Miracle-dz/UniFAR-FTUs huggingface dataset:
Internalização da permease de lactose de Kluyveromyces lactis em resposta a fontes de carbono

vii 1. INTRODUÇÃO. 1 2. REVISÃO DE LITERATURA. 3. REFERÊNCIAS BIBLIOGRÁFICAS. 3 7 4. ARTIGO CIENTÍFICO. 10 Resumo. 11 Introdução. 12 Material e Métodos. 14 Microrganismos e condições de cultivo. 14 Efeito da concentração de açúcar e da presença de 2-DG e 6-DG na localização de Lac12GFP. 14 Microscopia de fluorescência. 14 Medida das taxas de captação de lactose[C]. 15 Efeito de LiCl no crescimento de K. lactis e na internalização de Lac12-GFP. 15 Resultados. 16 Discussão. 20 Referências Bibliográficas. 23 Legendas. 26 Figuras. 28
The Influence of Ketosis on the Rectal Microbiome of Chinese Holstein Cows

Received: Revised: Accepted: Published online: July 07, 2018 December 06, 2018 January 31, 2019 March 22, 2019 This study was conducted to analyze the changes in microbial populations of rectal content of dairy cattle with and without ketosis. The plasma β-hydroxybutyric acid (BHBA) levels of 350 cows were measured and twenty-two post-parturient dairy cows with BHBA levels >1.2 mmol/L were selected and diagnosed with ketosis (KET group). According to statistical pairing rule, 22 dairy cows with BHBA levels <0.60 mmol/l formed the control groups (CON group). The profile of the microbial community of the rectal content samples was detected using high-throughput sequencing analysis of hypervariable V4 region of microbe. The average effective sequences of each sample were 84983, ranging from 64090 to 94470. The Principal Co-ordinates Analysis (PCoA) showed that there were distinctly different clusters of the rectal microbial community between KET and CON cows. Beta diversity analysis was evaluated differences in samples of species complexity. At the phylum level, the percentage of Euryarchaeota of the KET cows was less than (P<0.05) in the CON group. At the genus level, the percentages of Ruminococcaceae-UGG-014, Methanobrevibacter, Erysipelotrichaceae-UGG-009, and Atopobium of the KET cows were less than (P<0.05) those found in the CON group. The percentage of Lachnospiraceae was greater (P<0.05) in KET cows compared with CON cows. Lachnospiraceae is related to butyrate production and an increased amount may be an important causative agent of ketosis in dairy cattle. Our findings give a complete picture of current knowledge of the population structure of the rectal microbial ecosystem between KET and CON cows and enhance our understanding about the rectal microbial ecology that may be useful in the prevention of ketosis. ©2019 PVJ. All rights reserved
lifelines: survival analysis in Python

One frustration of data scientists and statisticians is moving between programming languages to complete projects. The most common two are R and Python. For example, a survival analysis model may be fit using R’s survival-package (Terry M Therneau, 2015) or flexsurv (Christopher Jackson, 2016), but needs to be deployed into a Python system. Previously, this may have meant using Python libraries to call out to R (still shuffling between two languages, but now abstracted), or translating the fitted model to Python (likely to introduce bugs). Libraries like Patsy (Nathaniel J. Smith et al., 2018) and Statsmodels (Skipper Seabold et al., 2017) have helped data scientists and statisticians work in solely in Python. lifelines extends the toolbox of data scientists so they can perform common survival analysis tasks in Python. Its value comes from its intuitive and well documented API, its flexibility in modeling novel hazard functions, and its easy deployment in production systems & research stations along side other Python libraries. The internals of lifelines uses some novel approaches to survival analysis algorithms like automatic differentiation and meta-algorithms. We present high-level descriptions of these novel approaches next. One goal of lifelines is to be pure Python so as to make installation and maintenance simple. This can be at odds with users’ desire for high-performance model fitting. Though Python is becoming more and more performant, datasets are getting larger and larger at a faster rate. Internally, lifelines uses some interesting tricks to improve performance. These approaches can be applied to other Python libraries. For example, the Cox proportional hazard model with Efron’s tie-handling method has a complicated partial-likelihood (Wikipedia contributors”, 2019):
The complete chloroplast genome of Aralia atropurpurea (Araliaceae, the ginseng family) from the Sino-Himalayan region, China

