Miracle-dz/UniFAR-FTUs huggingface dataset:
HLA class-I and class-II restricted neoantigen loads predict overall survival in breast cancer

ABSTRACT Tumors acquire numerous mutations during development and progression. When translated into proteins, these mutations give rise to neoantigens that can be recognized by T cells and generate antibodies, representing an exciting direction of cancer immunotherapy. While neoantigens have been reported in many cancer types, the profiling of neoantigens often focused on the class-I subtype that are presented to CD8 + T cells, and the relationship between neoantigen load and clinical outcomes was often inconsistent among cancer types. In this study, we described an informatics workflow, REAL-neo, for identification, quality control (QC), and prioritization of both class-I and class-II human leukocyte antigen (HLA) bound neoantigens that arise from somatic single nucleotide mutations (SNM), small insertions and deletions (INDEL), and gene fusions. We applied REAL-neo to 835 primary breast tumors in the Cancer Genome Atlas (TCGA) and performed comprehensive profiling and characterization of the detected neoantigens. We found recurrent HLA class-I and class-II restricted neoantigens across breast cancer cases, and uncovered associations between neoantigen load and clinical traits. Both class-I and class-II neoantigen loads from SNM and INDEL were found to predict overall survival independent of tumor mutational burden (TMB), breast cancer subtypes, tumor-infiltrating lymphocyte (TIL) levels, tumor stage, and age at diagnosis. Our study highlighted the importance of accurate and comprehensive neoantigen profiling and QC, and is the first to report the predictive value of neoantigen load for overall survival in breast cancer.
Nonlinear Behavior of High-Intensity Ultrasound Propagation in an Ideal Fluid

In this paper, nonlinearity associated with intense ultrasound is studied by using the one-dimensional motion of nonlinear shock wave in an ideal fluid. In nonlinear acoustics, the wave speed of different segments of a waveform is different, which causes distortion in the waveform and can result in the formation of a shock (discontinuity). Acoustic pressure of high-intensity waves causes particles in the ideal fluid to vibrate forward and backward, and this disturbance is of relatively large magnitude due to high-intensities, which leads to nonlinearity in the waveform. In this research, this vibration of fluid due to the intense ultrasonic wave is modeled as a fluid pushed by one complete cycle of piston. In a piston cycle, as it moves forward, it causes fluid particles to compress, which may lead to the formation of a shock (discontinuity). Then as the piston retracts, a forward-moving rarefaction, a smooth fan zone of continuously changing pressure, density, and velocity is generated. When the piston stops at the end of the cycle, another shock is sent forward into the medium. The variation in wave speed over the entire waveform is calculated by solving a Riemann problem. This study examined the interaction of shocks with a rarefaction. The flow field resulting from these interactions shows that the shock waves are attenuated to a Mach wave, and the pressure distribution within the flow field shows the initial wave is dissipated. The developed theory is applied to waves generated by 20 KHz, 500 KHz, and 2 MHz transducers with 50, 150, 500, and 1500 W power levels to explore the effect of frequency and power on the generation and decay of shock waves. This work enhances the understanding of the interactions of high-intensity ultrasonic waves with fluids.
An Energy-Efficient Level Shifter for Ultra Low-Voltage Digital LSIs

This brief presents a fast and energy-efficient level shifter with wide conversion range. To achieve both energy-efficient and high-speed voltage level conversion, a novel architecture combined with multi-threshold CMOS technique is employed in the proposed circuit. A mixed-threshold current mirror circuit is proposed to solve the reduced swing issue in the prior arts. Moreover, auxiliary bias circuits are inserted to guarantee that the low-threshold pull down networks could be strongly cut off while in leaking state. As a result, the power consumption would be reduced to a great extent. Measurement results based on SMIC 55-nm MTCMOS process demonstrate that the proposed level shifter could provide robust voltage conversion from 0.12V to 1.2V. At the target voltage of 0.3V, the proposed level shifter shows a propagation delay of 17.86ns, a static power of 73.95pW, and an energy per transition of 26.59fJ for input frequency of 1MHz.
A proteomic and genomic investigation into the role of lamin A in colorectal cancer cell motility

