Miracle-dz/UniFAR-FTUs huggingface dataset:
The efficiency of adenovirus transformation of rodent cells is inversely related to the rate of viral E1A gene expression

While the products of the type 5 adenovirus E1A and E1B genes can initiate pathways leading to a transformed rodent cell, little is known about how the rate of viral early gene expression influences the efficiency of this process. An adenovirus mutant [E1a(r) virus] that expresses its viral E1A and E1B genes at as much as a 100-fold-reduced rate relative to wild-type virus in infected CREF or HeLa cells transforms CREF cells at an 8-fold-higher efficiency than wild-type virus. Additional studies show that the reduction in viral E1A gene expression is solely responsible for this transformation phenotype, and at this low rate of viral E1A gene expression both E1A gene products must be expressed. Unlike previously characterized viruses which transform CREF cells at frequencies greater than wild-type virus, the foci obtained following E1a(r) virus infection were indistinguishable from those arising from wild-type virus by several criteria (morphological characteristics and anchorage-independent growth). Surprisingly, an analysis of viral early gene expression from a panel of wild-type- and E1a(r) virus-transformed CREF cell lines showed similar average rates of both viral E1A and E1B gene expression. By using an adenovirus-transformed cell line that is cold-sensitive for maintenance of the transformed cell phenotype, we show that both wild-type and the E1a(r) viruses can transform these cells at equally high efficiencies at the nonpermissive temperature of 32 degrees C. Our findings suggest that the process leading to a fully transformed cell involves multiple stages, with an early stage being facilitated by a reduced rate of viral E1A gene expression.
SIGNR3‐dependent immune regulation by Lactobacillus acidophilus surface layer protein A in colitis

Intestinal immune regulatory signals govern gut homeostasis. Breakdown of such regulatory mechanisms may result in inflammatory bowel disease (IBD). Lactobacillus acidophilus contains unique surface layer proteins (Slps), including SlpA, SlpB, SlpX, and lipoteichoic acid (LTA), which interact with pattern recognition receptors to mobilize immune responses. Here, to elucidate the role of SlpA in protective immune regulation, the NCK2187 strain, which solely expresses SlpA, was generated. NCK2187 and its purified SlpA bind to the C‐type lectin SIGNR3 to exert regulatory signals that result in mitigation of colitis, maintenance of healthy gastrointestinal microbiota, and protected gut mucosal barrier function. However, such protection was not observed in Signr3−/− mice, suggesting that the SlpA/SIGNR3 interaction plays a key regulatory role in colitis. Our work presents critical insights into SlpA/SIGNR3‐induced responses that are integral to the potential development of novel biological therapies for autoinflammatory diseases, including IBD.
Lentivirus‐mediated platelet‐derived factor VIII gene therapy in murine haemophilia A

Summary. Background: Previous studies from our laboratory have demonstrated that lineage‐targeted synthesis of factor VIII (FVIII) under the direction of the platelet‐specific integrin αIIb gene promoter (2bF8) can correct the murine haemophilia A phenotype even in the presence of high titer inhibitory antibodies in a transgenic mouse model. Objective: In this study, we assessed the efficacy of using a genetic therapy approach to correct haemophilia A in FVIII‐deficient (FVIIInull) mice by transplantation of bone marrow (BM) transduced with a lentivirus (LV)‐based gene transfer cassette encoding 2bF8. Results: Functional FVIII activity (FVIII:C) was detected in platelet lysates from treated mice and the levels were similar to 2bF8 heterozygous transgenic mice. Mice transplanted with 2bF8 LV‐transduced BM survived tail clipping and we did not detected inhibitory or non‐inhibitory FVIII antibodies over the period of this study (11 months). Furthermore, BM transferred from the primary transplant recipients into FVIIInull secondary recipients demonstrated sustained platelet‐FVIII expression leading to correction of the haemophilia A phenotype showing that gene transfer occurred within long‐term repopulating haematopoietic stem cells. Conclusions: These results demonstrate that ectopic expression of FVIII in platelets by lentivirus‐mediated bone marrow transduction/transplantation may be a promising strategy for gene therapy of haemophilia A in humans.
Aminotransferases: demonstration of homology and division into evolutionary subgroups.