Abstract Aralia atropurpurea (Araliaceae) is a perennial medicinal herb endemic to southwest China. In this study, the complete chloroplast (cp) genome of A. atropurpurea was reported and phylogenetic analysis was conducted. The cp genome of A. atropurpurea is 156,272 bp in length, consisting two inverted repeats (IRs, 25,963 bp), a small single copy (SSC, 18,080 bp), and a large single copy (LSC, 86,266 bp) region. It encodes 133 genes including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum-likelihood tree shows A. atropurpurea grouping with the other two Aralia sect. Aralia species, and a close relationship between Aralia and Panax.
In silico Studies of Parasporin Proteins: Structural and Functional Insights and Proposed Cancer Cell Killing Mechanism for Parasporin 5 and 6

Background: Cancer is the leading cause of death in the world and the new types of cancer are diagnosed regularly but the advancement in their treatment is relatively slow and not to mention very costly. Parasporins (PS), parasporal inclusion proteins from Bacillus thuringiensis, possess specific cytotoxicity against different cancer cells which has suggested them to be potential for cancer treatment due to their specific binding to cancer cells. Methods: Computational investigation were performed to exploit their physicochemical characteristics, structural properties including three dimensional (3D) model, model quality analysis, phylogenetic assessment and functional analysis along with the cancer-cell killing mechanism of PS-5 and PS-6 proteins using standard tools of bioinformatics. Results: PS proteins were found to be slightly acidic based on their isoelectric points i.e., pI ranging from 5.126. 19, and the instability indices (29.0342.31) indicate their highly stable nature in test tubes and higher aliphatic indices (62.54-94.75) indicate their thermostability, a feature suitable for high-level industrial production. In silico analysis of cellular localization predicts that the parasporins are mostly located in the cytoplasm and few in the plasma membrane but devoid of any signal peptide. The generated 3D models of PS proteins upon verification by Ramachandran plot analysis confirmed that our prediction lies in the good quality model range and facilitated the understanding of the very protein folding, assembly into complexes and cell killing mechanisms. It could be hypothesized that the PS-5 protein might induce apoptosis or act as βpore forming toxin to kill specific cancer cells while PS-6 might act simply as pore forming toxin. Conclusions: The theoretical overview of this research would facilitate the researchers with valuable insights of the PS protein structures, cancer cell killing mechanism of PS-5 and PS-6 proteins eventually in tumor microenvironment and their receptor molecules with a view to develop anti-cancer drugs.
Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress

Prosthetic joint replacement failure has a huge impact on quality of life and hospitalization costs. A leading cause of prosthetic joint infection is bacteria-forming biofilm on the surface of orthopedic devices. Staphylococcus epidermidis is an emergent, low-virulence pathogen implicated in chronic infections, barely indistinguishable from aseptic loosening when embedded in a mature matrix. The literature on the behavior of quiescent S. epidermidis in mature biofilms is scarce. To fill this gap, we performed comparative analysis of the whole proteomic profiles of two methicillin-resistant S. epidermidis strains growing in planktonic and in sessile form to investigate the molecular mechanisms underlying biofilm stability. After 72-h culture of biofilm-forming S. epidermidis, overexpression of proteins involved in the synthesis of nucleoside triphosphate and polysaccharides was observed, whereas planktonic bacteria expressed proteins linked to stress and anaerobic growth. Cytological analysis was performed to determine why planktonic bacteria unexpectedly expressed proteins typical of sessile culture. Images evidenced that prolonged culture under vigorous agitation can create a stressful growing environment that triggers microorganism aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. The choice of a unique late time point provided an important clue for future investigations into the biofilm-like behavior of planktonic cells. Our preliminary results may inform comparative proteomic strategies in the study of mature bacterial biofilm. Finally, there is an increasing number of studies on the aggregation of free-floating bacteria embedded in an extracellular matrix, prompting the need to gain further insight into this mode of bacterial growth.
Fibrous bone tissue engineering scaffolds prepared by wet spinning of PLGA

