Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperature-dependent growth kinetics of Escherichia coli ML 30 in glucose-limited continuous culture

Detailed comparison of growth kinetics at temperatures below and above the optimal temperature was carried out with Escherichia coli ML 30 (DSM 1329) in continuous culture. The culture was grown with glucose as the sole limiting source of carbon and energy (100 mg liter(-1) in feed medium), and the resulting steady-state concentrations of glucose were measured as a function of the dilution rate at 17.4, 28.4, 37, and 40 degrees C. The experimental data could not be described by the conventional Monod equation over the entire temperature range, but an extended form of the Monod model [mu = mu(max) x (s - s(min))/(Ks + s - s(min))], which predicts a finite substrate concentration at 0 growth rate (s(min)), provided a good fit. The two parameters mu(max) and s(min) were temperature dependent, whereas, surprisingly, fitting the model to the experimental data yielded virtually identical Ks values (approximately 33 microg liter(-1)) at all temperatures. A model that describes steady-state glucose concentrations as a function of temperature at constant growth rates is presented. In similar experiments with mixtures of glucose and galactose (1:1 mixture), the two sugars were utilized simultaneously at all temperatures examined, and their steady-state concentrations were reduced compared with to growth with either glucose or galactose alone. The results of laboratory-scale kinetic experiments are discussed with respect to the concentrations observed in natural environments.
Pro-survival Effects of 17β-Estradiol on Osteocytes Are Mediated by Nitric Oxide/cGMP via Differential Actions of cGMP-dependent Protein Kinases I and II*

Background: Estrogens prevent bone loss in part by preventing osteocyte apoptosis. Results: Anti-apoptotic effects of 17β-estradiol in osteocytes require NO/cGMP-mediated stimulation of Akt and Akt- and cGMP-dependent protein kinase (PKG)-dependent phosphorylation of BAD. Conclusion: PKG types I and II serve independent anti-apoptotic functions in 17β-estradiol-treated osteocytes, converging on BAD. Significance: These novel mechanisms of 17β-estradiol-mediated bone protection provide a rationale for developing NO/cGMP-based therapies for osteoporosis. Estrogens promote bone health in part by increasing osteocyte survival, an effect that requires activation of the protein kinases Akt and ERK1/2, but the molecular mechanisms involved are only partly understood. Because estrogens increase nitric oxide (NO) synthesis and NO can have anti-apoptotic effects, we examined the role of NO/cGMP signaling in estrogen regulation of osteocyte survival. Etoposide-induced death of MLO-Y4 osteocyte-like cells, assessed by trypan blue staining, caspase-3 cleavage, and TUNEL assays, was completely prevented when cells were pre-treated with 17β-estradiol. This protective effect was mimicked when cells were pre-treated with a membrane-permeable cGMP analog and blocked by pharmacological inhibitors of NO synthase, soluble guanylate cyclase, or cGMP-dependent protein kinases (PKGs), supporting a requirement for NO/cGMP/PKG signaling downstream of 17β-estradiol. siRNA-mediated knockdown and viral reconstitution of individual PKG isoforms demonstrated that the anti-apoptotic effects of estradiol and cGMP were mediated by PKG Iα and PKG II. Akt and ERK1/2 activation by 17β-estradiol required PKG II, and cGMP mimicked the effects of estradiol on Akt and ERK, including induction of ERK nuclear translocation. cGMP induced BAD phosphorylation on several sites, and experiments with phosphorylation-deficient BAD mutants demonstrated that the anti-apoptotic effects of cGMP and 17β-estradiol required BAD phosphorylation on Ser136 and Ser155; these sites were targeted by Akt and PKG I, respectively, and regulate BAD interaction with Bcl-2. In conclusion, 17β-estradiol protects osteocytes against apoptosis by activating the NO/cGMP/PKG cascade; PKG II is required for estradiol-induced activation of ERK and Akt, and PKG Iα contributes to pro-survival signaling by directly phosphorylating BAD.
Developing a test program for the DoD 2400 bps vocoder selection process

