Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Gene Cluster in Klebsiella pneumoniae Which Includes citX, a Gene Required for Biosynthesis of the Citrate Lyase Prosthetic Group

ABSTRACT The biosynthesis of the 2′-(5"-phosphoribosyl)-3′-dephospho-coenzyme A (CoA) prosthetic group of citrate lyase (EC 4.1.3.6), a key enzyme of citrate fermentation, proceeds via the initial formation of the precursor 2′-(5"-triphosphoribosyl)-3′-dephospho-CoA and subsequent transfer to apo-citrate lyase with removal of pyrophosphate. In Escherichia coli, the two steps are catalyzed by CitG and CitX, respectively, and the corresponding genes are part of the citrate lyase gene cluster, citCDEFXG. In the homologous citCDEFG operon of Klebsiella pneumoniae, citX is missing. A search for K. pneumoniae citX led to the identification of a second genome region involved in citrate fermentation which comprised the citWX genes and the divergent citYZ genes. The citX gene was confirmed to encode holo-citrate lyase synthase, whereas citW was shown to encode a citrate carrier, the third one identified in this species. The citYZ genes were found to encode a two-component system consisting of the sensor kinase CitY and the response regulator CitZ. Remarkably, both proteins showed ≥40% sequence identity to the citrate-sensing CitA-CitB two-component system, which is essential for the induction of the citrate fermentation genes in K. pneumoniae. A citZ insertion mutant was able to grow anaerobically with citrate, indicating that CitZ is not essential for expression of citrate fermentation genes. CitX synthesis was induced to a basal level under anaerobic conditions, independent of citrate, CitB, and CitZ, and to maximal levels during anaerobic growth with citrate as the sole carbon source. Similar to the other citrate fermentation enzymes, CitX synthesis was apparently subject to catabolite repression.
Non-canonical Maturation of Two Papain-family Proteases in Toxoplasma gondii*

Background: Toxoplasma gondii expresses several cathepsin proteases, but little is known about how they are activated. Results: Toxoplasma cathepsin B protease localizes to lysosome-like compartment, and its maturation requires a parasite cathepsin L protease. Conclusion: Maturation of Toxoplasma cathepsin B is unconventionally nonself-dependent. Significance: The unusual maturation of Toxoplasma cathepsin B suggests a novel mechanism of protease activation within the endolysosomal system. Proteases regulate key events during infection by the pervasive intracellular parasite Toxoplasma gondii. Understanding how parasite proteases mature from an inactive zymogen to an active enzyme is expected to inform new strategies for blocking their actions. Herein, we show that T. gondii cathepsin B protease (TgCPB) does not undergo self-maturation but instead requires the expression of a second papain-family cathepsin protease, TgCPL. Using recombinant enzymes we also show that TgCPL is capable of partially maturing TgCPB in vitro. Consistent with this interrelationship, antibodies with validated specificity detected TgCPB in the lysosome-like vacuolar compartment along with TgCPL. Our findings also establish that TgCPB does not localize to the rhoptries as previously reported. Accordingly, rhoptry morphology and rhoptry protein maturation are normal in TgCPB knock-out parasites. Finally, we show that although maturation of TgCPL is independent of TgCPB, it may involve an additional protease(s) in conjunction with self-maturation.
Stackelberg thresholds on parallel networks with horizontal queues

We study Stackelberg routing games on parallel networks with horizontal queues, in which a coordinator (leader) controls a fraction α of the total flow on the network, and the remaining players (followers) choose their routes selfishly. The objective of the coordinator is to minimize a system-wide cost function, the total travel-time, while anticipating the response of the followers. Nash equilibria of the routing game (with zero control) are known to be inefficient in the sense that the total travel-time is sub-optimal. Increasing the compliance rate α improves the cost of the equilibrium, and we are interested in particular in the Stackelberg threshold, i.e. the minimal compliance rate that achieves a strict improvement. In this work, we derive the optimal Stackelberg cost as a function of the compliance rate α, and obtain, in particular, the expression of the Stackelberg threshold.
Estimating Personality Constructs from Archival Data

