Miracle-dz/UniFAR-FTUs huggingface dataset:
Microscopic vascular invasion by hepatocellular carcinoma in liver transplant patients.

Background A characteristic of Hepatocellular Carcinoma (HCC) is to invade the portal venous system in the liver as a means of spread within the liver and systemically. The ensuing Portal Vein Thrombosis (PVT) is a poor prognosis parameter and often diagnosed radiologically pre-treatment. More limited Microvascular Portal Invasion (microPVI) is typically diagnosed on examination of tumors removed after treatment by resection or transplant. The biological characteristics and subsets of PVI are incompletely characterized. Aims To examine HCC patients with and without microPVI to understand the clinical relationships to other tumor and clinical characteristics and to survival. Methods A cohort of 270 liver transplant patients with HCC without macroscopic PVT that were available to us was examined. Patients with (165) and without (105) microPVI were compared for survival and clinical features. Results The mean survival of patients with and without microPVI was significantly different: 86.6 versus 110.5 months, p=0.007. The microPVI+ patients differed from microPVI- patients in having a significantly larger number of tumor nodules, tumor size and higher serum levels of both Alpha-Fetoprotein (AFP) and almost significant for higher Gamma-Glutamyl Transpeptidase (GGT, p=0.053). Survival in microPVI+ patients related significantly to serum GGT (p=0.006) but not to AFP levels. The incidence of microPVI increased with increase in tumor size and survival decreased significantly with increase in tumor size for microPVI patients. Increase in tumor size was also associated with significantly higher serum GGT levels in patients who were microPVI+, but not in those who were microPVI. Furthermore, patients with microPVI who had prolonged survival significantly differed from those with shorter survival in respect only to tumor size and serum GGT levels. Conclusion These findings draw attention to a group of patients with microPVI who have long survival and to the usefulness of serum GGT levels in their evaluation and prognosis.
Response to Interactive comments on: “Long-term Brown Carbon and Smoke Tracer Observations in Bogotá, Colombia: Association to Medium-Range Transport of Biomass Burning Plumes” by-Juan Manuel Rincón-Riveros et al

We thank the three anonymous reviewers for their thoughtful feedback, and constructive comments, which undoubtedly helped to improve our manuscript. The three reviewers accurately pointed out that the manuscript was missing an uncertainty analysis associated with the reported eBC and BrC concentrations, and they all emphasized the need to perform a sensitivity analysis for the parameters involved in the attribution of BrC and Black Carbon, to make the calculations more transparent. We addressed these issues (and all the other comments).
Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer

Hereditary breast and ovarian cancer syndrome, caused by a germline deleterious variant in the BRCA1 or BRCA2 genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 96-sample validation set consisting of samples from cell lines and deidentified patient samples, including the well-characterized NA12878 sample from HapMap/1000 Genomes.
Public Dose Assessment during the Operational States of APR1400

Normal operation of nuclear power plants (NPPs) involved production and release of radionuclides to the environment. Solid, liquid and gaseous effluents were discharged to the environment either periodically or continuously. Gaseous and liquid effluents were especially of interest since they were readily dispersed in waterways and the atmosphere [1]. Atmospheric dispersion (X/Q) and deposition (D/Q) factors determined the dispersal and subsequent deposition of radionuclides in the atmosphere. X/Q and D/Q were determined from atmospheric parameters of wind speed, wind direction and environment temperature. These factors were also influenced by atmospheric stability, i.e. how the air was mixed in the atmosphere [2]. Hydrological dispersion of radionuclide was determined from the concentration of aqueous solution released, the rate of release and dilution rate in the water body [3]. Exposure to radionuclides occurred through many pathways; plume, ground deposition, inhalation, taking food and water and performing activities in the environment. These contributed doses externally to the body, the gastro intestinal – lower large intestine (GILLI), bone, liver, kidneys, lungs, thyroid, skin, pancreas, spleen, gastro intestinal – upper large intestine (GI-ULI), airways, uterus, bone marrow and stomach. The effects of radiation were also influenced by the age of the person; adult, teenager, child, or infant [4]. Exposure to radionuclides posed health risks. Risks were reduced by setting limits to doses received by the public to normal operation of NPPs [5]. Taking the gaseous and liquid source terms of NPP normal operation, the dose to public could be estimated to address compliance with set limits. This study aimed at analyzing radiological dose resulting from the normal operation of a Nuclear Power Plant (NPP) to ensure compliance with the set standard regulations of radioactive effluent releases.
G502 APPLICATION OF MT AND GRAVITY METHOD TO POTENTIAL ANALYSIS OF KEPAHIANG GEOTHERMAL, BENGKULU

