Miracle-dz/UniFAR-FTUs huggingface dataset:
The Importance of the Strictly Conserved, C-terminal Glycine Residue in Phosphoenolpyruvate Carboxylase for Overall Catalysis

Phosphoenolpyruvate carboxylase (PEPC) is a “multifaceted,” allosteric enzyme involved in C4 acid metabolism in green plants/microalgae and prokaryotes. Before the elucidation of the three-dimensional structures of maize C4 leaf and Escherichia coli PEPC, our truncation analysis of the sorghum C4 homologue revealed important roles for the enzyme's C-terminal α-helix and its appended QNTG961 tetrapeptide in polypeptide stability and overall catalysis, respectively. Collectively, these functional and structural observations implicate the importance of the PEPC C-terminal tetrapeptide for both catalysis and negative allosteric regulation. We have now more finely dissected this element of PEPC structure-function by modification of the absolutely conserved C-terminal glycine of the sorghum C4 isoform by site-specific mutagenesis (G961(A/V/D)) and truncation (ΔC1/C4). Although the C4 polypeptide failed to accumulate in a PEPC- strain (XH11) of E. coli transformed with the Asp mutant, the other variants were produced at wild-type levels. Although neither of these four mutants displayed an apparent destabilization of the purified PEPC homotetramer, all were compromised catalytically in vivo and in vitro. Functional complementation of XH11 cells under selective growth conditions was restricted progressively by the Ala, ΔC1 and Val, and ΔC4 modifications. Likewise, steady-state kinetic analysis of the purified mutant enzymes revealed corresponding negative trends in kcat and kcat/K0.5 (phosphoenolpyruvate) but not in K0.5 or the Hill coefficient. Homology modeling of these sorghum C-terminal variants against the structure of the closely related maize C4 isoform predicted perturbations in active-site molecular cavities and/or ion-pairing with essential, invariant Arg-638. These collective observations reveal that even a modest, neutral alteration of the PEPC C-terminal hydrogen atom side chain is detrimental to enzyme function.
Generation of human hepatocytes by stem cell technology: definition of the hepatocyte

Since 1999, numerous articles have reported the generation of hepatocytes from different types of extrahepatic stem or precursor cells. This opens exciting new possibilities for pharmacology and toxicology, as well as for cell therapy. Hepatocyte marker expression, including albumin, cytokeratin 18, c-met, α-fetoprotein and cytochrome P450 3A4 and -2B6, has been observed after transplantation of different types of human stem cells into the liver of laboratory animals or in vitro after incubation with cytokines. These intriguing observations have prompted scientists to classify stem cell-derived cell populations as hepatocytes. However, this conclusion may be premature. It has been shown that factors of the liver microenvironment can induce expression of a limited number of hepatocyte marker genes in nonhepatic cell types. To conclude on the grounds of a limited number of markers that these cells are true hepatocytes is not indicated. In this case one should carefully evaluate crucial hepatocyte-defining enzymatic properties. The present article: i) reviews studies describing the fate of extrahepatic human stem and precursor cells in livers of laboratory animals, including the possibility of cell fusion; and ii) critically discusses the phenotype of stem cells after application of various differentiation protocols aimed at generating human hepatocytes. In addition, the necessary criteria needed for defining a true hepatocyte are suggested. Establishing the necessary properties for stem cell-derived hepatocytes is timely and reasonable, and thus avoids further misleading semantic confusion. Finally, it is essential to understand that the definition of a bona fide hepatocyte should not be limited to qualitative assays, such as reverse transcriptase polymerase chain reaction and immunohistochemistry, but has to include a quantitative analysis of enzymatic activities, which allows direct comparison with primary hepatocytes. Although the stem cell-derived-hepatocyte does not yet exist there is a good chance that this aim may be achieved in the future.
Role of Temperature in Mediating Morning and Evening Emergence Chronotypes in Fruit Flies Drosophila melanogaster