A total of 150 amino acid sequences of vitamin B6-dependent enzymes are known to date, the largest contingent being furnished by the aminotransferases with 51 sequences of 14 different enzymes. All aminotransferase sequences were aligned by using algorithms for sequence comparison, hydropathy patterns and secondary structure predictions. The aminotransferases could be divided into four subgroups on the basis of their mutual structural relatedness. Subgroup I comprises aspartate, alanine, tyrosine, histidinol-phosphate, and phenylalanine aminotransferases; subgroup II acetylornithine, ornithine, omega-amino acid, 4-aminobutyrate and diaminopelargonate aminotransferases; subgroup III D-alanine and branched-chain amino acid aminotransferases, and subgroup IV serine and phosphoserine aminotransferases. (N-1) Profile analysis, a more stringent application of profile analysis [Gribskov, M. , McLachlan, A. D. and Eisenberg, D. (1987) Proc. Natl Acad. Sci. USA 84, 4355-4358], established the homology among the enzymes of each subgroup as well as among all subgroups except subgroup III. However, similarity of active-site segments and the hydropathy patterns around invariant residues suggest that subgroup III, though most distantly related, might also be homologous with the other aminotransferases. On the basis of the comprehensive alignment, a new numbering of amino acid residues applicable to aminotransferases (AT) in general is proposed. In the multiply aligned sequences, only four out of a total of about 400 amino acid residues proved invariant in all 51 sequences, i.e. Gly(314AT)197, Asp/Glu(340AT)222, Lys(385AT)258 and Arg(562AT)386, the number not in parentheses corresponding to the structure of porcine cytosolic aspartate aminotransferase. Apparently, the aminotransferases constitute a group of homologous proteins which diverged into subgroups and, with some exceptions, into substrate-specific individual enzymes already in the universal ancestor cell.
Label-free chemical/biochemical sensing device based on an integrated microfluidic channel within a waveguide resonator

In this article we propose a novel label-free chemical/biochemical sensing device based on a waveguide resonator with an integrated microfluidic channel. This device is intended for the characterisation and detection of cells and various chemical substances from within a variety of micro-litre test samples. This paper outlines the design of the prototype device and describes the fabrication of the microfluidic network and microwave resonator. Initial testing of the prototype at X-band is examined with promising results. Finally, we propose a Low Temperature Co-fired Ceramic (LTCC) integration scheme for the miniaturization of the device for use in the THz regime.
Rainfall prediction climatological station of Banjarbaru using arima kalman filter

Time series analysis is a method built in a particular time sequence for prediction. One of the models in time series analysis used for prediction is the ARIMA model introduced by Box and Jenkins. As time goes by, the ARIMA model was developed by applying algorithms, one of which was the Kalman Filter algorithm. This study aims to estimate the parameters of the ARIMA model used as the Kalman Filter’s initial value to forecast rainfall using ARIMA and ARIMA Kalman Filter. Determination of the ARIMA model is done by dividing the data into training and testing. The results obtained from the three training data have the same model, namely ARIMA (0,0,0) × (0,1,1)12 models but with different parameter values than those used as initial values for the Kalman Filter. The results obtained using the ARIMA model with Kalman Filter significantly affect the initial data of 90% training data model parameters with an RMSE value of 155,13. Then predictions are made, the results obtained by ARIMA Kalman Filter can follow the actual data, but from June to October, the prediction results cannot approach the actual data. According to events in the field, June to October is the dry season, where rainfall is deficient
Constellation Selection in Network Coded Distributive Antenna System

Relays can improve wireless links by providing an extra path to the direct path which together form a virtual multiple antenna system. Network Coded-Distributive Antenna System (NC-DAS) and Plain-Distributive Antenna System (P-DAS) are examples of realizations of such scenario. Although the asymptotic diversity gain for both the schemes is comparable, the network coded scheme can further take advantage of the redundancy and the extra dimension provided by the relay link. This extra signal dimension can be very useful when multilevel modulation is employed as it gives the possibility for a better spread of the modulation signal points within the augmented signal space. This article presents a simple and effective Constellation Selection (CS) scheme for all the three links within the NC-DAS system. This selection procedure improves the bit error probability in both AWGN and Rayleigh fading channels. Two different detections schemes are considered in the paper. Joint detection where the both users are decoded simultaneously and detection with successive cancelation where the strongest user is detected first followed by cancelation and maximum ratio combining. Analytical expressions for the error probability supported by simulation results are presented. The obtained results show that constellation selection provides good performance gain as compared to the case of same constellation.
How much do the benefits cost? Effects of a home-based training programme on cardiovascular fitness, quality of life, programme cost and adherence for patients with coronary disease