Lamins are type V intermediate filament proteins found at the nuclear envelope. Expression of lamin A in colorectal cancer (CRC) tumours is correlated with poor prognosis and expression of lamin A in CRC cell lines promotes greatly increased cell motility. The aim of this study was to identify proteins that promote cell motility in response to lamin A expression and to investigate lamin A regulated changes in gene/protein expression and cytoskeletal organisation that might underpin the increased cell motility. The effects of lamin A expression were studied using quantitative proteomic and genomic methods using cells from the colorectal cancer cell line SW480 which had been transfected with GFP-lamin A (SW480/lamA) or GFP as a control (SW480/cntl). A biochemical fractionation technique was optimised for the preparation of cytoskeletal fractions which were analysed by 2D DIGE (2D difference in-gel electrophoresis) to reveal accurate and reproducible changes in the representation of proteins within the cytoskeleton in SW480/lamA cells compared to controls. The majority of proteins identified were either components of the actin/intermediate filament cytoskeleton, protein chaperones or translation initiation/elongation factors. Interestingly, tissue transglutaminase 2, a protein which modifies elements of the cytoskeleton and is associated with cancer progression, was highly over-represented in the cytoskeleton fraction of SW480/lamA cells. Ingenuity Pathway Analysis was used to analyse genome-wide Affymetrix microarray analysis of SW480/cntl and SW480/lamA cell lines. A highly significant interaction network was identified which clustered together genes linked to cancer, cellular movement and cellular growth and proliferation. Epithelial markers such as CDH1 were down-regulated and mesenchymal markers such as FN1 were up-regulated in cells expressing GFP-lamin A, which suggested that lamin A over-expression may lead to an epithelial-mesenchymal transition (EMT). As A-type lamins are known to modulate downstream effects of TGFβ signalling, and TGFβ is an inducer of EMT, changes in genes involved in TGFβ signalling were investigated. Knockdown of lamin A using siRNA led to decreased expression of TGFBI and SNAI2 followed by reduced cell motility. The data suggest that expression of lamin A in CRC cells causes changes in the organisation of the actin cytoskeleton and in TGFβ signalling, potentially involving an epithelial to mesenchymal transition, leading to increased cell motility and an increased risk of death from cancer.
Recognition of Landscape Key Areas in a Coal Mine Area of a Semi-Arid Steppe in China: A Case Study of Yimin Open-Pit Coal Mine

The ecological integrity and biodiversity of steppes were destroyed under the long-term and high-intensity development of open-pit coal mines in China, causing desertification, steppe degradation, landscape function defect, and so on. As a source of species maintenance and dispersal, an ecological source is a key area for preservation in order to restore the ecological security pattern of the larger landscape. The purpose of this study was to establish a landscape key area recognition model to identify the landscape key areas (LKA) surrounding an open pit coalmine located in semi-arid steppe. This study takes the Yimin open pit mining area as a case study. We assessed Landsat 5 Thematic Mapper (TM) and Landsat 8 Operational Land Imager (OLI) remote sensing images taken during the peak season of vegetation growth from July to August in 1999, 2006, 2011, and 2017. From these images, we identified the main landscape types and vegetation coverage grades in order to identify the ecological land. Next, we applied the three indices of Importance of Patch Connectivity, Habitat Quality, and Ecosystem Service Value to calculate the comprehensive results that identify ecological land. Finally, the ecological land quality results of different years are superimposed and averaged, and then Very Important Patch (VIMP), Important Patch (IMP), and General Patch (GEP) areas were used for LKA extraction. Our results showed LKA to cover 177.35 km2, accounting for 20.01% of the total study area. The landscape types identified as LKA are primarily grassland (47.37%), wetland (40.27%), and shrubland (11.88%), indicating that landscape type correlates strongly with its value as a landscape key area. The proposed landscape key area recognition model could enrich the foundations for ecological planning and ecological security pattern construction in order to support ecological protection and restoration in semi-arid steppe areas affected by coal mining.
Dynamical study of the class of difference equation Xn+1= Xn-2q+1/A+BXn-2qXn-q+1