Following decades of research under controlled laboratory conditions, there has been growing interest in the recent past to study circadian rhythms in nature. Recent studies conducted under natural conditions have been fruitful in exploring several characteristics of circadian rhythms that remained cryptic and previously masked under standard laboratory conditions, reemphasizing that the complexity of circadian rhythms in nature increases multifold under the influence of multiple zeitgebers. However, our understanding of the contributions of different zeitgebers in shaping various rhythm characteristics still remains elusive. Previously, Vaze et al. reported that chronotype differences between the morning emerging (early) and evening emerging (late) populations of Drosophila melanogaster are considerably enhanced under natural conditions compared to standard laboratory conditions. In the present study, we assess the role of 2 primary zeitgebers in nature—light and temperature—individually and in unison in driving chronotype differences. We report that when provided independently, temperature cycles enhance divergence between the early and late chronotypes more strongly than light, but when together, light and temperature appear to act antagonistically and that appropriate phase difference between light and temperature cycles is essential to promote chronotype divergence. Thus, our study highlights the importance of light and temperature, as well as their interaction with circadian clocks in mediating early and late chronotypes in fruit flies D. melanogaster.
Creating a critical mass eliminates the effects of stereotype threat on women's mathematical performance.

BACKGROUND Women in mathematical domains may become attuned to situational cues that signal a discredited social identity, contributing to their lower achievement and underrepresentation. AIM This study examined whether heightened in-group representation alleviates the effects of stereotype threat on women's mathematical performance. It further investigated whether single-sex testing environments and stereotype threat influenced participants to believe that their ability was fixed (fixed mindset) rather than a trait that could be developed (growth mindset). SAMPLE AND METHOD One hundred and forty-four female participants were assigned randomly to a self-as-target or group-as-target stereotype threat condition or to a control condition. They completed a modular arithmetic maths test and a mindset questionnaire either alone or in same-sex groups of 3-5 individuals. RESULTS Participants solved fewer mathematical problems under self-as-target and group-as-target stereotype threat when they were tested alone, but these performance deficits were eliminated when they were tested in single-sex groups. Participants reported a weaker growth mindset when they were tested under stereotype threat and in single-sex groups. Moreover, evidence of inconsistent mediation indicated that single-sex testing environments negatively predicted mindset but positively predicted mathematical performance. CONCLUSIONS These findings suggest that single-sex testing environments may represent a practical intervention to alleviate stereotype threat effects but may have a paradoxical effect on mindset.
A Fast and Secure Elliptic Curve Based Authenticated Key Agreement Protocol For Low Power Mobile Communications

The increasing progress in wireless mobile communication has attracted an important amount of attention on the security issue. To provide secure communication for mobile devices, authenticated key agreement protocol is an important primitive for establishing session key. So far, several protocols have been proposed to provide robust mutual authentication and key establishment for wireless local area network (WLAN). In this paper we present a fast and secure authenticated key agreement (EC-SAKA) protocol based on elliptic curve cryptography. Our proposed protocol provides secure mutual authentication, key establishment and key confirmation over an untrusted network. The new protocol achieves many of the required security and performance properties. It can resist dictionary attacks mounted by either passive or active networks intruders. It can resist Man-In-The Middle attack. It also offers perfect forward secrecy which protects past sessions and passwords against future compromise. In addition, it can resist known- key and resilience to server attack. Our proposed protocol uses ElGamal signature techniques (ECEGS). We show that our protocol meets the above security attributes under the assumption that the elliptic curve discrete logarithm problem is secure. Our proposed protocol offers significantly improved performance in computational and communication load over comparably many authenticated key agreement protocols such as B-SPEKE, SRP, AMP, PAK-RY, PAK-X, SKA, LR-AKE and EC-SRP.
Divergent molecular mechanisms underlying the pleiotropic functions of macrophage inhibitory cytokine‐1 in cancer