Having a self-healing capacity, bone is very well known to regenerate itself without leaving a scar. However, critical size defects due to trauma, tumor, disease, or infection involve bone graft surgeries in which complication rate is relatively at high levels. Bone tissue engineering appears as an alternative for grafting. Fibrous scaffolds are useful in tissue engineering applications since they have a high surface-to-volume ratio, and adjustable, highly interconnected porosity to enhance cell adhesion, survival, migration, and proliferation. They can be produced in a wide variety of fiber sizes and organizations. Wet spinning is a convenient way to produce fibrous scaffolds with consistent fiber size and good mechanical properties. In this study, a fibrous bone tissue engineering scaffold was produced using poly(lactic-co-glycolic acid) (PLGA). Different concentrations (20%, 25%, and 30%) of PLGA (PLA:PGA 75:25) (Mw = 66,000-107,000) were wet spun using coagulation baths composed of different ratios (75:25, 60:40, 50:50) of isopropanol and distilled water. Scanning electron microscopy (SEM) and in vitro degradation studies were performed to characterize the fibrous PLGA scaffolds. Mesenchymal stem cells were isolated from rat bone marrow, characterized by flow cytometry and seeded onto scaffolds to determine the most appropriate fibrous structure for cell proliferation. According to the results of SEM, degradation studies and cell proliferation assay, 20% PLGA wet spun in 60:40 coagulation bath was selected as the most successful condition for the preparation of wet-spun scaffolds. Wet spinning of different concentrations of PLGA (20%, 25%, 30%) dissolved in dichloromethane using different isopropanol:distilled water ratios of coagulation baths (75:25, 60:40, 50:50) were shown in this study.
Cellular dialogues that enable self-organization of dynamic spatial patterns

Cells form spatial patterns by coordinating their gene expressions. How a group of mesoscopic numbers (hundreds-to-thousands) of cells, without pre-defined morphogens and spatial organization, self-organizes spatial patterns remains incompletely understood. Of particular importance are dynamic spatial patterns - such as spiral waves that perpetually move and transmit information over macroscopic length-scales. We developed an open-source, expandable software that can simulate a field of cells communicating with any number of cell-secreted molecules in any manner. With it and a theory developed here, we identified all possible “cellular dialogues” - ways of communicating with two diffusing molecules - and core architectures underlying them that enable diverse, self-organized dynamic spatial patterns that we classified. The patterns form despite widely varying cellular response to the molecules, gene-expression noise, and spatial arrangement and motility of cells. Three-stage, “order-fluctuate-settle” process forms dynamic spatial patterns: cells form long-lived whirlpools of wavelets that, through chaos-like interactions, settle into a dynamic spatial pattern. These results provide a blueprint to help identify missing regulatory links for observed dynamic-pattern formations and in building synthetic tissues.
Axon-like protrusions promote small cell lung cancer migration and metastasis

Metastasis is the main cause of death in cancer patients but remains a poorly understood process. Small cell lung cancer (SCLC) is one of the most lethal and most metastatic types of human cancer. SCLC cells normally express neuroendocrine and neuronal gene programs but accumulating evidence indicates that these cancer cells become relatively more neuronal and less neuroendocrine as they gain the ability to metastasize. Here we show that mouse and human SCLC cells in culture and in vivo can grow cellular protrusions that resemble axons. The formation of these protrusions is controlled by multiple neuronal factors implicated in axonogenesis, axon guidance, and neuroblast migration. Disruption of these axon-like protrusions impairs cell migration in culture and inhibits metastatic ability in vivo. The co-option of developmental neuronal programs is a novel molecular and cellular mechanism that contributes to the high metastatic ability of SCLC.
Toughness in Santa Inês lamb meat has negative impact on consumer evaluation