Article history: Received 25 October 2019 Received in revised form 10 February 2020 Accepted 14 February 2020 This work is devoted to present a study of the class of the difference equations xn+1 = xn−2q+1 A + Bxn−2q+1xn−q+1, q = 1,2, . ⁄ with arbitrary initial data, where A and B are arbitrary parameters, and q is an arbitrary nonnegative integer. We present a detailed investigation of the behavior of the solution, including their dependence on parameters and initial conditions. Local and global stabilities of the equilibrium points are discussed. The existence of a periodic solution is studied. Numerical simulations are given to assure the correctness of the analytical results. This study improves and surpasses studies of several forms of difference equations that have been investigated earlier by many researchers.
Ficus deltoidea leaves methanol extract promote wound healing activity in mice

Wound healing is a normal process in skin tissue in response to injury. Ficus deltoidea leaves contain phytochemicals, which can play a role in wound healing. This study aimed to assess the wound healing activity of methanol extract of Ficus deltoidea leaves on artificial wounds in mice. In total 28 mice (2-3 months old, 20-30 g in weight) were randomly distributed into 7 treatment groups namely group I without treatment (negative control), group II were given povidone iodine 10% (positive control), group III was given a basic ointment and group IV-VII was treated with methanolic extract of Ficus deltoidea leaves with concentrations of 20, 40, 60 and 80% respectively. In all test animals, the wound was made with a length of 1 cm, and applied to the treatment according to the group, twice a day for 15 days. At the end of the treatment, wound healing activities were determined by measuring the percentage of wound contractions, Hydroxyproline estimates, and total new tissue DNA. Studies showed that the methanol extract of Ficus deltoidea leaves was able to heal wounds starting at a concentration of 20%. Mice treated with 80% extract resulted in the highest DNA and hydroxyproline content. The higher the concentration of the extract, the greater the healing effect of the wound. In summary, methanol extract of Ficus deltoidea leaves have potential for wound healing in mice.
Effect of feeding untreated or urea treated groundnut hull supplemented with different protein sources on blood parameters of Sudan desert lambs.

Hematology and serum biochemistry from thirty Sudan desert lambs (of an average body weight and age 18.0 ± 0.5 kg and 4-5 months respectively) fed diets contained untreated (UGH) or urea treated groundnut hull (TGH) with different protein supplementations (groundnut cake (GNC), cotton seeds cake (CSC) and fish byproducts (FBP) were investigated. The lambs given six dietary treatments; diets A, B and C were contained TGH supplemented with GNC, CSC and FBP respectively, while diets D, E and F were contained UGH supplemented with GNC, CSC and FBP respectively. Jugular blood samples were taken at 0, 45 and 90 days. There were significant differences between experimental diets in hemoglobin concentration (Hb), red blood cells (RBC), mean corpuscular hemoglobin (MCH) and mean corpuscular volume (MCV) concentrations, while other parameters were similar. Increasing feeding periods resulted in higher increase in Hb, WBC, MCHC and MCH concentrations, while PCV and MCV concentrations decreased. The same trend was observed in total serum protein, urea and triglycerides concentrations with higher values recorded for lambs fed A, B or C diets, while, no differences were found on serum albumin and globulin concentrations. Serum P, K and Na recorded higher values for lambs fed in A and B diets than other experimental diets. as experimental period increased (from 0 to 45 and 90days) serum K and Na concentrations were decreased significantly, while no significant variations in the values of serum Ca and inorganic P. Ration × period interaction had no significant effects on concentration of serum K and Na from A, B and C diets, while there were significant variations on concentration of serum Ca and P. The study revealed that inclusion of TGH supplemented with GNC, CSC or FBP in the diets of growing Sudan desert sheep had positive effects on the haematological and serum biochemical parameters.
Output, Uncertainty and Fuel Prices in the EU Countries