The scores from a test program often receive close scrutiny when used for the selection of a vocoder algorithm. However, the test program itself is equally important to the proper evaluation and selection of a vocoder. It must translate user requirements into test procedures and test conditions that ensure the selected vocoder performs adequately. Furthermore, since the test program defines a significant portion of the evidence that will be used to make a selection, the integrity of the selection relies heavily on the structure of the test program. The test program is also constrained by finite resources of time, money, and personnel. In 1995, the DoD Digital Voice Processing Consortium (DDVPC) created a test program for the purpose of selecting a new 2400 bps federal standard vocoder. This test program demonstrated a process of selecting proper test methods and defining proper test conditions to assess required performance, complexity and implementation requirements. This paper discusses the motivation for the structure of the 1995 test program and provides a description of the actual test.
Molecular Predictors of Response to Chemotherapy in Non-Small Cell Lung Cancer

Lung cancer is the leading cause of cancer-related mortality in the United States with 222,520 new cases and 157,300 deaths anticipated in 2010. The primary objective of any cancer treatment is to improve patient outcomes including overall survival and quality of life while minimizing treatment toxicity. As our knowledge of the molecular mechanisms involved in the pathogenesis of lung cancer evolves, improved methods of therapeutic selection may help clinicians better realize these goals. Such selection may be accomplished by examining biomarkers within patients' tumors that may provide prognostic information such as risk of recurrence in early stage disease or predict benefit from specific therapies regardless of disease stage. Three such biomarkers have emerged-excision repair cross-complementation group 1, the regulatory subunit of the ribonucleotide reductase enzyme, and thymidylate synthase-and are actively being evaluated in patients with non-small cell lung cancer. This review will focus on the role of these biomarkers as predictive and/or prognostic markers in the selection of chemotherapy regimens in non-small cell lung cancer patients.
Drifting Toward Invisibility: The Transition to the Electronic Task Board

The task board is one of the most important information radiators used by an agile team to track their progress. When teams make the transition to using electronic team tracking tools, they often stop using the physical information radiators such as the task board. This transition from using a physical tool to an electronic tool can have unintended side effects for teams. In this experience report, the focus is on sharing the problems teams can encounter with transparency if they do not manage the transition to electronic tools well. We discuss the implications for agile development teams along with the strengths and weaknesses of physical and electronic information radiators.
An Efficient Searchable Encryption Scheme using Multi-Indices in Cloud Computing Environments

A Searchable Encryption System enables the clients to search encrypted keywords without compromising the security of the original data. Also, malicious users are able to take advantage of the Searchable Encryption Systems. At the same time, however, they can impose overloads to the system using a Brute force attack. As a result, it could be exposed through retrieving the critical information such as keys and generating huge amount of false queries. Therefore, we propose a novel Searchable Encryption Scheme based on multi-indices by Bloom filter to deal with Brute force attacks efficiently.
Title Determining the directional contact range of two convexpolyhedra

The directional contact range of two convex polyhedra is the range of positions that one of the polyhedron may locate along a given straight line so that the two polyhedra are in collision. Using the contact range, one can quickly classify the positions along a line for a polyhedron as “safe” for free of collision with another polyhedron, or “unsafe” for the otherwise. This kind of contact detection between two objects is important in CAD, computer graphics and robotics applications. In this paper we propose a robust and efficient computation scheme to determine the directional contact range of two polyhedra. We consider the problem in its dual equivalence by studying the Minkowski difference of the two polyhedra under a duality transformation. The algorithm requires the construction of only a subset of the faces of the Minkowski difference, and resolves the directional range efficiently. It also computes the contact configurations when the boundaries of the polyhedra are in contact.
Gait Development On A Direct Drive , Quadrupedal Robot

