Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of p53 and Its Isoforms in Human Breast Carcinoma Cells

In breast carcinoma, disruption of the p53 pathway is one of the most common genetic alterations. The observation that the p53 can express multiple protein isoforms adds a novel level of complexity to the outcome of p53 mutations. p53 expression was analysed by Western immunoblotting and immunohistochemistry using monoclonal antibodies DO-7, Pab240, and polyclonal antiserum CM-1. The more frequently p53-positive nuclear staining has been found in the invasive breast tumors. One of the most intriguing findings is that mutant p53 appears as discrete dot-shaped regions within the nucleus of breast cancer cells. In many malignant cells, the nucleolar sequestration of p53 is evident. These observations support the view that the nucleolus is involved directly in the mediation of p53 function or indirectly by the control of the localization of p53 interplayers. p53 expressed in the nuclear fraction of breast cancer cells revealed a wide spectrum of isoforms. p53 isoforms ΔNp53 (47 kDa) and Δ133p53β (35 kDa), known as dominant-negative repressors of p53 function, were detected as the most predominant variants in nuclei of invasive breast carcinoma cells. The isoforms expressed also varied between individual tumors, indicating potential roles of these p53 variants in human breast cancer.
Systematic Effects on Tangential and Radial Arc Statistics: The Finite Source Size and Ellipticities of the Lens and Source

It has been recognized that the arc statistics of gravitational lensing are a useful probe of the density profile of clusters of galaxies. We examine several systematic effects that are important in predicting the number of arcs, with particular attention to the difference between tangential and radial arcs. First, we derive an analytic expression for the cross section for radial arcs taking account of the source size and find that a moderate source size enhances the cross section for radial arcs, while a larger source size (≳1'' in our example) suppresses the number of radial arcs. On the other hand, tangential arcs are much less sensitive to the source size. Next, we numerically calculate the cross section for arcs considering the lens and source ellipticities. We find that the numbers of both tangential and radial arcs are highly enhanced by both ellipticities, by 1 or 2 orders of magnitude. The number ratio of radial to tangential arcs is, however, not so affected if the threshold axis ratio of arcs is large (≳7). The number ratio therefore still remains a good statistic for probing the density profile of lens objects if the source-size effect is correctly taken into account.
Mitochondrial diversity and phylogenetic structure of Mahabadi goat population

On the basis of the previously mentioned archaeological studies and bio-geography, it is likely that the molecular studies of diversity in Iranian goats will yield new understanding of the origin and process of goat domestication, and will contribute to the resolution of goat phylogeny. More than 20 breed of goats have been recognized in Iran but only breeds namely Abstract The genetic diversity and phylogenetic structure was analyzed in Mahabadi goat population by mitochondrial DNA sequences. Phylogenetic analysis was carried out using hyper variable region 1 (896bp) obtained form 30 animals. Mahabadi goat proved to be extremely diverse (average haplotype diversity of 0.999) and the nucleotide diversity values 0.022. A total of 30 Mahabadi goats were grouped into six haplotypes and the large majority of haplotypes were present in 15 animals. All Mahabadi haplotypes were classified into a haplogroup and revealed remarkably high genetic distances within the population when compared with other Asian goat populations, indicating high genetic variation in the Mahabadi goat. These results indicate high- divergence status of the Mahabadi goat and will influence breeding and conservation strategies adopted for this breed.
NIK-dependent RelB Activation Defines a Unique Signaling Pathway for the Development of Vα14i NKT Cells

A defect in RelB, a member of the Rel/nuclear factor (NF)-κB family of transcription factors, affects antigen presenting cells and the formation of lymphoid organs, but its role in T lymphocyte differentiation is not well characterized. Here, we show that RelB deficiency in mice leads to a selective decrease of NKT cells. RelB must be expressed in an irradiation-resistant host cell that can be CD1d negative, indicating that the RelB expressing cell does not contribute directly to the positive selection of CD1d-dependent NKT cells. Like RelB-deficient mice, aly/aly mice with a mutation for the NF-κB–inducing kinase (NIK), have reduced NKT cell numbers. An analysis of NK1.1 and CD44 expression on NKT cells in the thymus of aly/aly mice reveals a late block in development. In vitro, we show that NIK is necessary for RelB activation upon triggering of surface receptors. This link between NIK and RelB was further demonstrated in vivo by analyzing RelB+/− × aly/+ compound heterozygous mice. After stimulation with α-GalCer, an antigen recognized by NKT cells, these compound heterozygotes had reduced responses compared with either RelB+/− or aly/+ mice. These data illustrate the complex interplay between hemopoietic and nonhemopoietic cell types for the development of NKT cells, and they demonstrate the unique requirement of NKT cells for a signaling pathway mediated by NIK activation of RelB in a thymic stromal cell.
DNA Methylation and Normal Chromosome Behavior in Neurospora Depend on Five Components of a Histone Methyltransferase Complex, DCDC