SUMMARY Meat tenderness is a major attribute for consumers worldwide. However, few studies investigate the importance of lamb meat tenderness for Brazilian consumers. This study assessed consumers’ evaluation of lamb meat with high shear forces. Eight lambs were slaughtered at 32.5±2.5kg of live weight and 5 to 6 months of age. The Longissimus dorsi muscle from both half carcasses was randomly assigned to four different postmortem processes: Tough Meat (TM), obtained by cold shortening, Fresh Meat (FM), Aging for 3 (A3) and 7 (A7) days postmortem . The variables measured were the sarcomere length, shear force (WBSF) and myofibrillar fragmentation index. We also applied the sensory analysis using affective acceptance tests with hedonic scale of nine points to measure texture, juiciness and overall quality of the meat. The postmortem processing for TM resulted in shorter sarcomere and greater shear values (p <0.05) compared to all other samples, while FM, A3 and A7, did not differ between the samples. Myofibrillar fragmentation was greater for A7 compared to TM (p <0.05), while FM and A3 showed intermediate values that did not differ between the treatments. In the sensory analysis, TM samples received significantly lower scores (p <0.01) for all attributes compared to other treatments and the attributes were not different between the post rigor processes. Consumers identified and evaluated negatively the meat samples with high WBSF. However, further studies are needed to elucidate the impact of smaller differences in WBSF, at intermediate values, on consumers’ evaluation.
Acoustic Feedback and Echo Cancellation in Speech Communication Systems

During the last decades, signal processing techniques have been developed to attenuate the undesired effects caused by the acoustic coupling between loudspeaker and microphone in communication systems. In public address (PA) or sound reinforcement systems, the acoustic coupling causes the system to have a closed-loop transfer function that, depending on the amplification gain, may become unstable. Consequently, the maximum stable gain (MSG) of the system has an upper limit. In teleconference or hands-free communication systems, the acoustic coupling causes the speaker to receive back his/her voice signal after talking, which sounds like an echo and disturbs the communication. The use of adaptive filters to identify the acoustic coupling path and estimate the resulting acoustic signal, which is subtracted from the microphone signal, is the state-of-art approach to remove the influence of the acoustic coupling in PA and teleconference systems. This approach is very attractive because, in theory, it would completely remove the effects caused by the acoustic coupling if the adaptive filter exactly matches the acoustic coupling path. And it has been applied to develop acoustic feedback cancellation (AFC) and acoustic echo cancellation (AEC) methods for PA and teleconference systems, respectively. In a PA system, however, a bias is introduced in the adaptive filter coefficients if the traditional gradient-based or least-squares-based adaptive filtering algorithms are used. This issue occurs because the system input signal and the loudspeaker signal are highly correlated, mainly for colored signals as speech, and limits the performance of the AFC methods available in the literature. This work aims to primarily investigate the use of cepstral analysis to develop more effective AFC methods. It is proved that the cepstra of the microphone signal and the error signal may contain time domain information about the system, including its open-loop impulse response. Then, two new AFC methods are proposed: the AFC method based on the cepstrum of the microphone signal (AFC-CM) and the AFC method based on the cepstrum of the error signal (AFC-CE). The AFC-CM and AFC-CE methods estimate the feedback path impulse response from the cesptra of the microphone signal and error signal, respectively, to update the adaptive filter. Simulation results demonstrated that, for speech signals in a PA system with one microphone and one loudspeaker, the AFC-CM and AFC-CE methods can estimate the feedback path impulse
Automatic Haiku Generation Using VSM

In this paper, we present our current research progress in using an AI approach and modern Web 2.0 techniques to automatically create "modern haiku" poetry from text harvested from the blogosphere. Our haikus are generated using keyword seeds and the semantics of these keywords to extract lines from blogs to create a well-rounded poem. We believe this approach will yield much more human-understandable haiku poetry with much more realism than other traditional AI approaches as the language used in blogs is current as well as the events and cultural references. Our algorithm is based on formulating relationships between sentences as vectors using Vector Space Model (VSM) and then comparing relationships between sentences pairs using angle measurements based on simple cosine metric between the formed vectors.
Blood cells morphology of Testudo graeca and Testudo hermanni Testudines Testudinidae from Turkey

Here, the morphology of peripheral blood cells (erythrocytes, leukocytes and thrombocytes) of Testudo graeca and T. hermanni was studied in Wright’s stained blood smears. In both species, heterophils were notable as dominant cells in blood smears. For eosinophils and basophils, nucleus could not be clearly distinguished because of intensive granulation in the cytoplasm, and it was observed that thrombocytes were close to spherical for T. hermanni and spindle-shaped for T. graeca.
Histomorphological and histochemical studies on Harderian gland of Kadaknath fowl.