An analysis of geothermal potential in KepahiangBengkulu area using gravity and MT measurements of PSDG has been done. The analysis was conducted on 286 gravity points and 37 MT points spread over the southern part of Mount Kaba to Babakan Bogor hot springs. Kepahiang geothermal system is related to the volcanic activity of Mount Kaba which is still preserving the residual heat from the magma. Based on the gravity residual anomaly, the structure that controls the emerging Sempiang hot springs is estimated to be Sempiang fault that in near north-south direction, while Babakan Bogor hot springs is estimated to be controlled by the Sumatra fault. The cap rocks scatter around Sempiang hot springs start from near ground surface with thickness of between 1500 meters to 2500 meters. Cap rock is a unit of Young Lava of Kaba with resistivity < 10 Ohm-m and density is 2.2 gr/cm 3 . Geothermal reservoir is estimated to be located under the cap rocks scatter around Sempiang hot springs as indicated by values of 10-60 Ohm-m in resistivity and density is 2.4 gr/cm 3 . The top of reservoir is estimated to be 1500 meters below the ground surface, these rocks are volcanic products of Old Kaba in form of either lava or pyroclastic. Kepahiang geothermal prospect area scatters 19 km 2 wide around Sempiang hot springs which is bound by contrast resistivity and fault. It has potential geothermal of 133 MWe with the assumption of reservoir temperature (geochemistry) is 250 0 C. Calculation of geothermal potential is included in the classification of expected reserves, as well as the extent and thickness of reservoir rock and fluid physical parameters are estimated based on data integrated geosciences detail depicted in the model tentatively. Keywords— Kepahiang Geothermal, Gravity, MT
Role of the V-ATPase a3 subunit in osteoclast maturation and function

Bone resorption involves osteoclast-mediated acidification via a vacuolar type H+-ATPase (V-ATPase) found in lysosomes and at the ruffled border membrane. V-ATPases are proton pumps that include the a3 subunit, one of four isoforms (a1-a4) in mammals. The a3 isoform is enriched in osteoclasts where it is essential for bone resorption. Over 50% of humans with osteopetrosis have mutations in the a3 subunit and a3 mutations in mouse also result in osteopetrosis. A mouse founder with an osteopetrotic phenotype was identified in an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. This mouse bears a dominant missense mutation in the Tcirg1 gene that encodes the a3 subunit resulting in the replacement of a highly conserved amino acid, arginine 740, with serine (R740S). The heterozygous mice (+/R740S) exhibit high bone density but otherwise have a normal appearance, size and weight. Osteoblast parameters are unaffected whereas osteoclast number and marker expression are increased along with a decreased number of apoptotic osteoclasts. V-ATPases from +/R740S osteoclast membranes have severely reduced proton transport along with wild type levels of ATP hydrolysis, indicating that the R740S mutation uncouples ATP hydrolysis from proton transport. The mutation however has no effect on ruffled border formation or polarization of +/R740S osteoclasts. Mice homozygous for R740S (R740S/R740S) have more severe osteopetrosis than +/R740S mice and die by postnatal day 14. Similarly to the mouse models that lack the a3 subunit (oc/oc and Tcirg1-/-) R740S/R740S osteoclasts do not polarize and lack ruffled border membranes. However R740S/R740S osteoclasts exhibit unique phenotypic traits, including increased apoptosis and defective early stage autophagy. Intracellular and extracellular acidification is absent in R740S/R740S osteoclasts, providing evidence for a requirement for lysosomal acidification for cytoplasmic distribution of key osteoclast enzymes such as TRAP and other important osteoclast phenotypic traits. This work provides evidence that the a3 subunit of V-ATPases and the proton pumping function of a3-containing V-ATPases play a major role in osteoclast survival, maturation and function. %%%%PhD
Knowledge Management as a Catalyst to Building Resilient and Effective Human Capital in Manufacturing Companies