The development of dynamic, quadrupedal robots is becoming an increasing topic of interest with the growing demand for robotic interaction in the human environment, but they require adaptable control schemes to address the challenges encountered while traversing real world terrains. In this study, we explore improvements to both physical and control methods to a quadrupedal system in order to achieve fast, stable walking and trotting gaits. This analysis includes an investigation of physical compliance, 5-bar kinematics for trajectory shaping, and the implementation of ground and obstacle contact sensing. Structural and mechanical improvements were made to reduce undesired compliance to generate faster, more stable gaits. Contact sensing was implemented for identifying obstacles and deviations in surface level for negotiation of varying terrain. Overall, the incorporation of these features greatly enhances the mobility of the dynamic quadrupedal robot and helps to establish a basis for overcoming obstacles.
Measures of the DSM–5 mixed-features specifier of major depressive disorder

During the past two decades, a number of studies have found that depressed patients frequently have manic symptoms intermixed with depressive symptoms. While the frequency of mixed syndromes are more common in bipolar than in unipolar depressives, mixed states are also common in patients with major depressive disorder. The admixture of symptoms may be evident when depressed patients present for treatment, or they may emerge during ongoing treatment. In some patients, treatment with antidepressant medication might precipitate the emergence of mixed states. It would therefore be useful to systematically inquire into the presence of manic/hypomanic symptoms in depressed patients. We can anticipate that increased attention will likely be given to mixed depression because of changes in the DSM–5. In the present article, I review instruments that have been utilized to assess the presence and severity of manic symptoms and therefore could be potentially used to identify the DSM–5 mixed-features specifier in depressed patients and to evaluate the course and outcome of treatment. In choosing which measure to use, clinicians and researchers should consider whether the measure assesses both depression and mania/hypomania, assesses all or only some of the DSM–5 criteria for the mixed-features specifier, or assesses manic/hypomanic symptoms that are not part of the DSM–5 definition. Feasibility, more so than reliability and validity, will likely determine whether these measures are incorporated into routine clinical practice.
Linkage between EGFR family receptors and nuclear factor kappaB (NF‐κB) signaling in breast cancer

In the United States there are 225,000 new cases of invasive breast cancer annually, and at least 50,000 women are diagnosed with ductal carcinoma in situ (DCIS). Breast cancer is a collection of disorders of mammary epithelial cells with distinct pathological characteristics and diverse clinical manifestations. Breast cancers are divided broadly into four classes by the level of the biomarkers HER2 (erbB2/neu) and the estrogen receptor (ER). Histologic grade is also an important modifier of breast cancer taxonomy and behavior. Broadly speaking, breast cancer can be divided into those that are HER2‐positive, containing cancers that are both ER‐positive and negative, cancers that are ER‐positive and divided into high‐grade and low‐grade tumors, and the remaining but important class of cancers that are both ER‐negative and HER2‐negative. These last cancers are called basal‐like and were first recognized as a distinct group by gene expression arrays. Nuclear factor kappaB (NF‐κB) is family of multifunctional transcription factors that when activated generate pleotrophic changes in target cells. Elevated levels of active NF‐κB are detected in many human diseases including breast cancers. High‐level active NF‐κB is detected in specific subclasses of breast cancers briefly described above, predominantly in ER‐negative and epidermal growth factor family receptor (EGFR) overexpressing breast cancers (predominantly HER2 amplified cancers). This article is focused on the role of NF‐κB activation initiated by the EGFR family receptors in subclasses of breast cancer. The combined influence of EGFR family receptors and NF‐κB signaling on the transformation of ER‐negative human mammary epithelial cell is illustrated. J. Cell. Physiol. 209: 645–652, 2006. © 2006 Wiley‐Liss, Inc.
Characterization of Peptides Released from Mitochondria