Multifunctional macrophage inhibitory cytokine‐1, MIC‐1, is a member of the transforming growth factor‐β (TGF‐β) superfamily that plays key roles in the prenatal development and regulation of the cellular responses to stress signals and inflammation and tissue repair after acute injuries in adult life. The stringent control of the MIC‐1 expression, secretion, and functions involves complex regulatory mechanisms and the interplay of other growth factor signaling networks that control the cell behavior. The deregulation of MIC‐1 expression and signaling pathways has been associated with diverse human diseases and cancer progression. The MIC‐1 expression levels substantially increase in cancer cells, serum, and/or cerebrospinal fluid during the progression of diverse human aggressive cancers, such as intracranial brain tumors, melanoma, and lung, gastrointestinal, pancreatic, colorectal, prostate, and breast epithelial cancers. Of clinical interest, an enhanced MIC‐1 expression has been positively correlated with poor prognosis and patient survival. Secreted MIC‐1 cytokine, like the TGF‐β prototypic member of the superfamily, may provide pleiotropic roles in the early and late stages of carcinogenesis. In particular, MIC‐1 may contribute to the proliferation, migration, invasion, metastases, and treatment resistance of cancer cells as well as tumor‐induced anorexia and weight loss in the late stages of cancer. Thus, secreted MIC‐1 cytokine constitutes a new potential biomarker and therapeutic target of great clinical interest for the development of novel diagnostic and prognostic methods and/or cancer treatment against numerous metastatic, recurrent, and lethal cancers. J. Cell. Physiol. 224: 626–635, 2010. © 2010 Wiley‐Liss, Inc.
Lung Nodule Classi cation Based on Deep Convolutional Neural Networks in Chest X-Ray Images Classi cação de Nódulos Pulmonares Baseada em Redes Neurais Convolucionais Profundas

Lung cancer, which is characterized by the presence of nodules, is the most common type of cancer around the world, as well as one of the most aggressive and deadliest cancer, with 20% of total cancer mortality. Lung cancer screening can be performed by radiologists analyzing chest X-ray (CXR) images. However, the detection of lung nodules is a di cult task due to their wide variability, human limitations of memory, distraction and fatigue, among other factors. These di culties motivate the development of computer-aided diagnosis (CAD) systems for supporting radiologists in detecting lung nodules. Lung nodule classi cation is one of the main topics related to CAD systems. Although convolutional neural networks (CNN) have been demonstrated to perform well on many tasks, there are few explorations of their use for classifying lung nodules in CXR images. In this work, we proposed and analyzed a pipeline for detecting lung nodules in CXR images that includes lung area segmentation, potential nodule localization, and nodule candidate classi cation. We presented a method for classifying nodule candidates with a CNN trained from the scratch. The e ectiveness of our method relies on the selection of data augmentation parameters, the design of a specialized CNN architecture, the use of dropout regularization on the network, inclusive in convolutional layers, and addressing the lack of nodule samples compared to background samples balancing mini-batches on each stochastic gradient descent iteration. All model selection decisions were taken using a CXR subset of the Lung Image Database Consortium and Image Database Resource Initiative (LIDC/IDRI) dataset separately. Thus, we used all images with nodules in the Japanese Society of Radiological Technology (JSRT) dataset for evaluation. Our experiments showed that CNNs were capable of achieving competitive results when compared to state-of-the-art methods. Our proposal obtained an area under the free-response receiver operating characteristic (AUC) curve of 7.51 considering 10 false positives per image (FPPI), and a sensitivity of 71.4% and 81.0% with 2 and 5 FPPI, respectively.
A review on fault prognostics in integrated health management

Integrated Health Management (IHM) is an advanced technology which integrated artificial intelligence with advanced test and information technologies. Having gone through fault detection, isolation and reconfiguration and immerged with the state of arts reasoning technologies, IHM monitors and controls the function of critical systems and components in order to ensure safe and efficient operation. An IHM system usually comprises seven functional modules, namely data acquisition, signal/feature extraction, condition assessment, diagnostics, prognostics, decision reasoning and human interface. Among them, fault prognostics are not only the core of IHM, but also an important guarantee to reduce the costs of life-cycle maintenance, and to improve system security. Fault prognostics is the process to project the current health state of equipment into the future taking into account estimates of future usage profiles. It may report health status at a future time, or may estimate the remaining useful lifetime (RUL) of a machine given its projected usage profile. In recent years, fault prognostics are under unprecedented attentions. And it is becoming the most challenging research area which is so-called crystal ball of IHM. Based on the theory, methods and routes adopted in the practical application, fault prognostics is generally fallen into three main categories, namely model-based approaches, knowledge-based approaches and data-based approaches. Then, based on the analysis of some typical applications on each approaches, the strengths and weaknesses of each approach are further discussed. Finally, according to the current research situation at home and abroad, the future development trend of fault prognostics is also presented.
IL-21 Is Important for Induction of KLRG1+ Effector CD8 T Cells during Acute Intracellular Infection