The study argues that human capital development from a knowledge management perspective helps to shape attitudes and foster ethical values for higher productivity. Human capital is central to productivity in an economy and if well groomed, may result in sustainable development of a society. Human cultures vary, but application of knowledge management perspectives lead to cooperation, collaboration, team work and understanding that all people desire to live in a safe and secure world. Knowledge management is an idea-generating process that must be shared within the organization through tacit means or explicit knowledge which leads to the alignment and integration of human resources’ skills, competences and abilities to the positions held by the various incumbents in the organization. Knowledge management also implies the product value and features should match the cultural and physical inclinations of that community for it to be of any use or market value. Thus, fusion of knowledge management into human capital development leads to development of employees who are able to make decisions in uncertain scenarios and make organizations successful and sustainable. This was a case study of twenty manufacturing companies and both qualitative and quantitative instrumentation were used. The study found out that use of knowledge management as a discipline to guide policy formulation and decisions in organizations was a farfetched idea. No organization used knowledge as one of the co-competences. The study recommends use of research to create knowledge so that decisions are made based on empirical evidence.
Toward closure between predicted and observed particle viscosity
over a wide range temperature and relative humidity

Atmospheric aerosols can exist in amorphous semi-solid or glassy phase states whose viscosity varies with atmospheric temperature and relative humidity. The temperature and humidity dependence of viscosity has been hypothesized to be predictable from the combination of a water-organic binary mixing rule of the glass transition temperature, a glass transition temperature scaled viscosity fragility parameterization, and a water uptake parameterization. This work presents a closure study between predicted and observed viscosity for sucrose and citric acid. Viscosity and glass transition temperature as a function of 5 water content are compiled from literature data and used to constrain the fragility parameterization. New measurements characterizing viscosity of sub-100 nm particles using the dimer relaxation method are presented. These measurements extend the available data of temperature and humidity dependent viscosity to−28oC. Predicted relationships agree well with observations at room temperature and with measured isopleths of constant viscosity at ~10 Pa s and warmer than −28oC. Discrepancies at colder temperatures are observed for sucrose particle. Simulations with the kinetic multi-layer model of gas-particle interac10 tions suggest that the observed deviations at colder temperature for sucrose can be attributed to kinetic limitations associated with water uptake at the timescales of the dimer relaxation experiments. Using the available information, updated equilibrium phase-state diagrams (−80oC < T < 40oC and 0<RH < 100%) for sucrose and citric acid are constructed and associated equilibration timescales are identified.
EFFECTIVENESS OF ESCAPE VENT SHAPE IN TRAPS FOR CATCHING LEGAL-SIZED LOBSTER, HOMARUS AMERICANUS, AND HARVESTABLE-SIZED CRABS, CANCER BOREALIS AND CANCER IRRORATUS 1

During 1976 a study was conducted to find an escape vent that would select similar sized lobsters as the rectangular vent, yet retain Cancer crabs ;;;. 90 mm carapace width. Analysis of the size composition of research and commercial catches from experimental traps revealed that circular (58 mm in diameter) and rectangular (44.5 x 152.4 mm) vents release shorts and retain legal lobsters (;;;'81 mm carapace length) equally well, and decidedly more marketable-sized crabs were captured in traps with circular vents. Length-width relationship shows that crabs ;;;. 90 10m carapace width have lengths ;;;. 58 mm, thus precluding the possibility of marketable-sized crabs exiting through an opening 58 mm in diameter. Escapementstudies for lobsters confirm that with the present minimumlegal size of33/'6 in, a 58-mm diameter vent will select legals and allow most of the sublegals to escape. Accordingly, the Maine Department ofMarine Resources recommends that either circular (;;;'58 mm in diameter) or oblong (;a.44.5 x 152.4 mm) escape vents be incorporated in all crab and lobster traps along the Maine coast.
Markery nowotworowe w raku nerki Tumour markers in renal cell carcinoma

