Miracle-dz/UniFAR-FTUs huggingface dataset:
AN EFFICIENT CORE ARCHITECTURE FOR PROTEIN SEQUENCE ALIGNMENT

This paper presents efficient biological sequence alignment core architecture to reduce execution time of the wellknown dynamic programming-based (DP) pairwise sequence alignment algorithms i.e. the Smith Waterman algorithm. The PE was prototyped in the Xilinx Virtex 5 FPGA with further improvements have been done in the scheduling strategy of alignment matrix computation and substitution coefficients’ pre-loading onto the processing elements in folded systolic arrays. Implementation rresults showed that the new hardware architecture for the protein sequence alignment achieved over 100x speed-up performance, compared to the well-known SSEARCH 35 ‘software-only implementation’ and more than ~1.6x speed up improvement against our previously implemented core in Virtex 5 FPGA.
Fermented feed for laying hens: effects on egg production, egg quality, plumage condition and composition and activity of the intestinal microflora

1. An experiment with a total of 480 hens (Babcock) was carried out from 16 to 38 weeks of age to evaluate the suitability of wet fermented feed (feed water ratio, 1:1·2–1:1·4) for layers, taking aspects of nutrition and gastrointestinal health into consideration. The production performance, egg shell quality, plumage condition, litter dry matter (DM) content, as well as the composition and activity of the intestinal microbial flora were analysed. 2. Fermented feed was characterised by a high concentration of lactic acid (160–250 mmol/kg feed) and a moderate level of acetic acid (20–30 mmol/kg feed), high numbers of lactic acid bacteria (log 9–10 CFU/g feed) and a pH of approximately 4·5. Feed fermentation reduced the concentration of dietary sugar from 32·1 to 7·3 g/kg DM and the phytate bound phosphorus from 2·7 to 1·9 g/kg DM. 3. Fermented feed seemed to loose attractiveness for the birds quite rapidly, resulting in a more aggressive behaviour and a poorer plumage condition than in birds given dry feed. The use of fermented feed reduced the litter DM content. 4. During the experimental period, the body weight gain of hens receiving fermented feed was 80 g higher than of hens fed the dry mash. Presumably because of an extended adaptation time to the feed, the onset of lay occurred later when hens were fed on fermented feed, resulting in non-significantly reduced total egg production (75 vs. 82%). 5. There was no significant difference between groups with respect to the total egg mass production (g/d/hen, 42 and 45 for fermented feed and dry mash, respectively). Throughout the experimental period, the feed DM intake of hens fed with fermented feed was lower than that of hens receiving the dry mash (110 vs. 125 g). From week 26 to 37, fermented feed improved the feed conversion as compared with the dry mash (g feed DM/g egg mass, 2·28 vs. 2·53). 6. The use of fermented feed increased egg weight in the period from 34 to 37 weeks (61·4 vs. 60·0) and increased shell weight (g/100 g egg weight, 10·2 vs. 9·9) and shell stiffness (N/mm, 161 vs. 150) of eggs collected at 37 weeks. 7. The feeding of fermented feed increased intestinal health by acidification of the upper digestive tract, forming a natural barrier towards infection with acid sensitive pathogens, e.g. E. coli, Salmonella and Campylobacter. 8. It was concluded that fermented wet feed offers potential benefits for health and nutrition, but may become suitable for layers only after the practical problems related to this feeding form have been overcome. However, an early adaptation of the birds during the rearing period seems to be necessary.
Targeted inhibition of interleukin‐6 with CNTO 328 sensitizes pre‐clinical models of multiple myeloma to dexamethasone‐mediated cell death