Conserved ATP-dependent proteases ensure the quality control of mitochondrial proteins and control essential steps in mitochondrial biogenesis. Recent studies demonstrated that non-assembled mitochondrially encoded proteins are degraded to peptides and amino acids that are released from mitochondria. Here, we have characterized peptides extruded from mitochondria by mass spectrometry and identified 270 peptides that are exported in an ATP- and temperature-dependent manner. The peptides originate from 51 mitochondrially and nuclearly encoded proteins localized mainly in the matrix and inner membrane, indicating that peptides generated by the activity of all known mitochondrial ATP-dependent proteases can be released from the organelle. Pulse-labeling experiments in logarithmically growing yeast cells revealed that ∼6–12% of preexisting and newly imported proteins is degraded and contribute to this peptide pool. Under respiring conditions, we observed an increased proteolysis of newly imported proteins that suggests a higher turnover rate of respiratory chain components and thereby rationalizes the predominant appearance of representatives of this functional class in the detected peptide pool. These results demonstrated a constant efflux of peptides from mitochondria and provided new insight into the stability of the mitochondrial proteome and the efficiency of mitochondrial biogenesis.
Urinary CCN2 (CTGF) as a possible predictor of diabetic nephropathy: preliminary report.

BACKGROUND It is currently impossible to reliably predict which diabetic patients will develop nephropathy and progress to kidney failure. Microalbuminuria, often regarded as a predictor of overt diabetic renal disease is, in fact, an indicator of established glomerular damage. We have shown that glomerular expression of the prosclerotic cytokine CCN2 (CTGF) is greatly up-regulated early in experimental and in human diabetes and mesangial cell exposure to CCN2 increases its production of extracellular matrix (ECM) molecules responsible for glomerulosclerosis. As an early marker, we therefore investigated the presence of CCN2 in urine and the relationship to diabetes and/or renal disease in an experimental model of diabetes and in a limited patient population. METHODS Urine samples from (1) healthy rats, (2) rats made diabetic by streptozotocin (STZ), (3) healthy human volunteers, (4) diabetic patients with renal disease, and (5) diabetic patients without renal disease were examined by Western blotting and/or enzyme-linked immunosorbent assay (ELISA) for qualitative and quantitative analysis of the of CCN2. RESULTS Low levels of urinary CCN2 were present in healthy, control rats, but were increased approximately sevenfold overall in STZ-diabetic animals. CCN2 levels were the highest at week 3 of diabetes, then decreased with time, but remained significantly elevated over controls even after 32 weeks. Consistently low levels of urinary CCN2 were also detected in healthy volunteers (mean value, 7.1 CCN2/mg creatinine). However, levels were elevated approximately sixfold in the majority of diabetic patients with nephropathy. A small number of the diabetic patients not yet exhibiting evidence of renal involvement demonstrated CCN2 urinary levels that were ninefold greater than controls. The remaining normoalbuminuric diabetic patients demonstrated CCN2 levels indistinguishable from those of healthy volunteers. Analysis by Western blotting confirmed the identity of the urinary CCN2. A molecular species equivalent to full-length CCN2 (37/39 kD doublet) was present in healthy controls. In contrast, the nephropathic group demonstrated multiple CCN2 bands. CONCLUSION These findings support our hypothesis that CCN2 is up-regulated early in the evolution of glomerulosclerosis, including that of diabetes. We contend that urinary CCN2 may both stage nephropathy and predict those patients who are destined for progressive glomerulosclerosis and end-stage renal disease (ESRD). Cross-sectional and prospective studies of larger, well-defined diabetic patients groups will be required to prove this hypothesis, and are ongoing.
In vitro adhesion of lactic acid bacteria to canine small intestinal mucus

