Miracle-dz/UniFAR-FTUs huggingface dataset:
mTORC1-Activated S6K1 Phosphorylates Rictor on Threonine 1135 and Regulates mTORC2 Signaling

ABSTRACT The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes important for nutrient and growth factor signaling. While mTOR complex 1 (mTORC1) regulates mRNA translation and ribosome biogenesis, mTORC2 plays an important role in the phosphorylation and subsequent activation of Akt. Interestingly, mTORC1 negatively regulates Akt activation, but whether mTORC1 signaling directly targets mTORC2 remains unknown. Here we show that growth factors promote the phosphorylation of Rictor (rapamycin-insensitive companion of mTOR), an essential subunit of mTORC2. We found that Rictor phosphorylation requires mTORC1 activity and, more specifically, the p70 ribosomal S6 kinase 1 (S6K1). We identified several phosphorylation sites in Rictor and found that Thr1135 is directly phosphorylated by S6K1 in vitro and in vivo, in a rapamycin-sensitive manner. Phosphorylation of Rictor on Thr1135 did not affect mTORC2 assembly, kinase activity, or cellular localization. However, cells expressing a Rictor T1135A mutant were found to have increased mTORC2-dependent phosphorylation of Akt. In addition, phosphorylation of the Akt substrates FoxO1/3a and glycogen synthase kinase 3α/β (GSK3α/β) was found to be increased in these cells, indicating that S6K1-mediated phosphorylation of Rictor inhibits mTORC2 and Akt signaling. Together, our results uncover a new regulatory link between the two mTOR complexes, whereby Rictor integrates mTORC1-dependent signaling.
Synthesizing Fast Intrusion Prevention/Detection Systems from High-Level Specifications

To build survivable information systems (i.e., systems that continue to provide their services in spite of coordinated attacks), it is necessary to detect and isolate intrusions before they impact system performance or functionality. Previous research in this area has focussed primarily on detecting intrusions after the fact, rather than preventing them in the first place. We have developed a new approach based on specifying intended program behaviors using patterns over sequences of system calls. The patterns can also capture conditions on the values of system-call arguments. At runtime, we intercept the system calls made by processes, compare them against specifications, and disallow (or otherwise modify) those calls that deviate from specifications. Since our approach is capable of modifying a system call before it is delivered to the operating system kernel, it is capable of reacting before any damage-causing system call is executed by a process under attack. We present our specification language and illustrate its use by developing a specification for the ftp server. Observe that in our approach, every system call is intercepted and subject to potentially expensive operations for matching against many patterns that specify normal/abnormal behavior. Thus, minimizing the overheads incurred for pattern-matching is critical for the viability of our approach. We solve this problem by developing a new, low-overhead algorithm for matching runtime behaviors against specifications. A salient feature of our algorithm is that its runtime is almost independent of the number of patterns. In most cases, it uses a constant amount of time per system call intercepted, and uses a constant amount of storage, both independent of either the size or number of patterns. These benefits make our algorithm useful for many other intrusion detection methods that employ pattern-matching. We describe our algorithm, and evaluate its performance through experiments.
Airway hyperresponsiveness in asthma: not just a matter of airway inflammation