Abstract : As part of a leadership research program at the U.S. Military Academy involving cadets in the Class of 1998, this report examined the viability of using archival data on prior cadets to estimate a variety of personality constructs among current cadets. Two sets of archival personality data on prior cadet classes were obtained. The first involved a short form administration of the ABLE inventory to cadets in the Class of 1994. The second involved the administration of the NEO Personality Inventory to the Class of 1996. Scores on the 12 scales contained in these inventories were used as archival criteria. Archival predictors were then sought from other and questionnaire items administered to cadets at the same point in time as the original inventories. For each scale, a different 20-item pool of predictors was developed from the archival items having the strongest zero order correlations with that scale. A series of multiple regression analyses was then used to predict scores on each scale. An average R2 of . 39 per scale was obtained after cross validation. Both the original scales and their analogs tended to manifest similar relationships with two external criteria examined, leadership performance and attrition.
Investigation of Single-Cell Dynamic Faults in Deep-Submiron Memory Technologies

This paper presents single-cell dynamic fault models for deep-submicron semiconductor memories together with their associated tests (test primitives). The test primitives are evaluated industrially, together with the traditional tests, using 65nm technology 131 Kbytes embedded SRAMs. The test results are reported, and their analysis shows the increasing importance of dynamic faults and tests, and the exceptional effectiveness of using back-to-back operations (with complementary data values) along bit lines during memory testing.
Signaling over MIMO Multi-Base Systems: Combination of Multi-Access and Broadcast Schemes

A new structure for multi-base systems is studied in which each user receives data from two nearby base stations, rather than only from the strongest one. This system can be considered as a combination of broadcast and multi-access channels. By taking advantages of both perspectives, an achievable rate region for a discrete memoryless channel modeled by Pr(y1,y2|x1,x2 ) is derived. In this model, x1 and x2 represent the transmitted signals by the transmitter one and two, respectively, and y1 and y2 denote the received signals by the receiver one and two, respectively. In this derivation, it is assumed that each transmitter is unaware of the data of the other transmitter, and therefore x1 and x2 are independent. To investigate the advantage of this scheme, an efficient signaling method which works at a corner point of the achievable region for multiple-antenna scenarios is developed. In the proposed scheme, each base station only requires the state information of the channels between the other base station and each user. In this paper, the signaling scheme is elaborated for the case that each transmitter/receiver is equipped with three antennas. It is proven that in such a scenario, the multiplexing gain of four is achievable, which outperforms any other conventional schemes
Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy

To identify biomarker candidates associated with early IgA nephropathy (IgAN) and thin basement membrane nephropathy (TBMN), the most common causes presenting isolated hematuria in childhood, a proteomic approach of urinary exosomes from early IgAN and TBMN patients was introduced. The proteomic results from the patients were compared with a normal group to understand the pathophysiological processes associated with these diseases at the protein level. The urinary exosomes, which reflect pathophysiological processes, collected from three groups of young adults (early IgAN, TBMN, and normal) were trypsin‐digested using a gel‐assisted protocol, and quantified by label‐free LC‐MS/MS, using an MSE mode. A total of 1877 urinary exosome proteins, including cytoplasmic, membrane, and vesicle trafficking proteins, were identified. Among the differentially expressed proteins, four proteins (aminopeptidase N, vasorin precursor, α‐1‐antitrypsin, and ceruloplasmin) were selected as biomarker candidates to differentiate early IgAN from TBMN. We confirmed the protein levels of the four biomarker candidates by semi‐quantitative immunoblot analysis in urinary exosomes independently prepared from other patients, including older adult groups. Further clinical studies are needed to investigate the diagnostic and prognostic value of these urinary markers for early IgAN and TBMN. Taken together, this study showed the possibility of identifying biomarker candidates for human urinary diseases using urinary exosomes and might help to understand the pathophysiology of early IgAN and TBMN at the protein level.
Functionalization of Fe3O4 NPs by Silanization: Use of Amine (APTES) and Thiol (MPTMS) Silanes and Their Physical Characterization