Interleukin (IL)‐6‐mediated signalling attenuates the anti‐myeloma activity of glucocorticoids (GCs). We therefore sought to evaluate whether CNTO 328, an anti‐IL‐6 monoclonal antibody in clinical development, could enhance the apoptotic activity of dexamethasone (dex) in pre‐clinical models of myeloma. CNTO 328 potently increased the cytotoxicity of dex in IL‐6‐dependent and ‐independent human myeloma cell lines (HMCLs), including a bortezomib‐resistant HMCL. Isobologram analysis revealed that the CNTO 328/dex combination was highly synergistic. Addition of bortezomib to CNTO 328/dex further enhanced the cytotoxicity of the combination. Experiments with pharmacologic inhibitors revealed a role for the p44/42 mitogen‐activated protein kinase pathway in IL‐6‐mediated GC resistance. Although CNTO 328 alone induced minimal cell death, it potentiated dex‐mediated apoptosis, as evidenced by increased activation of caspases‐8, ‐9 and ‐3, Annexin‐V staining and DNA fragmentation. The ability of CNTO 328 to sensitize HMCLs to dex‐mediated apoptosis was preserved in the presence of human bone marrow stromal cells. Importantly, the increased activity of the combination was also seen in plasma cells from patients with GC‐resistant myeloma. Taken together, our data provide a strong rationale for the clinical development of the CNTO 328/dex regimen for patients with myeloma.
The Metabolic Syndrome: A Brain Disease?

The incidence of obesity with, as consequence, a rise in associated diseases such as diabetes, hypertension and dyslipidemia − the metabolic syndrome − is reaching epidemic proportions in industrialized countries. Here, we provide a hypothesis that the biological clock which normally prepares us each morning for the coming activity period is altered due to a modern life style of low activity during the day and late‐night food intake. Furthermore, we review the anatomical evidence supporting the proposal that an unbalanced autonomic nervous system output may lead to the simultaneous occurrence of diabetes type 2, dyslipidemia, hypertension and visceral obesity.
Use of delphi method in obtaining requirements for the game structural masonry

The article presents the achievement of the project requirements for the development of learning material from the formulation of a game which simulates the management of a work in the building system in structural masonry. The methodology for obtaining these requirements goes through literature survey and application of the Delphi method with a group of 12 specialists (Professor, Researcher and Game Designer Professional) who develop their professional activities in this building system. The game will serve to qualify the students of civil engineering undergraduate courses, production engineering and architecture that will act as work managers in this system.
Immune Dysfunction and Bacterial Coinfections following Influenza

Secondary pulmonary infections by encapsulated bacteria including Streptococcus pneumoniae and Staphylococcus aureus following influenza represent a common and challenging clinical problem. The reasons for this polymicrobial synergy are still not completely understood, hampering development of effective prophylactic and therapeutic interventions. Although it has been commonly thought that viral-induced epithelial cell damage allows bacterial invasiveness, recent studies by several groups have now implicated dysfunctional innate immune defenses following influenza as the primary culprit for enhanced susceptibility to secondary bacterial infections. Understanding the immunological imbalances that are responsible for virus/bacteria synergy will ultimately allow the design of effective, broad-spectrum therapeutic approaches for prevention of enhanced susceptibility to these pathogens.
High Peritoneal Permeability is Not Associated with Higher Mortality or Technique Failure in Patients on Automated Peritoneal Dialysis

Background Patients on continuous ambulatory peritoneal dialysis (CAPD) who have high small-molecule peritoneal transport have increased mortality. Objective To investigate the impact of baseline peritoneal transport characteristics on patient and technique survival in incident peritoneal dialysis (PD) patients, most of whom are on automated PD (APD), with the use of icodextrin. Design Retrospective observational cohort study. Setting A single PD unit. Patients and Methods 193 new patients that began PD between January 2000 and September 2004, and had an initial peritoneal equilibration test within 6 months of commencement of PD. Patients were divided into low (L), low average (LA), high average (HA), and high (H) peritoneal transport groups. Death-censored technique failure and patient survival were examined. Results Of the 193 patients, 151 (78.1%) were on APD or on APD with icodextrin or on CAPD with icodextrin. At the end of 1, 3, and 5 years, patient survival was 91%, 82%, and 67% in LA group; 95%, 77%, and 69% in HA group; and 96%, 71%, and 71% in H group. Technique survival was 100%, 90%, and 77% in LA group; 96%, 84%, and 72% in HA group; and 92%, 87%, and 77% in H group. High peritoneal permeability did not predict worse patient survival or technique failure, while age, diabetes, a lower glomerular filtration rate, and high body mass index (≥ 30 kg/m2) were independent predictors of death. Conclusion This study suggests that higher peritoneal transport is not a significant independent risk factor for either mortality or death-censored technique failure. The favorable outcome for high transporters in this study may be due to improved management of volume status by the increased use of APD and the use of icodextrin-based dialysis fluid.
Type 1 Interferons and the Virus-Host Relationship: A Lesson in Détente