According to the most recent definition, bronchial asthma is a chronic inflammatory disorder of the airways associated with reversible airway obstruction and increased airway responsiveness to a variety of stimuli.1 An intuitive inference from this definition is that a causal relationship may exist between airway inflammation and airway hyperresponsiveness. Along this line of reasoning, most of the research in the last two decades in this field was aimed at identifying inflammatory cell products possibly responsible for the pathogenesis of bronchial asthma and airway hyperresponsiveness.2 However, the common observation that the asthmatic airways are equally hyperresponsive to a variety of different stimuli does challenge the idea that a single inflammatory cell or mediator may be central to the pathogenesis of asthma and airway hyperresponsiveness and focuses on the importance of an altered mechanical response of the target organ. This view has been recently corroborated by the finding that airway responsiveness of normal individuals may become similar to that of asthmatics by simply changing the pattern of breathing during the bronchial challenge.3It is therefore legitimate to wonder how much of airway hyperresponsiveness is due to inflammation or to inherent predisposing factors. The aims of the present review are to show that airway narrowing in asthma is the ultimate result of an interaction between complex and multiple mechanisms not necessarily and uniquely related to airway inflammation, and to revisit the evidence on which the theorem “airway inflammation equal to airway hyperresponsiveness” has been constructed. Airway calibre in vivo is the result of a delicate balance between the force generated by the airway smooth muscle (ASM) and a number of opposing factors.4 The latter are mainly represented by autonomic mechanisms that tend to limit the ASM tone and by mechanical forces that oppose ASM shortening. ### AIRWAY SMOOTH MUSCLE (ASM) Although it is widely …
Peak experiences in nature: implications for psychological well-being and environmental behaviour

The aim of the research presented here was to investigate the relevance of ecopsychology principles for contemporary counselling psychology; specifically, whether peak experiences in nature may lead to greater psychological well-being and more environmental behaviours. Theory and research from a variety of different fields that informed a better understanding of the associations and outcomes of peak experiences in nature were carefully considered. The method includes a quantitative survey design with 305 participants who responded to measures of contact with nature, mystical experiences in natural and human-built environments, psychological well-being, and environmental behaviour. Twenty semi-structured interviews were also completed, where participants were asked about the qualities and outcomes of their significant experiences in natural and human-built settings. Quantitative data analysis revealed significant relationships between mystical experiences in nature, psychological well-being, and environmental behaviour, with differences in the strength of these relationships according to gender and religious affiliation. Qualitative analysis suggested that spiritual and peak experiences in nature may lead to long-term psychological well-being as a consequence of changes in self and personality, the formation of vivid memories that could be drawn upon in the present, and increased contact with nature. Interview participants also discussed a desire to protect and care for environments that were able to elicit significant affective experiences. Implications for contemporary ecopsychology, counselling psychology, and urban design are discussed.
ParCube

How can we efficiently decompose a tensor into sparse factors, when the data do not fit in memory? Tensor decompositions have gained a steadily increasing popularity in data-mining applications; however, the current state-of-art decomposition algorithms operate on main memory and do not scale to truly large datasets. In this work, we propose ParCube, a new and highly parallelizable method for speeding up tensor decompositions that is well suited to produce sparse approximations. Experiments with even moderately large data indicate over 90% sparser outputs and 14 times faster execution, with approximation error close to the current state of the art irrespective of computation and memory requirements. We provide theoretical guarantees for the algorithm’s correctness and we experimentally validate our claims through extensive experiments, including four different real world datasets (Enron, Lbnl, Facebook and Nell), demonstrating its effectiveness for data-mining practitioners. In particular, we are the first to analyze the very large Nell dataset using a sparse tensor decomposition, demonstrating that ParCube enables us to handle effectively and efficiently very large datasets. Finally, we make our highly scalable parallel implementation publicly available, enabling reproducibility of our work.
Expression of growth hormone receptor and its mRNA in hepatic cirrhosis.