In this paper the results concerning the synthesis of magnetite (Fe3O4) nanoparticles (NPs), their functionalization using silane derivatives, such as (3-Aminopropyl)triethoxysilane (APTES) and (3-mercaptopropyl)trimethoxysilane (MPTMS), and their exhaustive morphological and physical characterization by field emission scanning electron microscopy (FE-SEM) with energy dispersion X-ray spectrometer (EDX) analysis, AC magnetic susceptibility, UV-VIS and IR spectroscopy, and thermogravimetric (TGA) analyses are reported. Two different paths were adopted to achieve the desired functionalization: (1) the direct reaction between the functionalized organo-silane molecule and the surface of the magnetite nanoparticle; and (2) the use of an intermediate silica coating. Finally, the occurrence of both the functionalization with amino and thiol groups has been demonstrated by the reaction with ninhydrin and the capture of Au NPs, respectively.
Reliability of counting actinic keratoses before and after brief consensus discussion: the VA topical tretinoin chemoprevention (VATTC) trial.

OBJECTIVE To assess the reliability of counts of actinic keratoses (AKs) and the effect of a brief joint discussion of discrepancies on that reliability. DESIGN AND INTERVENTION Seven dermatologists independently counted AKs on the face and ears before and after a brief joint discussion of discrepancies. SETTING AND PATIENTS A volunteer sample of 9 patients from the ongoing VA (Department of Veterans Affairs) Topical Tretinoin Chemoprevention (VATTC) Trial. All participating individuals are veterans and have had 2 or more keratinocyte carcinomas (basal or squamous cell carcinoma) in the 5 years before enrollment in the study. MAIN OUTCOME MEASURE Standard deviation of estimates of the Poisson regression parameter for the dermatologists. RESULTS Substantial variation was found among the dermatologists in their AK counts. The SD of the parameter estimates for the dermatologists decreased from 0.45 to 0.24 after the brief joint discussion, a 47% decrease (P =.076). The variation attributable to the dermatologists also decreased substantially (chi(2)(6) decrease, 94 to 12). CONCLUSIONS Actinic keratoses are common, and there is a continuous spectrum of lesions that ranges from sun-damaged skin to squamous cell carcinoma in situ. Clinical distinguishing features may be difficult to delineate precisely. Counts of AK are commonly performed, but appear to be unreliable, even when performed by experienced dermatologists. Joint discussion of discrepancies may enhance the reliability of these counts, although substantial variation remains. Research that relied on these counts must be reevaluated in light of the marked variation among expert observers. Future studies should consider measures to assess and enhance reliability.
Incorporating prosodic information and language structure into speech recognition systems

Some of the major research issues in the field of speech recognition revolve around methods of incorporating additional knowledge sources, beyond the short-time spectral information of the speech signal, into the recognition process. These knowledge sources, which may include information about prosody, language structure, semantics, and dialogue context, are difficult to quantify with regard to the task of language understanding, and are even more difficult to interface with the statistically motivated architectures such as Hidden Markov Models that are used for acoustic processing. The fundamental goal of this research is to further our understanding of how to incorporate prosodic features and language structure into recognition systems. Each of these two domains has proven to be particularly difficult to use effectively, especially for speaker independent tasks where most of the elements of these knowledge domains vary significantly between speakers. To accomplish this goal, we look at the effectiveness of using word graphs as an interface mechanism between recognition and language systems, develop the Observation Dependent Hidden Markov Model (ODHMM) which is able to adaptively alter transition probabilities based on the dynamics of spectral features, and apply temporal and suprasegmental information to the task of segmenting audio classes for broadcast news transcription.
A novel role for α3β1 integrins in extracellular matrix assembly