The interface between an infectious agent and its host represents the ultimate battleground for survival: The microbe must secure a niche for replication, whereas the host must limit the pathogen's advance. Among the host's arsenal of antimicrobial factors, the type 1 interferons (IFNs) induce potent defense mechanisms against viruses and are key in the host-virus standoff. Viruses have evolved multiple tricks to avoid the immediate antiviral effects of IFNs and, in turn, hosts have adapted use of this innate cytokine system to galvanize multiple additional layers of immune defense. The plasticity that exists in these interactions provides us with a lesson in détente.
Investimentos em Ativos Imobilizados para Instalação de Usina de Reciclagem de Resíduos de Construção Civil de Médio Porte na Zona Leste de São Paulo

Novas ferramentas de gerenciamento e manejo dos residuos gerados em obras tem despertado interesse e sido objeto de varias pesquisas conduzidas pelo setor da Construcao Civil. Dentre estas, destaca-se a reciclagem, uma vez que proporciona a reducao dos volumes descartados e a necessidade de aquisicao de materia-prima natural, ocasionando ganhos economicos significativos e reducao do impacto ambiental. Este trabalho estima os investimentos em ativos imobilizados necessarios para instalacao de uma Usina de Reciclagem de Entulho, (URE) de medio porte a ser localizada na zona Leste da cidade de Sao Paulo, trazendo tambem comparacoes entre precos de comercializacao de agregados naturais e reciclados produzidos em URE e jazidas pesquisadas nos municipios de Sao Paulo, Guarulhos e Osasco, no intuito de se estabelecer um comparativo entre ambos e demonstrar a vantagem economica de aquisicao do reciclado. Para tal, esta pesquisa, qualitativa e exploratoria, apresenta um estudo de caso em que foram realizadas visitas tecnicas a usinas de mesmo porte e entrevistas com gestores, de forma a se identificar investimentos indispensaveis a implantacao da URE em estudo. Os resultados obtidos demonstraram a grande demanda da Zona Leste de Sao Paulo em relacao a reciclagem de residuos de construcao, atestando a viabilidade da usina estudada. Observou-se tambem que os precos de comercializacao dos agregados reciclados nas URE pesquisadas foram inferiores aos agregados naturais, demonstrando a viabilidade economica de sua utilizacao.
Essays on conflict-related migration and development in the case of Afghanistan

This dissertation explores the relationship between conflict-related migration and development within the (post-) conflict setting of Afghanistan. Taking advantage of two unique micro-level datasets seldom available for such a high-risk environment, these studies tackle a range of issues related to the causes and consequences of conflict-related migration, and also assess an important policy response. Moreover, the varied types of migration are considered including cross-border flows, internal displacement and return migration. The ability to do so is not simply convenient but appropriate given the prevalence of these three particular migration trends in Afghanistan over the last four decades.
Model-Based Adaptation of Mixed-Criticality Multiservice Systems for Extreme Physical Environments

An increasingly important trend in the design of industry-strength embedded systems is the integration of multiple services with varying criticality levels into a common computing platform. Such systems are characterized as mixed-criticality multiservice systems (MCMSs). An MCMS has to survive in rigorous environments posed by industry-level requirements. Such survival, however, is becoming continuously more challenging due to the growing system complexity and integrating more and more services. While existing works typically target reliability-driven design optimization to improve the system robustness rather than deal with the surviving problem of the system in extreme physical environments, this paper addresses the problem by enabling the service capability transitions of an MCMS to adapt to the environments. This paper proposes a service capability model to capture the importance of functional modules for the criticality of different services. A model-based service-capability transition mechanism is designed to automatically identify the maximum allowed service capability under a given physical environment. A case study of the proposed techniques was performed on an industrial Ethernet switch which is a typical MCMS, to validate the capability of adaptation to high and low temperatures. The experimental results demonstrate the significant potential of our approach to improve system survivability under extreme physical environments.
Evolução do aprendizado na expansão da cana-de-açúcar para Goiás: o papel dos centros de pesquisa / Evolution of learning in sugarcane growth in the brazilian state of Goiás: the role of the research centers