Microsporidia, a latent opportunistic infection associated with mild inflammation, is characterized by a strong CD8 T cell response, which has been shown to be CD4 T cell dependent. In this manuscript, we demonstrate that CD4 help is provided via IL-21 production, a common γ-chain cytokine closely related to IL-2. The peak of IL-21 expression, observed during the acute infection, is associated with an elevated IL-21+ CD4 T subset, and these cells bear a phenotypic resemblance to T follicular helper cells. We observed that, during per-oral microsporidial infection, IL-21 was critical for the generation of an optimal effector CD8 T cell immunity. Sharply decreased effector KLRG1+ CD8 response was observed in IL-21R knockout mice, and although these cells exhibited reduced functional properties, they retained the ability to proliferate. The role of IL-21 in the generation of CD8 effectors was cell intrinsic, as stronger defects were observed in the IL-21–deficient compartment from the bone marrow chimeric mice (IL-21R knockout/wild-type). These findings are different from those reported for viral infections in which IL-21 has been primarily associated with the generation and maintenance of CD8 memory response. To the best of our knowledge, this report demonstrates a critical role for IL-21 in the generation of a primary effector CD8 T cell response to an infectious disease model.
Differential effects of specific phosphodiesterase isoenzyme inhibitors on bovine oocyte meiotic maturation.

The differential regulation of cAMP levels within the oocyte and somatic (cumulus) cell compartments of the bovine follicle, and the subsequent regulation of oocyte meiotic maturation was examined through specific cell-type localisation of phosphodiesterases (PDEs). Selective PDE inhibitors were used to modulate cAMP levels in each of the two follicular compartments and to examine their effects on oocyte meiotic maturation. Ovaries were obtained from an abattoir and cumulus-oocyte complexes (COC) were aspirated from antral follicles into culture medium supplemented with 4 mg/ml BSA and 2mM 3-isobutyl-1-methylxanthine (IBMX). COC, denuded oocytes (DO), or mural granulosa cells (MGC) were cultured either with or without forskolin or FSH, in the presence of specific PDE inhibitors; either milrinone (PDE3 inhibitor), cilostamide (PDE3 inhibitor), or rolipram (PDE4 inhibitor). COC/DO cultures were assessed for meiotic progression and cAMP content, and MGC for cAMP production. The type 3 PDE inhibitor, but not the type 4, prevented spontaneous meiotic maturation and elevated intraoocyte cAMP in cultured denuded oocytes. In contrast, the type 4 PDE inhibitor had no effect on the oocyte, but elevated mural granulosa and cumulus cell cAMP production. The results of this study indicate that specific PDE subtypes are differentially localised within the two compartments of the bovine follicle-the type 3 PDE in the oocyte and the type 4 PDE in the granulosa cells. In addition, oocyte cAMP levels are primarily regulated in bovine oocytes by its degradation by PDE, whereas granulosa cell cAMP levels are controlled mainly by active adenylate cyclase, with both sources able to participate in oocyte meiotic regulation.
Cooperative Estimation via Altruism

A novel approach, based on the notion of altruism, is presented to cooperative estimation in a system comprising two information-sharing estimators. The underlying assumption is that the system’s global mission can be accomplished even if only one of the estimators achieves satisfactory performance. The notion of altruism motivates a new definition of cooperative estimation optimality that generalizes the common definition of minimum mean square error optimality. Fundamental equations are derived for two types of altruistic cooperative estimation problems, corresponding to heterarchical and hierarchical setups. Although these equations are hard to solve in the general case, their solution in the Gaussian case is straightforward and only entails the largest eigenvalue of the conditional covariance matrix and its corresponding eigenvector. Moreover, in that case the performance improvement of the two altruistic cooperative estimation techniques over the conventional (egoistic) estimation approach is shown to depend on the problem’s dimensionality and statistical distribution. In particular, the performance improvement grows with the dispersion of the spectrum of the conditional covariance matrix, rendering the new estimation approach especially appealing in ill-conditioned problems. The performance of the new approach is demonstrated using a numerical simulation study.
Cholesterol‐rich lipid rafts are involved in neuropeptide FF anti‐nociceptin/orphanin FQ effect

