings by fusing high-resolution IKONOS satellite images and airborne laser scanning data. With the high spatial resolution, rich spectral signature of IKONOS images and the very accurate positioning information of laser data, our data fusion methods show an efficient way to exploit the complementary characteristics of these two kinds of dataset for the purpose of building detection. In order to simplify the complexity of processing, a top to down strategy is generally applied to extract features of objects from coarsely to finely, and multiple cues are also derived and fused at different processing levels. The paper describes the developed framework and experimental results in detail, and also discusses both the advantage and deficiencies of the approach.
Eprosartan mesylate, an angiotensin II receptor antagonist

The title compound, eprosartan mesylate {systematic name: 2-butyl-1-(4-carboxybenzyl)-5-[(E)-2-carboxy-3-(thiophen-2-yl)prop-1-enyl]-1H-imidazol-3-ium methanesulfonate}, C23H25N2O4S+·CH3O3S−, one of the angiotensin II-receptor antagonists, is effective in regulating hypertension, induced or exacerbated by angiotensin II, and in the treatment of congestive heart failure, renal failure and glaucoma. In the eprosartan residue, which appears in this crystal in the cationic imidazolium form, the benzene ring plane is almost orthogonal to that of the imidazole ring, making a dihedral angle of 87.89 (2)°. The thiophene ring forms dihedral angles of 66.54 (2) and 67.12 (2)° with the benzene and imidazole rings, respectively. The imidazolium NH group and the H atom of the aromatic carboxyl group participate in hydrogen bonds with the the O atoms of the anion, thus forming centrosymmetric aggregates made up of two cations and two anions each. The second carboxyl group further links the above-mentioned aggregates through a conventional centrosymmetric hydrogen-bonding motif into infinite chains along [011].
MMP9 Processing of HSPB1 Regulates Tumor Progression

Matrix metalloproteinases regulate pathophysiological events by processing matrix proteins and secreted proteins. Previously, we demonstrated that soluble heat shock protein B1 (HSPB1) is released primarily from endothelial cells (ECs) and regulates angiogenesis via direct interaction with vascular endothelial growth factor (VEGF). Here we report that MMP9 can cleave HSPB1 and release anti-angiogenic fragments, which play a key role in tumorprogression. We mapped the cleavage sites and explored their physiological relevance during these processing events. HSPB1 cleavage by MMP9 inhibited VEGF-induced ECs activation and the C-terminal HSPB1 fragment exhibited more interaction with VEGF than did full-length HSPB1. HSPB1 cleavage occurs during B16F10 lung progression in wild-type mice. Also, intact HSPB1 was more detected on tumor endothelium of MMP9 null mice than wild type mice. Finally, we confirmed that secretion of C-terminal HSPB1 fragment was significantly inhibited lung and liver tumor progression of B16F10 melanoma cells and lung tumor progression of CT26 colon carcinoma cells, compared to full-length HSPB1. These data suggest that in vivo MMP9-mediated processing of HSPB1 acts to regulate VEGF-induced ECs activation for tumor progression, releasing anti-angiogenic HSPB1 fragments. Moreover, these findings potentially explain an anti-target effect for the failure of MMP inhibitors in clinical trials, suggesting that MMP inhibitors may have pro-tumorigenic effects by reducing HSPB1 fragmentation.
APPLICATION OF MYCORRHIZAE IN SUSTAINABLE DATE PALM CULTIVATION

Date palm (Phoenix dactylifera) is a significant and developing crop especially in the Arabian Peninsula, the Middle East and North Africa regions. The area under cultivation of this tree is increasing annually. Date palms usually grown under harsh and unfavorable growing conditions with low rainfall and high rates of evaporation as well as in soils with low organic matter and nutrient deficiencies. Hence, date palm cultivation becomes dependent on application of high levels of fertilizers as well as on irrigation. This may lead to salinization of soil and leaching of nutrients to deep soils that might affect ground water. Therefore, it is important that date palm plantations are managed in a sustainable way to reduce the impact of date palm cultivation on ecosystems while maximizing dates yield through using such practices as mycorrhizal fungi technology. The application of mycorrhizal fungi technology is an option that can benefit both agronomic plant health and ecosystems. Mycorrhizae confer numerous benefits to host plants including improved plant growth and mineral nutrition, water uptake, tolerance to diseases and stresses such as drought, temperature fluctuation, metal toxicity and salinity. Mycorrhizae may also play a role in the formation of stable soil aggregates, building up a macro porous structure of soil that allows penetration of water and air and prevents erosion. All of these beneficial effects on plant health and soil fitness mean that mycorrhizae have the potential to increase agricultural productivity and are crucial for the sustainable functioning of agricultural ecosystems. This study provides an insight into the application of mycorrhizae in date palm cultivation.