Direcionar a producao de cana-de-acucar para Goias nao foi um procedimento simples. O ambiente natural de maior parte do Estado, com um longo periodo sem chuvas e uma condicao pedologica adversa, impunha restricoes a esse cultivo. Por um longo periodo, Goias foi tido como improprio para um crescimento dinâmico da agroindustria canavieira. Porem, a situacao tem mudado para atender a expansao da demanda por etanol induzida pelo crescimento da frota de veiculos flex-fuel. Nessa etapa, o Estado tornou-se o segundo maior produtor de etanol e de cana-de-acucar do pais. A mudanca no panorama de Goias somente foi possivel por conta do aprendizado que permitiu aprimorar as formas de produzir cana-de-acucar nas condicoes de cerrado. Meu objetivo e analisar os esforcos feitos nessa direcao, tendo como foco o papel dos tres principais centros de pesquisa que trabalham com a atividade canavieira: Ridesa, IAC e CTC.
Adaptive Channel Hopping Algorithm for Reader Anti-collision in RFID systems

In RFID field, it is easy to interfere between adjacent channels as the frequency band and channel bandwidth are narrow. Especially, in case of the dense reader mode where the number of readers is more than the number of channels, the readers easily collide with each other. In this paper, we propose an algorithm to avoid reader collision in dense reader environment. First, we introduce the operation of our algorithm. And next, we show the simulation results of the proposed algorithm. Simulation results show performance improvement of our algorithm compared to existing LBT algorithm.
Biochemical Determination of Training Effects Using Insulin Clamp Technique

Tissue sensitivity to insulin was evaluated in 6 trained athletes and 9 untrained controls using the euglycemic insulin clamp technique. The amount of glucose metabolism is a measure of overall tissue sensitivity to insulin. During insulin clamp study comparable plasma glucose (80-90 mg/dl) and insulin (90-100 microU/ml) were achieved in both groups. The glucose infusion rate in the athletes (10.70 +/- 0.32 mg/kg/min) was significantly higher than in the controls (7.37 +/- 0.23 mg/kg/min). During euglycemic hyperinsulinemia plasma FFA decreased by 80% while glycerol showed only a 20% reduction in both groups. Urinary catecholamine concentrations in the athletes were similar to those in the controls, and these levels did not change during the insulin clamp period. From these results, it might be concluded that tissue sensitivity to exogenous insulin is 45% higher in trained athletes and that physical exercise can reduce the insulin requirements in insulin-dependent diabetic patients in addition to being beneficial to noninsulin-dependent diabetics.
Adversarial learning games with deep learning models

Deep learning has been found to be vulnerable to changes in the data distribution. This means that inputs that have an imperceptibly and immeasurably small difference from training data correspond to a completely different class label in deep learning. Thus an existing deep learning network like a Convolutional Neural Network (CNN) is vulnerable to adversarial examples. We design an adversarial learning algorithm for supervised learning in general and CNNs in particular. Adversarial examples are generated by a game theoretic formulation on the performance of deep learning. In the game, the interaction between an intelligent adversary and deep learning model is a two-person sequential noncooperative Stackelberg game with stochastic payoff functions. The Stackelberg game is solved by the Nash equilibrium which is a pair of strategies (learner weights and genetic operations) from which there is no incentive for either learner or adversary to deviate. The algorithm performance is evaluated under different strategy spaces on MNIST handwritten digits data. We show that the Nash equilibrium leads to solutions robust to subsequent adversarial data manipulations. Results suggest that game theory and stochastic optimization algorithms can be used to study performance vulnerabilities in deep learning models.
A Maneuvering-Board Approach to Path Planning with Moving Obstacles

In this paper we describe a new approach to the problem of path planning with moving obstacles. Our approach is based on the maneuvering board method commonly used for nautical navigation. We have extended this method to handle cases where obstacles may maneuver at any time and where knowledge of the position and velocity of the obstacles may be uncertain.
Neurogenic Intermittent Claudication in Lumbar Spinal Canal Stenosis: The Clinical Relationship Between the Local Pressure of the Intervertebral Foramen and the Clinical Findings in Lumbar Spinal Canal Stenosis