Histomorphological and histochemical studies were conducted on the Harderian gland of the Kadaknath fowl at different age groups from day old to more than 32 week of age. The black coloured Harderian gland was situated ventral and postero-medial aspect of the eyeball. The Harderian gland was covered by thin connective tissue capsule and divided into different lobules of variable sizes by connective tissue trabeculae made up of mainly reticular fibers. The epithelium of corpus glandulae and excretory duct was lined by simple columnar epithelium of varying height. The apical portion of the glandular part was darkly stain and serous in nature while the basal portion was light stain and mucous in nature. Much amount of plasma cells, different sizes of lymphocytes, mast cells, macrophages and melanin pigments were present in the interlobular tissue of the gland. The activity for PAS and AMPS reaction was more towards the apex of the glandular unit than the base.
Polymorphisms in the and genes of the SUMO-conjugating system and breast cancer risk

SUMOylation consists in the covalent conjugation of small ubiquitin-related modifiers to target proteins. SUMOylation participates in processes that are tightly linked to tumorigenesis, and genetic variability in the SUMO-conjugating system may influence the development of breast cancer. We recently reported that variation in the gene encoding the SUMO-conjugating enzyme may affect the grade of breast tumors. Following comprehensive analyses for detection of putative functional polymorphisms in 14 genes of the SUMO system, we selected one coding SNP in and seven tag SNPs in for association analyses. Results were based on 1,021 cases, and 1,015 matched controls from the population-based GENICA study. Odds ratios (OR) and 95% confidence intervals (CI) were estimated by conditional logistic regression. To explore the association with polymorphisms closely linked to the genotyped variants, multiple imputation based on HapMap data was applied. The study revealed associations of four polymorphisms with risk of grade 1 tumors. Comparison of genotype and haplotype models indicated that the best representation of risk solely relied on rs7187167 under dominant penetrance. Women carrying the rare allele showed an increased risk of grade 1 tumors compared with common homozygotes (OR 1.87, 95% CI 1.18–2.95). This effect appeared to be stronger in women with a family history of breast or ovarian cancer. Imputation of polymorphisms in a 300-kb region around the genotyped polymorphisms identified no variants with stronger associations. Our findings suggest that genetic variation in may affect the risk of grade 1 breast tumors.
Toxicity and serum metabolomics investigation of Mn-doped ZnS quantum dots in mice

Purpose Mn-doped ZnS quantum dots (QDs) with special luminescent properties have been widely researched and applied in various fields. Thus, their release toxicity and security cannot be ignored. Methods In the present study, the toxicity and non-targeted metabolomics of Mn-doped ZnS QDs were investigated after single intravenous injection. Serum metabolites were evaluated based on gas chromatography–mass spectrometry together with multivariate statistical analyses [principal component analysis, partial least squares discriminant analysis, and orthogonal PLS-DA]. Results The modified metabolites (variable importance in the projection (VIP) >1 and p<0.05) revealed that Mn-doped ZnS QDs exposure disturbed glycolysis, tricarboxylic acid cycle, ketoplasia, glutaminolysis, and amino acid and lipid metabolism. The behavior, coefficients of organs, and histological changes were the same as in the control group, and the disturbance of hematology and serum biochemistry was not dose- or time-dependent. Conclusion Our study provides a general observation regarding the toxicity and potential metabolic responses of mice exposed to Mn-doped ZnS QDs.
Iris-Face Fusion and Security Analysis Based on Fisher Discriminant

Abstract With the development of society and science technology, the information security becomes more and more important for people and nation. In this paper, we focus on the technology of iris-face fusion in multi-mode sense in order to find an algorithm to get a better recognition performance. Firstly, we introduce the feature extraction of iris and face, and fusion the features using different algorithms. By simulation, we find out the recognition performance with different fusion methods, which provide some new conclusions. In order to improve the performance of recognition system, we classify these features with fisher discriminant analysis again. Then we analyze the security of recognition system from the aspect of influence of leak in biology features. Finally, experiments were designed to demonstrate the effectiveness of the proposed algorithms.