To study the biological role of α3β1 integrins in cell adhesion, migration, and in the deposition of extracellular matrix, we stably expressed the human α3 integrin subunit in the α4, α5 integrin deficient CHO cell line B2. The expression of α3β1 integrins enhanced cell adhesion on entactin (also known as nidogen), but not on fibronectin. Using recombinant GST-fusion proteins that span the entire length of the entactin molecule, we located cell adhesive activity to the G2 domain of entactin. These results suggest that the α3β1 integrin functions as an adhesion receptor interacting with the G2 domain of entactin. On the other hand, the expression of α3β1 integrins did not confer the ability to migrate on entactin. Strikingly, the expression of α3β1 dramatically increased the deposition of entactin and fibronectin into the pericellular matrix. This was accompanied by increased binding activity of the 29 kDa amino-terminal domain of fibronectin. Thus, similar to α5β1 integrins, α3β1 integrins can play an important role in modulating the assembly of pericellular matrices. However, unlike fibronectin deposition supported by α5β1, α3β1 supported fibronectin deposition into pericellular matrix was not inhibited by antibodies binding to the RGD containing cell adhesion domain of fibronectin, demonstrating that the two processes are mechanistically distinct. The role of α3β1 in pericellular matrix assembly potentially implicates this receptor in the assembly and/or recognition of entactin-containing pericellular matrices, an observation consistent with its apparent role in the renal glomerulus of the mammalian kidney. SUMMARY
Accommodating for different levels of proficiency in the English classroom : With focus on ability grouping

This study investigated the perceived strategies used to deal with mixed ability classes of four English teachers, two working at a year 4-9 compulsory school, and two at an upper secondary school in Sweden. The same teachers were asked about their attitudes towards and experience of ability grouping. The findings of the latter part of this investigation were discussed in reference to research concerning the field of ability grouping.Semi structured interviews were used. Strategies used by teachers included grouping devices, issues of communication, giving individual attention inside and outside the classroom and encouraging self- and peer reviewing. Two teachers in the 4-9 school used ability grouping sparingly but clearly and had experienced an ability grouping of a year nine class which was perceived to have predominantly positive results in academic terms and both positive and negative results in social areas. The teachers of upper secondary school did not use ability grouping – either on democratic grounds or because it was perceived to be unacceptable in the particular school climate. Because the research in ability grouping is diverse, many of the teachers’ attitudes could be supported, and refuted in the research. The teachers using ability grouping felt themselves to be going against research made, but were confident in the decisions they made. Further investigations about maximum numbers of students in heterogeneous classes and time spent with an extra teacher contra own teacher were encouraged.
Bayesian Hierarchical Model for Estimating Gene Expression Intensity Using Multiple Scanned Microarrays

We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sen-sitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at the high end. Our method is generic and can be applied to data from any organism, for imaging with any scanner that allows varying the laser power, and for extraction with any image analysis software. Results from a self-self hybridization data set illustrate an improved precision in the estimation of the expression of genes compared to what can be achieved by applying standard methods and using only a single scan.
Aristotle, emotions, and education

Contents: Introduction: Fusing heart and head Aristotelian moral development Aristotle and the 'paradox of moral education' Aristotle on the non-expendability of emotions Teaching justified anger the Aristotelian way Emotional intelligence versus Aristotle Emulation: an Aristotelian virtue for the young Aristotelian friendship between parents and children What can Aristotle teach us about generosity? Aristotelian agreeableness and teaching Is teaching an Aristotelian praxis? Conclusion Bibliography Index.
Cre-loxP Recombination System for Large Genome Rearrangements in Lactococcus lactis