Summary Selected probiotic lactic acid bacteria have several documented health effects. For many of these health effects, adhesion to the intestinal mucosa is of primary importance. In the current study, the adhesive ability to canine small intestinal mucus of four lactic acid bacteria intended for human use, two for animal use and two strains isolated from dogs was assessed. The strains for human use were specifically chosen because they have documented health effects and have been proven to be safe. One strain for human use, Lactobacillus rhamnosus (ATCC 53103), was found to adhere significantly better than all other strains. Pretreatment of the strains with canine jejunal chyme, to simulate digestion, dramatically reduced the adhesion of all strains tested. However, three of the strains intended for human use were still adhering better than the strains from animal origin. The results show that probiotic strains from human origin and intended for human use also adhere to canine intestinal mucus. This warrants further investigation of these strains for use in dogs.
Tree-based Convolution: A New Neural Architecture for Sentence Modeling

This paper proposes a new convolutional neural architecture based on tree-structures, called the tree-based convolutional neural network (TBCNN). Two variants take advantage of constituency trees and dependency trees, respectively, to model sentences. Compared with traditional"flat"convolutional neural networks (CNNs), TBCNNs explore explicitly sentences' structural information; compared with recursive neural networks, TBCNNs have shorter propagation paths, enabling more effective feature learning and extraction. We evaluated our model in two widely applied benchmarks---sentiment analysis and question classification. Our models outperformed most state-of-the-art results, including both existing neural networks and dedicated feature/rule engineering.
Arabic Dialect Handling in Hybrid Machine Translation

In this paper, we describe an extension to a hybrid machine translation system for handling dialect Arabic, using a decoding algorithm to normalize non-standard, spontaneous and dialectal Arabic into Modern Standard Arabic. We prove the feasibility of the approach by measuring and comparing machine translation results in terms of BLEU with and without the proposed approach. We show in our tests that on real-live broadcast input with transcriptions of dialectal speech we achieve an increase on BLEU of about 1%, and on web content with dialect text of about 2%.
Research on Data Use: A Framework and Analysis

One of the central lessons from research on data use in schools and school districts is that assessments, student tests, and other forms of data are only as good as how they are used. But what influences how they are used? This relatively straightforward question turns out to be fairly complex to answer. Data use implicates a number of processes, conditions, and contexts. It involves interpretive processes, as using data requires that the user interpret the data and construct implications for next steps. It implicates social and organizational conditions, since the data use unfolds in the context of a multileveled organizational system. And, because data can be a source of power, particularly in the current accountability environment, data use also involves power relations. In this article, we put forward a framework for understanding the phenomenon of data use in the context of data use interventions. We draw on existing research and theory to identify key dimensions of data use that we should attend to and offer a way to understand how these dimensions might interact. In so doing, we provide guidance for studying the pathways between data use interventions and various outcomes of value.
Développement de méthodes d'ordonnancement efficaces et appliquées dans un système de production mécanique

L’evolution continue des environnements de production et l’augmentation des besoins des clients, demandent un processus de production plus rapide et efficace qui controle plusieurs parametres en meme temps. Nous nous sommes interesses au developpement de methodes d’aide a la decision qui permettent d’ameliorer l’ordonnancement de la production. L’entreprise partenaire (Norelem) fabrique des pieces de precision mecanique, il faut donc prendre en compte les differentes contraintes de ressources (humaines et d’outillage) existantes dans l’atelier de production.Nous avons aborde l’etude d’un atelier d’ordonnancement de type open shop ou chemin ouvert, ou une tâche peut avoir de multiples sequences de production puisque l’ordre de fabrication n’est pas fixe et l’objectif a minimiser est le temps total de sejour. Des contraintes d’affectation de ressources humaines (multi-competences) et de disponibilite d’outillage ont ete prises en compte.Des modeles mathematiques lineaires et non-lineaires ont ete developpes pour decrire la problematique. Etant donne que les methodes exactes sont limitees aux instances de petites tailles a cause des temps de calcul, des methodes de resolution approchees ont ete proposees et comparees. De plus, nous avons aborde l’optimisation multi-objectif en considerant trois objectifs, la minimisation du temps total de sejour et l’equilibrage de charge des ressources (humaines et machines). L’efficacite des methodes est prouvee grâce a des tests sur des instances theoriques et l’application au cas reel