Analiza econometrică a comerţului exterior în timp Ţurcan Sandu, Pârţachi Ion Academia de Studii Economice din Moldova Simpozion Ştiinţific Internaţional al Tinerilor Cercetători Nr. 3(39) / 2005 / ISSN 1561-4042 Disponibil online 19 November, 2018. Descarcări-2. Vizualizări-165 ----------------------------------------------------------------------------------------------------------------------------------Câştigurile salariale, indicatori de bază în evoluţia pieţei forţei de muncă. Studiu comparativ în baza datelor judeţului Bacău şi Regiunii de Centru a Republicii Moldova Pârţachi Ion, Ciomârtan Vasilica-Lăcrămioara Academia de Studii Economice din Moldova Economica Nr. 4(106) / 2018 / ISSN 1810-9136 Disponibil online 5 January, 2019. Descarcări-4. Vizualizări-184 ----------------------------------------------------------------------------------------------------------------------------------Economie comportamentală în sistemul sanitar Ghiţulescu Virgiliu1, Stancu Stelian1, Pârţachi Ion2, Petrică Andreea-Cristina2, Tindeche Alexandu1, Liţă Iulian1, Wang Xin1 1 Academia de Studii Economice din Bucureşti, 2 Academia de Studii Economice din Moldova
Spatio-temporal investigation of doxorubicin in a 3D heterogeneous tumor microenvironment

Doxorubicin (Adriamycin) is a type of chemotherapy drugs using to treat diseases such as breast cancer, bladder cancer, Kaposi’s sarcoma, and lymphoma. Additionally, it can be first prescribed to reduce tumor size. The ratio of killed cells is varied depending on the clinical dosage regimen. Hence, the exact dosage of the drug must be administered to prevent the toxicity that could impair the immune system or leading to heart failure. In the present study, a 3D heterogeneous geometry with a solid tumor and healthy tissue is modeled for the drug delivery investigation. At the first stage, the physical properties of tumor microenvironment are obtained. Then, a five-compartmental model is used to evaluate the free, bound and internalized drug via the convection–diffusion-reaction (CDR) equation. Results are shown that a percent increase of 37.5% and 47.1% for the 75 mg m−2 to 50 mg m−2 in the AUC of bound drug and free drug concentration, respectively. The free and bound drugs have the same trend in time showing an apex at the earliest time of injection and then drops to the lowest amount about 9 hours after treatment. Moreover, the internalized drug has a different trend in time. It increases and reaches a constant amount of drug concentration in the cells. Besides, the fraction of surviving cells is also evaluated for both tumor and healthy tissues showing a 88.62% and 97.76% of surviving cells with 50 mg m−2 of doxorubicin after the treatment, respectively. This model is developed to predict the heterogenous distribution of doxorubicin in three different drug concentrations for patient-specific drug treatment. This model could be used for different drugs to show the rate of perfusion and the ability to kill cancerous cells regarding their different doses and toxicity effects.
Subsampled Factor Models for Asset Pricing: The Rise of Vasa

We propose a new method, VASA, based on variable subsample aggregation of model predictions for equity returns using a large-dimensional set of factors. To demonstrate the effectiveness, robustness, and dimension reduction power of VASA, we perform a comparative analysis between state-of-the-art machine learning algorithms. As a performance measure, we explore not only the global predictive but also the stock-specific R2's and their distribution. While the global R2 indicates the average forecasting accuracy, we find that high variability in the stock-specific R2's can be detrimental for the portfolio performance, due to the higher prediction risk. Since VASA shows minimal variability, portfolios formed on this method outperform the portfolios based on more complicated methods like random forests and neural nets.
Theoretical and Numerical Analysis of Anterior Cruciate Ligament Injury and its Prevention

Anterior cruciate ligament (ACL) injury is one of major risks for most athletes. ACL injury can be caused by many risk factors such as anatomic risk factors, biomechanical risk factors and environmental risk factors. In this article, numerical and theoretical analysis are conducted to investigate biomechanical risk factors. An entire three-dimensional finite element knee model was built based on MRI data. Anterior Tibial Translations (ATT) at different knee flexion angles are simulated by finite element models. In the simulations, more attentions are given to material properties of different knee components and their effects on ACL injury. Mechanical response of ACL during sport activities is highly determined by its viscoelastic properties. Unfortunately, viscoelastic properties of two bundles of ACL will change dramatically even with several hours’ physical aging. As a consequence, ACL will experience mechanical ductile to brittle transition due to daily physical aging. Theory of physical aging from polymer science is, for the first time, introduced to understand ACL injury and its prevention. By analogy to physical aging of amorphous polymer materials, we think physical aging of two bundles of ACL will largely increase risk of ACL injury. Besides, physical aging will also build a heterogeneous stress and strain in ACL due to its natural anatomic structure, which is a large risk for athletes. The specific designed prevention programs for ACL injury such as plyometrics, strengthening and other neuromuscular training exercises [1] are believed to erase physical aging of ACL. ACL with less physical aging is less likely to get injured in sport activities. In this article, a virtual physical aging simulation is built to validate current hypothesis. Erasing physical aging of ACL may provide an accurate and quantitative way to prevent ACL injury.
Effects of Probiotic on Immune Response and Intestine Morphology of Broiler Chicks Exposed to Stress Induced by Corticosterone