Objective: To evaluate cost, adherence and effects on cardiovascular function and quality of life of a home-based cardiac rehabilitation programme for patients with coronary disease. Design: A randomized, prospective controlled trial. Setting: Department of Rehabilitation, University Hospital, Brazil. Subjects: Thirty-nine low-risk patients were assigned to a home exercise training group (n = 19) or a control group (n = 20). Interventions: The home group performed home-based training for three months with biweekly telephone monitoring. Main outcome measures: The aerobic capacity and the quality of life (Medical Outcomes Study 36-Item Short Form Survey (SF-36)) of all patients were evaluated before and after the three-month period. Adherence was evaluated weekly. Programme cost was estimated using the Brazilian Classification of Medical Procedures. Results: After training, the home group had higher peak Vo2 from 28.8 (6.4) to 31.7 (8.1) mL/kg per minute, peak heart rate from 135 (22) to 143 (20) bpm, work rate from 4780 (2021) to 7103 (3057) kpm/min and exercise time from 11.5 (1.9) to 13.6 (2.3) minutes (P ≤ 0.05). The control group showed reduction in peak Vo2 from 28.6 (6.6) to 26.8 (7.2) mL/kg per minute, peak Vo2 pulse from 15.5 (3.9) to 14.3 (3.8) mL/bpm and exercise time from 11.5 (2.3) to 11.4 (2.7) minutes (P ≤ 0.05). The home group reported improvements in all domains of SF-36. The control group showed improvement in only three domains of SF-36. In the home group the average cost per patient was US$502.71 and the adherence achieved 100%. Conclusion: The programme seems to provide an efficient low-cost approach to cardiac rehabilitation in low-risk patients.
Entity Search Based on the Representation Learning Model With Different Embedding Strategies

We focus on the problem of learning distributed representations for entity search queries, named entities, and their short descriptions. With our representation learning models, the entity search query, named entity, and description can be represented as low-dimensional vectors with minimal human preprocessing. Our goal is to develop a simple but effective model that can make the distributed representations of query-related entities similar to the query representation in the vector space. Hence, we propose three kinds of learning strategies, and the difference between them mainly lies in how to deal with the relationship between an entity and its description. We analyze the strengths and weaknesses of each learning strategy and validate our methods on public data sets, which contain various query types and different languages (i.e., English and Chinese). The experimental results indicate that our proposed methods can adapt to different types of entity search queries, and outperform the current state-of-the-art methods no matter the entity collection is homogeneous or heterogeneous. Besides, the proposed methods can be trained fast and can be easily extended to other similar tasks.
The Relationship between Postpartum Depression and Breastfeeding

Introduction: The purpose was to investigate the possible correlation or predictive relationship between breastfeeding and Postpartum Depression (PPD). Method: We conducted a prospective study in which 137 Arab women were assessed during pregnancy and postpartum. Current breastfeeding was correlated with postpartum outcomes (EPDS and MINI), employment, and use of formula at 2 and 4 months postpartum, as well as with other variables. Results: Women who were breastfeeding at 2 and 4 months had lower scores on EPDS (p < 0.0037 and p < 0.0001, respectively) and were less likely to be diagnosed with PPD at 4 months (p < 0.0025). Higher scores on EPDS and diagnosis of PPD at 2 months were predictive of lower rates of breastfeeding at 4 months (p < 0.0001 and p < 0.005, respectively). Women who were employed and using formula at 2 months were less likely to breastfeed at 4 months (p < 0.0001). Breastfeeding women at 2 months had lower scores on EPDS (p < 0.003) and were less likely to be diagnosed with PPD (p < 0.05) at 4 months. Discussion: The results indicate that women who breastfeed their infants reduced their risk of developing PPD, with effects being maintained over the first 4 months postpartum. PPD may also decrease the rate of breastfeeding, suggesting a reciprocal relationship between these variables.
Gluconeogenesis during endurance exercise in cyclists habituated to a long‐term low carbohydrate high‐fat diet

Blood glucose is an important fuel for endurance exercise. It can be derived from ingested carbohydrate, stored liver glycogen and newly synthesized glucose (gluconeogenesis). We hypothesized that athletes habitually following a low carbohydrate high fat (LCHF) diet would have higher rates of gluconeogenesis during exercise compared to those who follow a mixed macronutrient diet. We used stable isotope tracers to study glucose production kinetics during a 2 h ride in cyclists habituated to either a LCHF or mixed macronutrient diet. The LCHF cyclists had lower rates of total glucose production and hepatic glycogenolysis but similar rates of gluconeogenesis compared to those on the mixed diet. The LCHF cyclists did not compensate for reduced dietary carbohydrate availability by increasing glucose synthesis during exercise but rather adapted by altering whole body substrate utilization.
Compact cascaded branch line coupler using T-sections conversion

The branch line coupler has many applications such as phase shifters, vector modulators, amplifiers and mixers and etc. The conventional branch line coupler consists of four arms each have μ/4 length with different impedances. To broaden the bandwidth, the couplers need to be cascaded, but due to the cascading, the overall size will be very large. To minimize the overall size, a T-section conversion was used instead of each of the quarter wave length arms. The new cascaded coupler occupies 33.5% of the area needed for the conventional cascaded coupler. Added to the size reduction, the new cascaded branch line coupler has nearly the same frequency response and fractional bandwidth as the conventional cascaded branch line coupler.
Non-concave network utility maximization: A distributed optimization approach