account for about 2% of all new cancer cases diagnosed each year. Up to 70% of the cancers arise from renal parenchyma (renal cell), and the rest from renal pelvis (15%), ureter (8%), urethra (4%) and other sites (3%). Renal cell carcinoma (RCC) is a resistant tumour that responds poorly to chemotherapy and immunotherapy. Lack of well-defined and reliable prognostic factors and tumour markers makes treatment very difficult. Multiple attempts to discover meaningful prognostic factors that correlate closely with life expectancy, overall survival and response to treatment, have identified a whole new range of molecular markers that may be helpful in diagnosis, as well as patient selection. The current review summarizes the conventional prognostic factors such as tumour size, stage, histological grade and acute phase reactants as well as the whole range of genetic and molecular markers.
Antiinflammatory Activity of Slime Extract from Giant African Snail (Lissachatina fulica)

The present study aims to investigate the antiinflammatory activity of the slime extracts from the giant African snail, Lissachatina fulica. In this study, aqueous and ethanol extracts of the snail slime were evaluated for antiinflammatory activities in vitro. The aqueous extract showed greater antiinflammatory activities than that of the ethanol extract. The aqueous extract was further tested for antiinflammatory activity in vivo. For acute inflammation, the ear edema assay was used to screen the slime extract. The results revealed that application of 2 mg/ear extract or phenylbutzone could significantly reduce edema when compared with ethanol-treated ears. For chronic inflammatory test, the cotton pellet granuloma model was employed to determine the activity of the slime extract. It was found that 2.5 and 6.25 % extract could significantly reduce transudative and granuloma weights. Moreover, the extracts also reduced malondialdehyde and increased superoxide dismutase in the granuloma tissue of the induced rats. In conclusion, the slime extract showed antiinflammatory activity both in vitro and in vivo. The antiinflammatory activity was also observed against acute and chronic inflammations, which suggested that the slime extracts has the potential to be developed into antiinflammatory products.
DeepLN: an artificial intelligence-based automated system for lung cancer screening

Background Lung cancer causes more deaths worldwide than any other cancer. For early-stage patients, low-dose computed tomography (LDCT) of the chest is considered to be an effective screening measure for reducing the risk of mortality. The accuracy and efficiency of cancer screening would be enhanced by an intelligent and automated system that meets or surpasses the diagnostic capabilities of human experts. Methods Based on the artificial intelligence (AI) technique, i.e., deep neural network (DNN), we designed a framework for lung cancer screening. First, a semi-automated annotation strategy was used to label the images for training. Then, the DNN-based models for the detection of lung nodules (LNs) and benign or malignancy classification were proposed to identify lung cancer from LDCT images. Finally, the constructed DNN-based LN detection and identification system was named as DeepLN and confirmed using a large-scale dataset. Results A dataset of multi-resolution LDCT images was constructed and annotated by a multidisciplinary group and used to train and evaluate the proposed models. The sensitivity of LN detection was 96.5% and 89.6% in a thin section subset [the free-response receiver operating characteristic (FROC) is 0.716] and a thick section subset (the FROC is 0.699), respectively. With an accuracy of 92.46%±0.20%, a specificity of 95.93%±0.47%, and a precision of 90.46%±0.93%, an ensemble result of benign or malignancy identification demonstrated a very good performance. Three retrospective clinical comparisons of the DeepLN system with human experts showed a high detection accuracy of 99.02%. Conclusions In this study, we presented an AI-based system with the potential to improve the performance and work efficiency of radiologists in lung cancer screening. The effectiveness of the proposed system was verified through retrospective clinical evaluation. Thus, the future application of this system is expected to help patients and society.
A NUMERICAL STUDY OF WATER PROPAGATION AND BREAKING USING SPH METHOD