ABSTRACT We have used a new genetic strategy based on the Cre-loxP recombination system to generate large chromosomal rearrangements in Lactococcus lactis. Two loxP sites were sequentially integrated in inverse order into the chromosome either at random locations by transposition or at fixed points by homologous recombination. The recombination between the two chromosomal loxP sites was highly efficient (approximately 1 × 10−1/cell) when the Cre recombinase was provided in trans, and parental- or inverted-type chromosomal structures were isolated after removal of the Cre recombinase. The usefulness of this approach was demonstrated by creating three large inversions of 500, 1,115, and 1,160 kb in size that modified the lactococcal genome organization to different extents. The Cre-loxP recombination system described can potentially be used for other gram-positive bacteria without further modification.
Interference alignment feasibility in constant coefficient MIMO interference channels

We consider the K-link constant coefficient multiple-input-multiple-output interference channel (MIMO IFC) where inter-link interference is treated as Gaussian noise (Noisy MIMO IFC). Starting from Interference Alignment (IA) constraints, analytical conditions that need to be satisfied in order to admit an IA solution for such a MIMO IFC are derived. For a given degrees of freedom allocation, these conditions, along with a recursive algorithm to check its validity in a given K-link MIMO IFC, allow an analytical evaluation of the existence of IA solutions (or lack thereof). While such an attempt has been made recently for several interesting cases in published literature [1] [2], to the best of our knowledge, this is the first time that such conditions have been derived in full generality (including the multiple stream case). Moreover, for the cases addressed in [2] our approach evaluates the existence of IA solution with much lower complexity.
Cells expressing a major histocompatibility complex class I molecule with a single covalently bound peptide are highly immunogenic

The major histocompatibility complex (MHC) class I molecules expressed at the cell surface are associated with a large number of different peptides so that the density of a given MHC-peptide complex is relatively low. Here we describe the properties of MHC class I molecules genetically attached to a single antigenic peptide. Cells expressing these fusion proteins are recognized by T cells specific for the particular MHC-peptide complex. Coculture of naive splenocytes with cells expressing these MHC-peptide fusion proteins and the B7.1 antigen allows the induction of primary cytotoxic T lymphocytes (CTL) in vitro. Injection of these cells into naive mice enhances the frequency of specific CTL precursors and protects against a subsequent challenge with a tumor or a virus bearing the antigenic peptide. Soluble MHC- peptide fusions were also produced in which all three components, that is, the heavy chain, beta 2-microglobulin and the peptide, have fused into a single-chain protein. The availability of MHC class I molecules bound to a single peptide provides valuable tools for the manipulation of CTL responses and the analysis of the selection processes in the thymus.
Expression of calcium-binding proteins and selected neuropeptides in the human, chimpanzee, and crab-eating macaque claustrum

The claustrum is present in all mammalian species examined so far and its morphology, chemoarchitecture, physiology, phylogenesis and ontogenesis are still a matter of debate. Several morphologically distinct types of immunostained cells were described in different mammalian species. To date, a comparative study on the neurochemical organization of the human and non-human primates claustrum has not been fully described yet, partially due to technical reasons linked to the postmortem sampling interval. The present study analyze the localization and morphology of neurons expressing parvalbumin (PV), calretinin (CR), NPY, and somatostatin (SOM) in the claustrum of man (# 5), chimpanzee (# 1) and crab-eating monkey (# 3). Immunoreactivity for the used markers was observed in neuronal cell bodies and processes distributed throughout the anterior-posterior extent of human, chimpanzee and macaque claustrum. Both CR- and PV-immunoreactive (ir) neurons were mostly localized in the central and ventral region of the claustrum of the three species while SOM- and NPY-ir neurons seemed to be equally distributed throughout the ventral-dorsal extent. In the chimpanzee claustrum SOM-ir elements were not observed. No co-localization of PV with CR was found, thus suggesting the existence of two non-overlapping populations of PV and CR-ir interneurons. The expression of most proteins (CR, PV, NPY), was similar in all species. The only exception was the absence of SOM-ir elements in the claustrum of the chimpanzee, likely due to species specific variability. Our data suggest a possible common structural organization shared with the adjacent insular region, a further element that emphasizes a possible common ontogeny of the claustrum and the neocortex.