AIM To investigate the expression of growth hormone receptor (GHR) and mRNA of GHR in cirrhotic livers of rats with the intension to find the basis for application of recombinant human growth hormone (rhGH) to patients with liver cirrhosis. METHODS Hepatic cirrhosis was induced in Sprague-Dawley rats by administration of thioacetamide intraperitoneally for 9-12 weeks. Collagenase IV was perfused in situ for isolation of hepatocytes. The expression of GHR and its mRNA in cirrhotic livers was studied with radio-ligand binding assay, RT-PCR and digital image analysis. RESULTS One class of specific growth hormone-binding site, GHR, was detected in hepatocytes and hepatic tissue of cirrhotic livers. The binding capacity of GHR (R(T), fmol/mg protein) in rat cirrhotic liver tissue (30.8+/-1.9) was significantly lower than that in normal control (74.9+/-3.9) at the time point of the ninth week after initiation of induction of cirrhosis (n=10, P<0.05), and it decreased gradually along with the accumulation of collagen in the process of formation and development of liver cirrhosis (P<0.05). The number of binding sites (X10(4)/cell) of GHR on rat cirrhotic hepatocytes (0.86+/-0.16) was significantly lower than that (1.28+/-0.24) in control (n=10, P<0.05). The binding affinity of GHR among liver tissue, hepatocytes of various groups had no significant difference (P>0.05). The expression of GHR mRNA (riOD, pixel) in rat cirrhotic hepatic tissues (23.3+/-3.1) was also significantly lower than that (29.3+/-3.4) in normal control (n=10, P<0.05). CONCLUSION The growth hormone receptor was expressed in a reduced level in liver tissue of cirrhotic rats, and lesser expression of growth hormone receptors was found in a later stage of cirrhosis. The reduced expression of growth hormone receptor was partly due to its decreased expression on cirrhotic hepatocytes and the reduced expression of its mRNA in cirrhotic liver tissue.
Famílias fumicultoras no sul do Brasil: situação econômica dos associados à Associação dos Fumicultores do Brasil (Afubra)

this article is the result of a survey involving 1,200 family farmers in southern Brazil from a demand of the Tobacco Growers Association of Brazil to meet the socioeconomic profile of its members. The information presented here concern the economic aspects of the properties, highlighting the issues of debt, productive activities, consumption and income earned. Family farming in southern Brazil is directly linked to tobacco production and the analysis of other activities by producers is a key to the establishment of alternatives for agricultural production diversification that is now being gestated in that region. It was found that just over 60% of farmers interviewed had declared his situation as stable, but only 29.3% have no debt. Among the others, more than half have debt on costing and nearly 75% have debts relating to investments in property. Involvement of tobacco in total income of the properties is on average 68.59%. It should be noted, however, that the participation of tobacco on the revenue actually received (disregarding their own consumption and production of animal origin) is significantly higher.
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser

MOTIVATION Text-mining research in the biomedical domain has been motivated by the rapid growth of new research findings. Improving the accessibility of findings has potential to speed hypothesis generation. RESULTS We present the Arizona Relation Parser that differs from other parsers in its use of a broad coverage syntax-semantic hybrid grammar. While syntax grammars have generally been tested over more documents, semantic grammars have outperformed them in precision and recall. We combined access to syntax and semantic information from a single grammar. The parser was trained using 40 PubMed abstracts and then tested using 100 unseen abstracts, half for precision and half for recall. Expert evaluation showed that the parser extracted biologically relevant relations with 89% precision. Recall of expert identified relations with semantic filtering was 35 and 61% before semantic filtering. Such results approach the higher-performing semantic parsers. However, the AZ parser was tested over a greater variety of writing styles and semantic content. AVAILABILITY Relations extracted from over 600 000 PubMed abstracts are available for retrieval and visualization at http://econport.arizona. edu:8080/NetVis/index.html.
Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans.

We surveyed nucleotide variation at vermilion in population samples of Drosophila melanogaster from Africa, Asia and the Americas to test the hypothesis that the vermilion gene was a target of balancing selection and to improve our understanding of geographic differentiation. Patterns of polymorphism and divergence showed no evidence for non-neutral evolution. However, the frequency spectrum of polymorphic sites in some non-African samples departed from the neutral equilibrium expectation. Furthermore, there were high levels of linkage disequilibrium in non-African samples, despite apparently high rates of crossing over in the vermilion region. In the absence of comparable data from other loci in these same population samples, we cannot determine whether the unusual patterns of variation at vermilion reflect demographic as opposed to locus-specific events. We found surprisingly high levels of differentiation at vermilion between U.S. and Congo samples of D. simulans. In light of previously published allozyme and mtDNA data that provided no evidence for significant differentiation between African and non-African D. simulans populations, the vermilion data raise the possibility that both mtDNA and allozymes have been influenced by selection.
Benign and malignant phyllodes tumors: mammographic and sonographic findings.