A breaking wave is a violent natural event that involves highly complex phenomena, such as large deformation of free surface, turbulence, vortex generation, strong interaction between wave and structures, etc. In this work a wave breaking over an inclined surface is simulated using the Smoothed Particle Hydrodynamics (SPH). SPH is a meshless method that uses a Lagrangian referential to account the forces acting over a fluid particle. The formalism of SPH is based on the idea that the flow can be considered as a set of parts of fluid volume in motion using the concept of particles. This work uses a Weakly Compressible Smoothed Particle Hydrodynamics (WCSPH), where the pressure field is determined by a state equation. The code is validated with several benchmark cases, in which the most relevant parameters for the numerical stability of the analyses are varied. Finally, the model is applied to the simulation of breaking waves in coastal regions, determining shear stresses, important parameter for various applications in engineering, such as erosion.
SYSTEMATIC EVALUATION AND CHARACTERIZATION OF 3D SOLID STATE LIDAR SENSORS FOR AUTONOMOUS GROUND VEHICLES

Abstract. 3D LiDAR sensors play an important part in several autonomous navigation and perception systems with the technology evolving rapidly over time. This work presents the preliminary evaluation results of a 3D solid state LiDAR sensor. Different aspects of this new type of sensor are studied and their data are characterized for their effective utilization for object detection for the application of Autonomous Ground Vehicles (AGV). The paper provides a set of evaluations to analyze the characterizations and performances of such LiDAR sensors. After characterization of the sensor, the performance is also evaluated in real environment with the sensors mounted on top of a vehicle and used to detect and classify different objects using a state-of-the-art Super-Voxel based method. The 3D point cloud obtained from the sensor is classified into three main object classes “Building”, “Ground” and “Obstacles”. The results evaluated on real data, clearly demonstrate the applicability and suitability of the sensor for such type of applications.
Feature Extraction for Large-Scale Text Collections

Feature engineering is a fundamental but poorly documented component in Learning-to-Rank (LTR) search engines. Such features are commonly used to construct learning models for web and product search engines, recommender systems, and question-answering tasks. In each of these domains, there is a growing interest in the creation of open-access test collections that promote reproducible research. However, there are still few open-source software packages capable of extracting high-quality machine learning features from large text collections. Instead, most feature-based LTR research relies on "canned" test collections, which often do not expose critical details about the underlying collection or implementation details of the extracted features. Both of these are crucial to collection creation and deployment of a search engine into production. So in this regard, the experiments are rarely reproducible with new features or collections, or helpful for companies wishing to deploy LTR systems. In this paper, we introduce Fxt, an open-source framework to perform efficient and scalable feature extraction. Fxt can easily be integrated into complex, high-performance software applications to help solve a wide variety of text-based machine learning problems. To demonstrate the software's utility, we build and document a reproducible feature extraction pipeline and show how to recreate several common LTR experiments using the ClueWeb09B collection. Researchers and practitioners can benefit from Fxt to extend their machine learning pipelines for various text-based retrieval tasks, and learn how some static document features and query-specific features are implemented.
QUMEC: Software for Quantum Mechanics First Principle Calculation in 3-Dimensional Real Space

We present software on total energy calculation by quantum mechanics first principle method with a graphic user interface (GUI). Total energy calculation in this software is based on numerical analysis of time-dependent density functional (the used numerical method is finite difference time domain). QUMEC package has been equipped by common exchange-correlation energy terms with electron spin polarization calculation. With this package, users can calculate the total energy of the free particle, bulk materials, and materials with free surfaces at the atomic scale. The package is tested by several physical subjects, i.e., the surface energy of nano-LiCoO2 and diffusion constant of lithium atoms in LiNi0.5Mn1. 5O4.