This paper proposes an algorithm for optimal decentralized traffic engineering in communication networks. We aim at distributing the traffic among the available routes such that the network utility is maximized. In some practical applications, modeling network utility using non-concave functions is of particular interest, e.g., video streaming. Therefore, we tackle the problem of optimizing a generalized class of non-concave utility functions. The approach used to solve the resulting non-convex network utility maximization (NUM) problem relies on designing a sequence of convex relaxations whose solutions converge to that of the original problem. A distributed algorithm is proposed for the solution of the convex relaxation. Each user independently controls its traffic in a way that drives the overall network traffic allocation to an optimal operating point subject to network capacity constraints. All computations required by the algorithm are performed independently and locally at each user using local information and minimal communication overhead. The only non-local information needed is binary feedback from congested links. The robustness of the algorithm is demonstrated, where the traffic is shown to be automatically rerouted in case of a link failure or having new users joining the network. Numerical simulation results are presented to validate our findings.
Models for Maintenance Effort Prediction with Object-Oriented Cognitive Complexity Metrics

Software maintenance is the most desired, but most elusive and difficult task in software engineering. The cost of maintenance is as high as 60% to 80% of the total cost of the software. So, plenty of researches are going on in software maintenance. Though, object-oriented paradigm has made it easier, it remains the critical hotspot of research. One way of grappling with the maintenance problem, is to use the complexity metrics. Many studies were made to understand the relationship among complexity metrics, cognition, and maintenance. This paper wrestles with four newly proposed object-oriented cognitive complexity metrics to develop maintenance effort prediction models through various statistical techniques. Empirical study designs are made with hypotheses and experimented. Discussion on results prove the maintenance effort prediction models are more robust, more accurate, and can be employed to estimate the maintenance effort.
System architecture design of PCIe root complex based on SOPC

PCIe bus is widely applied because of its high-bandwidth, high reliability and low cost characteristic. Research on PCIe root complex architecture based on FPGA begin to receive attentions. However, current methods are usually expensive, code closure and poor flexibility. A new open source PCIe root system architecture based on Xilinx SOPC platform is proposed in this paper. The system is mainly composed of AXI-PCIe bridge, AXI interconnect, processing subsystem and DDR3 memory. The processing system runs the embedded Linux operating system for controlling and management functions. The AXI-PCIe bridge communicates with the specific PCIe endpoint device and provides the conversion logic for the PCIe domain address and the AXI domain address. They are connected by high performance AXI interconnect. This paper uses the gigabit ethernet card and network bandwidth testing tools to verify the proposed hardware and software design method. The architecture of this approach has the advantages of simple structure, powerful performance and easy expansion, which provides a feasible solution for new high-performance servers and large-scale PLC systems.
Phosphorylation of the Abelson murine leukemia virus transforming protein

The Abelson murine leukemia virus transforming gene product is a phosphorylated protein encoded by both viral and cellular sequences. This gene product has an amino-terminal region derived from the gag gene of its parent virus and a carboxyl-terminal region of (abl) derived from a normal murine cellular gene. Using a combination of partial proteolytic cleavage techniques and antisera specific for gag and abl sequences, we mapped in vivo phosphorylation sites to different regions of the protein. Phosphoproteins encoded by strain variants and transformation-defective mutants of Abelson murine leukemia virus with defined deletions in the primary sequence of the abl region were compared by two dimensional limit digest peptide mapping. Specific phosphorylation pattern differences for wild-type and mutant proteins probably represented deletions of specific phosphate acceptor sites in the abl region. An in vitro autophosphorylation activity copurified with the Abelson murine leukemia virus protein from transformation-competent strains. A peptide analysis of such in vitro reactions demonstrated that these phosphorylation sites were restricted to the amino-terminal region, and the specific sites appeared to be unrelated to the sites found on proteins phosphorylated in vivo. Thus, the autophosphorylation reaction probably correlates with an activity important in transformation, but the specific end product in vitro bears little resemblance to its function in vivo.
ADAR1 and PACT contribute to efficient translation of transcripts containing HIV-1 trans-activating response (TAR) element

Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase PKR, which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor eIF2α. This shuts down the synthesis of both host and viral proteins, allowing the cell to mount an effective antiviral response. PACT (protein activator of PKR) is a cellular protein activator of PKR, primarily functioning to activate PKR in response to cellular stress. Recent studies have indicated that during HIV-1 infection, PACT's normal cellular function is compromised and that PACT is unable to activate PKR. Using various reporter systems and in vitro kinase assays, we establish in this report that interactions between PACT, ADAR1 and HIV-1-encoded Tat protein diminish the activation of PKR in response to HIV-1 infection. Our results highlight an important pathway by which HIV-1 transcripts subvert the host cell's antiviral activities to enhance their translation.