The participation of a signaling platform to the anti‐nociceptin/orphanin FQ (N/OFQ) effect of neuropeptide FF (NPFF) receptors was investigated in both acutely dissociated neurons and SH‐SY5Y human neuroblastoma cells. The NPFF anti‐N/OFQ, not anti‐μ opioid effect, on the Ca2+ transient triggered by depolarization was reversed by methyl‐β‐cyclodextrin which depletes cholesterol from cell membranes. While the inactive α‐cyclodextrin had no effect. By using [35S]GTPγS binding assay, a significant 20% decrease in the activity of nociceptin/orphanin FQ peptide receptors induced by the NPFF analog 1DMe was observed in detergent‐resistant membranes, but not in total membranes of SH‐SY5Y cells. Moreover, siRNA knock‐down of G‐protein‐coupled receptor kinase 2 indicated that G‐protein‐coupled receptor kinase 2, but not protein kinase C, acted as the mediator in the NPFF anti‐N/OFQ process. These data indicate that cholesterol‐rich lipid rafts play an important role in the anti‐N/OFQ effect of NPFF receptors.
Epitope Mapping of Anti-MUC1 Mucin Protein Core Monoclonal Antibodies

A panel of 56 murine monoclonal antibodies against the MUC1 mucin was analysed for reactivity against purified MUC1 mucin and synthetic MUC1 mucin protein core-related peptides. In an ELISA assay, with purified normal urinary mucin as the target antigen, 48/56 (86%) of antibodies showed positive reactivity. A smaller proportion of antibodies, 31/56 (55%), reacted with a bovine serum albumin conjugate containing the synthetic peptide, APDTRPAPG. This peptide represents the hydrophilic region of the tandem repeat sequence of the MUC1 mucin core. These 31 anti-mucin core antibodies were then evaluated for reactivity with a set of overlapping heptamers with sequences based upon that of the 20-amino acid tandem repeat of the MUC1 protein core. For this purpose, the ‘Pepscan’ procedure was employed to detect antibody binding to peptides tethered at their carboxy termini to the polypropylene pins. Synthetic peptides binding to these antibodies were identified for 29 of the samples provided and epitopes or ‘minimum binding units’ were deduced for these. Most antibodies bound to epitopes of 4 amino acid residues with the sequence RPAP occurring most frequently.The results confirm that the short hydrophilic region PDTRPAP in the MUC1 mucin core is immunodominant in the induction of antibodies to the MUC1 mucin since half of the antibodies submitted reacted with this peptide.
Anti-Trypanosoma cruzi Immunoglobulin G1 Can Be a Useful Tool for Diagnosis and Prognosis of Human Chagas' Disease

ABSTRACT Two functionally distinct antibodies, categorized as conventional serology antibodies (CSA) and lytic antibodies (LA) have been described in Chagas' disease, based on their ability to bind to fixed epimastigotes (EPI) or live trypomastigotes (TRYPO), respectively. In this study, the profile of immunoglobulin G (IgG) subclasses of CSA and LA were analyzed by flow cytometry using serum samples from chronic chagasic patients with the indeterminate (IND), cardiac (CARD), and digestive (DIG) clinical forms of the disease. The results were expressed as percentage of positive fluorescent parasites (PPFP) for each sample. CSA showed a higher PPFP than LA for all samples. At serum dilutions between 1:256 and 1:2,048, IgG1 anti-EPI was able to distinguish chagasic from nonchagasic individuals. Different profiles of IgG subclasses were observed for CSA and LA. IgG1 and IgG2 were the main subclasses in CSA, whereas IgG1 and IgG3 were the predominant ones in LA. The reactivity of IgG2 anti-EPI was greater in IND and CARD than in DIG patients. Furthermore, a low level of IgG1 and IgG3 LA was associated with most of the CARD patients. On the other hand, a high level of IgG1 LA was associated with most of the IND patients. In summary, our findings indicate the potential of IgG1 anti-EPI for serological diagnosis of Chagas' disease, providing further evidence for a protective role of LA, and show that IgG1 anti-liveTrypanosoma cruzi TRYPO may be used to predict the risk of cardiac damage in Chagas' disease.