PURPOSE To characterize imaging findings that suggest the benign or malignant histologic nature of phyllodes tumors. MATERIALS AND METHODS Clinical and imaging findings were retrospectively reviewed in 46 women with 51 phyllodes tumors (32 benign, 19 malignant) identified at preoperative mammography. Thirty of these tumors were also evaluated with preoperative sonography. RESULTS Mammography showed nonspiculated soft-tissue masses in 49 tumors. Four masses contained calcifications; three of these masses were benign. The tumors were 1-20 cm in diameter; tumors 3 cm or larger were statistically significantly more likely to be malignant (P < .004). Sonography showed solid, hypoechoic masses in 28 cases. At sonography, cystic areas were more often seen in malignant than in benign tumors, but the difference was not statistically significant. CONCLUSION There is substantial overlap in the imaging characteristics of benign and malignant phyllodes tumors. A tumor diameter of 3 cm or greater appears to be associated with a higher likelihood of malignancy.
Block diagonalization eigenvalue based beamforming precoding design for downlink capacity improvement in multiuser MIMO channel

In order to fully benefit from multiple-input multiple-output (MIMO) channels, multiuser techniques are adopted in the 3rd generation partner project (3GPP) long term evolution (LTE) downlink system. The core task of multiuser MIMO system is to suppress multiuser interference and enhance the signal to interference plus noise ratio (SINR). As a classical MIMO scheme, block diagonalization (BD) algorithm could eliminate the multiuser interference completely. Unfortunately, it also reduces the desired receive power and then has capacity loss especially at low signal to noise ratio (SNR). On the other extreme, eigenvalue based beamforming (EBB) maximizes the useful power of receive signals and takes no action to depress multiuser interference making it an interference limited system with high SNRs. Based on such observations, this paper proposes an appropriate combination of the above two schemes. In order to reduce the computing complexity of the proposed scheme, we present an alternative algorithm named as interference sorting (IS). Simulations over spatial channel model (SCM) are carried out with framework of 3GPP LTE technical specifications. It is verified that proposed scheme leads to a remarkable capacity improvement both with low and high SNRs. And the IS algorithm could reduce the complexity of system significantly with indistinguishable performance loss.
Discrete Time Estimation of the Mean Doppler Frequency in Ultrasonic Blood Velocity Measurements

A new Doppler frequency estimator operating in the discrete time domain is derived from an analysis of the Doppler signal statistics. It is shown that the estimator gives a nearly unbiased estimate of the mean frequency of the signal spectrum, regardless of the spectrum shape. The discrete time implementation gives the advantage that, under specified conditions, the range-velocity product of a pulsed Doppler velocity meter can be increased.
Evidence for abnormal cortical functional connectivity during working memory in schizophrenia.

OBJECTIVE Disturbed neuronal interactions may be involved in schizophrenia because it is without clear regional pathology. Aberrant connectivity is further suggested by theoretical formulations and neurochemical and neuroanatomical data. The authors applied to schizophrenia a recently available functional neuroimaging analytic method that permits characterization of cooperative action on the systems level. METHOD Thirteen medication-free patients and 13 matched healthy comparison subjects performed a working memory (n-back) task and sensorimotor baseline task during positron emission tomography. "Functional connectivity" patterns, reflecting distributed correlated activity that differed most between groups, were extracted by a canonical variates analysis. RESULTS More than half the variance was explained by a single pattern showing inferotemporal, (para-)hippocampal, and cerebellar loadings for patients versus dorsolateral prefrontal and anterior cingulate activity for comparison subjects. Expression of this pattern perfectly separated all patient scans from comparison scans, thus showing promise as a trait marker. This result was validated prospectively by successfully classifying unrelated scans from the same patients and data from a new cohort. An additional 19% of variance corresponded to the pattern activated by the working memory task. Expression of this pattern was more variable in patients during working memory but not the control condition, suggesting inability to sustain a task-adequate neural network, consistent with the disconnection hypothesis. CONCLUSIONS Pronounced disruptions of distributed cooperative activity in schizophrenia were found. A pattern showing disturbed frontotemporal interactions showed promise as a trait marker and may be useful for future investigations.
Novel and conventional serum biomarkers predicting acute kidney injury in adult cardiac surgery—A prospective cohort study*