This experiment investigated the effects of different doses of Bacillus subtilis spore as a probiotic on the immune response, intestinal morphology and ileal dry matter digestibility in broiler chicks exposed to stress induced by corticosterone (CORT). Two hundred and eighty-eight one-day-old Ross 308 male broiler chicks were randomly assigned to six treatments in a completely randomized factorial design with and without CORT injection and 3 levels (0, 0.8×106, and 1.6×106 cfu/g) of B. subtilis spore supplementation. At 7 to 9 days of age (for 3 days), the chicks received one of the subcutaneous injections of CORT or corn oil (as control) at 2 mg/kg BW twice a day. The same injections were repeated at 25 to 27 days of age. Corticosterone injection led to significant (P<0.05) changes in intestinal morphology including villus height, ratio of villus height to crypt depth, and dry matter digestibility (as measured by TiO2 marker). These same parameters, however, increased in the experimental chicks relative to the control as a result of probiotic supplementation. Heterophil/lymphocyte ratio increased (P<0.05) as a result of corticosterone injection but exhibited no significant effect of probiotic supplementation. While corticosterone injection decreased lymphocyte density in the medulla of the bursa of Fabricius, this adverse effect was reversed by probiotic supplementation, which was more effective at a 1.6 × 106 concentration than at 0.8 × 106. As a general conclusion, it may be claimed that administration of B. subtilis-based probiotic alleviates certain negative effects of the stress induced by the corticosterone injection.
Design of a compact high gain printed octagonal array of spiral-based fractal antennas for DBS application

Abstract This paper presents a compact octagonal array of microstrip patch antennas for direct broadcast satellite (DBS) (12.2–12.7 GHz) services. The proposed single element of this array is a new fractal antenna, having considerably high gain and can heavily suppress cross polarization along the main beam direction. The single element is derived from a 2D spiral geometry. The corporate feed network of the array is designed in such a manner to make the structure very compact. The fabricated single element resonates at 12.51 GHz and gives a gain and bandwidth of 9.32 dBi and 280 MHz, respectively. The array resonates at 12.46 GHz and gives gain of 17.67 dBi and a bandwidth of 506 MHz, which ensures a 100% coverage of the entire DBS service band. The measured cross polarization of single element and array along the direction of main beam are −45.50 and −43.35 dB, respectively. Both the single element as well as the array maintains a reasonably good radiation efficiency of 86.70 and 82.20%, respectively.
Dual gated attentive-autoencoder for content-aware Recommendation

In recent years, content-aware recommendation of personalized products using automatic encoders has become the mainstream technology in the field of personalized recommendation systems. But the technology still faces the following main problems: 1.The automatic encoder structure ignores the inherent duality of the model and separates the training encoder from the decoder.2. The automatic encoder structure makes use of implicit feedback data and the difficulty of combining heterogeneous data.3. The traditional content-aware recommendation based on the auto-encoder ignores the neighboring merchandise information of the merchandise. In order to solve these problems, this paper proposes a dual gated attentive-autoencoder based on the door attention mechanism. The model is compared to the current optimal outcome model on the three recommended system public datasets. The experimental results show that the recall rate and the normalized damage cumulative gain of the auto-encoder content perception recommendation based on the dual-gate attention mechanism are better than the current optimal result model.
Plant population and row spacing effects on corn: Phenotypic traits of positive yield‐responsive hybrids

Corn ( Zea mays L.) hybrids differ in their yield response to plant population and/or row spacing changes. The objective of this study was to identify the hybrid phenotypic traits underlying intensive plant population and row spacing yield responses to help breeders select for hybrids to be placed in these possible management systems. In 2017 and 2018, six commercial hybrids were planted at 94,000, 109,000, 124,000