Study Design The clinical relationship between the local pressure of the intervertebral foramen and the clinical findings in lumbar spinal canal stenosis were evaluated. Objective To investigate the pathogenesis of neurogenic intermittent claudication in lumbar spinal canal stenosis. Summary of Background Data The genesis of neurogenic intermittent claudication is generally considered to result from nerve root ischemia; however, the exact pathogenesis of neurogenic intermittent claudication remains uncertain. Methods From a total of 20 lumbar spinal canal stenosis patients, 29 L5/S1 vertebral foramens were studied. All patients showed neurogenic intermittent claudication, and also showed neurologic abnormalities in L5 area. Intraoperatively, the local pressure of the intervertebral foramen was continuously measured using a micro-tip catheter transducer whereas the lumbar spine postures were changed under passive movement, and the relationships between the local pressure and the preoperative clinical findings in lumbar spinal canal stenosis were analyzed. Results The local pressure of the intervertebral foramen significantly increased during lumbar spine extension (P<0.001). The patients who demonstrated large changes in the local pressure between flexion and extension showed a significantly poor walking ability (P=0.003). Moreover, the patients who had 2-level lumbar spinal canal stenosis showed significantly smaller changes in the local pressure between flexion and extension than 1-level lumbar spinal canal stenosis patients (P=0.01). Conclusions The present study suggests that the genesis of neurogenic intermittent claudication in lumbar spinal canal stenosis may be greatly affected by the variation of the dynamic mechanical stress on the spinal nerve roots of the lumbar spine, rather than the static mechanical stress on the spinal nerve roots with each posture. Moreover, 2-level lumbar spinal canal stenosis patients demonstrated radicular symptoms with relatively less external stress on their spinal nerve roots in the vertebral foramen than that observed in 1-level lumbar spinal canal stenosis patients.
Lifestyle and Low-Back Pain: The Influence of Smoking and Obesity

The authors examined associations between back pain prevalence and lifestyle factors (smoking and obesity) using national survey data. Back pain prevalence rose with increasing levels of smoking, with a relative risk of 1.47 for persons reporting 50 or more pack-years of smoking. This association was strongest in persons under the age of 45 years, however, for whom the corresponding relative risk was 2.33. There were similar trends toward greater prevalence with Increasing body mass index, but prevalence rose substantially only in the most obese 20% of subjects (1.7 times higher than the lowest 20%). In a logistic regression, smoking and obesity contributed independent risk, even after controlling for age, education, exercise level, and employment status. Programs for back pain prevention may wish to test interventions for these lifestyle-related factors.
Nuclear Receptors and the Regulation of Drug‐Metabolizing Enzymes and Drug Transporters: Implications for Interindividual Variability in Response to Drugs

Erratic or unpredictable response to drugs remains a challenge of modern drug therapy. An important determinant of such interindividual differences in drug response is variability in the expression of drug‐metabolizing enzymes and/or transporters at sites of absorption and/or tissue distribution. Variable drug‐metabolizing enzyme and transporter expression can result in unpredictable exposure and tissue distribution of drugs and may manifest as adverse effects or therapeutic failure. In the past decade, important new insights have been made relating to the regulatory mechanisms governing the expression of drug‐metabolizing enzymes and transporters by ligand‐activated nuclear receptors. Specifically, there is compelling evidence to demonstrate that PXR, CAR, FXR, LXR, VDR, HNF4α, and AhR form a battery of nuclear receptors that regulate the expression of many important drug‐metabolizing enzyme and transporters. In this review, the authors focus on clinically important drug‐metabolizing enzymes such as CYP3A4, CYP2B6, CYP2C9, CYP2C19, UGT1A1, SULT2A1, and glutathione S‐transferases and their regulation by nuclear receptors. They also review the nuclear receptor–mediated regulation of drug transporters such as MDR1, MRP2, MRP4, BSEP, BCRP, NTCP, OATP1B3, and OATP1A2. Finally, they outline how the drug development process has been affected by the current understanding of the involvement of nuclear receptors in the regulation of drug disposition genes.