Objective:To compare the value of novel with conventional serum biomarkers in the prediction of acute kidney injury (AKI) in adult cardiac surgical patients according to preoperative renal function. Design:Single-center, prospective observational study. Setting:Tertiary hospital. Patients:One hundred adult cardiac surgical patients. Measurements and Main Results:We measured concentrations of plasma neutrophil gelatinase-associated lipocalin (NGAL), and serum cystatin C, and creatinine and urea at baseline, on arrival in the intensive care unit (ICU) and at 24 hours postoperatively. We assessed such biomarkers in relation to the development of AKI (>50% increase in creatinine from baseline) and to a composite end point (need for renal replacement therapy and in-hospital mortality). We defined an area under the receiver operating characteristic curve of 0.60–0.69 as poor, 0.70–0.79 as fair, 0.80–0.89 as good, and 0.90–1.00 as excellent in terms of predictive value. On arrival in ICU, plasma NGAL and serum cystatin C were of good predictive value, but creatinine and urea were of poor predictive value. After exclusion of patients with preoperative renal impairment (estimated glomerular filtration rate <60 mL/min), the predictive performance for AKI of all renal biomarkers on arrival in ICU remained unchanged except for cystatin C, which was of fair value in such patients. At 24 hours postoperatively, all renal biomarkers were of good predictive value. On arrival in ICU, novel biomarkers were superior to conventional biomarkers (p < 0.05). Plasma NGAL (p = 0.015) and serum cystatin C (p = 0.007) were independent predictors of AKI and of excellent value in the prediction of the composite end point. Conclusions:Early postoperative measurement of plasma NGAL was of good value in identifying patients who developed AKI after adult cardiac surgery. Plasma NGAL and serum cystatin C were superior to conventional biomarkers in the prediction of AKI and were also of prognostic value in this setting.
Lessons from sudden coronary death: a comprehensive morphological classification scheme for atherosclerotic lesions.

This review will reconsider the current paradigm for understanding the critical, final steps in the progression of atherosclerotic lesions. That scheme, largely an outgrowth of observations of autopsy tissues by Davies and colleagues,1 2 asserts that the cause of death in atherosclerotic coronary artery disease is rupture of an advanced atherosclerotic lesion. Although this assumption may be partially true, recent autopsy studies suggest that it is incomplete. To reconsider this paradigm, we reexamined the morphological classification scheme for lesions proposed by the American Heart Association (AHA). 3 4 This scheme is difficult to use for 2 reasons. First, it uses a very long list of roman numerals modified by letter codes that are difficult to remember. Second, it implies an orderly, linear pattern of lesion progression. This tends to be ambiguous, because it is not clear whether there is a single sequence of events during the progression of all lesions. We have therefore tried to devise a simpler classification scheme that is consistent with the AHA categories but is easier to use, able to deal with a wide array of morphological variations, and not overly burdened by mechanistic implications. The current paradigm is based on the belief that type IV lesions, or “atheromas,” described by the AHA are stable because the fatty, necrotic core is contained by a smooth muscle cell–rich fibrous cap. Virchow’s analysis5 in 1858 pointed out that historically, the term “atheroma” refers to a dermal cyst (“Grutzbalg”), a fatty …