Methylation of DNA and of Lysine 9 on histone H3 (H3K9) is associated with gene silencing in many animals, plants, and fungi. In Neurospora crassa, methylation of H3K9 by DIM-5 directs cytosine methylation by recruiting a complex containing Heterochromatin Protein-1 (HP1) and the DIM-2 DNA methyltransferase. We report genetic, proteomic, and biochemical investigations into how DIM-5 is controlled. These studies revealed DCDC, a previously unknown protein complex including DIM-5, DIM-7, DIM-9, CUL4, and DDB1. Components of DCDC are required for H3K9me3, proper chromosome segregation, and DNA methylation. DCDC-defective strains, but not HP1-defective strains, are hypersensitive to MMS, revealing an HP1-independent function of H3K9 methylation. In addition to DDB1, DIM-7, and the WD40 domain protein DIM-9, other presumptive DCAFs (DDB1/CUL4 associated factors) co-purified with CUL4, suggesting that CUL4/DDB1 forms multiple complexes with distinct functions. This conclusion was supported by results of drug sensitivity tests. CUL4, DDB1, and DIM-9 are not required for localization of DIM-5 to incipient heterochromatin domains, indicating that recruitment of DIM-5 to chromatin is not sufficient to direct H3K9me3. DIM-7 is required for DIM-5 localization and mediates interaction of DIM-5 with DDB1/CUL4 through DIM-9. These data support a two-step mechanism for H3K9 methylation in Neurospora.
Semantic Class Induction and Coreference Resolution

This paper examines whether a learningbased coreference resolver can be improved using semantic class knowledge that is automatically acquired from a version of the Penn Treebank in which the noun phrases are labeled with their semantic classes. Experiments on the ACE test data show that a resolver that employs such induced semantic class knowledge yields a statistically significant improvement of 2% in F-measure over one that exploits heuristically computed semantic class knowledge. In addition, the induced knowledge improves the accuracy of common noun resolution by 2-6%.
Bulk Loading of Calcium Indicator Dyes to Study Astrocyte Physiology: Key Limitations and Improvements Using Morphological Maps

Calcium signaling has been studied in astrocyte cell bodies using bulk loading of calcium indicator dyes, and astrocytes are known to display intracellular calcium transients. An assumption in recent data on the neuronal impact of somatic astrocyte calcium transients has been that bulk loading reflects signaling in relevant astrocyte compartments such as processes. We assessed bulk loading using Sholl analysis (Sholl, 1953) of astrocytes loaded with common calcium indicator dyes and compared these data with Sholl analysis of astrocyte morphology. In the CA1 region of the hippocampus from rats, we found that bulk loading of calcium indicator dyes only reports on calcium signals within the soma and in the most proximal processes, leaving ∼90% of the area of an astrocyte and its extensive processes unsampled. By using morphological reconstructions as “maps” after the imaging session, we present simple procedures that remedy these shortfalls and permit reliable detection of calcium transients in distal astrocyte processes. The data thus reveal limitations in the interpretation of astrocyte calcium imaging data gathered with bulk loading and provide refinements to minimize these shortcomings.
Teacher Salaries, State Collective Bargaining Laws, and Union Coverage

What are the causal effects of collective bargaining (CB) on teacher salaries? This seemingly simple question has been difficult to answer because (a) a national census (or near‐census) of CB data for school districts is not available, while individual coverage data from the CPS have substantial reporting error; (b) union wage effects depend not only on coverage but also on an array of CB law provisions difficult to quantify; (c) union coverage and possibly state CB laws are endogenous since each has been influenced by union sentiment among workers and voters; and (d) OLS estimates of the wage effect of CB coverage and laws are attenuated by measurement error and potentially biased due to endogeneity. We attempt to address these issues by accounting for the endogeneity of state laws and coverage using instruments that measure historical state‐level labor sentiment, by use of factor analysis to create indices of CB law strength, and by using two national data sets containing information on teacher salaries and coverage. Both measurement error and endogeneity bias appear to be important. Collective bargaining coverage has a substantial impact on teacher salaries. State level bargaining laws that enable collective bargaining provide the key mechanism through which higher salaries are obtained.
Multiple receptor systems promote CNS neural migration

To identify glial receptor systems in CNS migration, cerebellar granule neuron migration was assayed on glass fibers coated with polylysine, astroglial membranes (AM fibers), or the extracellular matrix proteins collagen (COLL fibers), fibronectin (FN fibers), and laminin (LAM fibers). By video microscopy, granule cells migrated along AM fibers with the cytology, neuron-fiber apposition, and dynamics seen on living glia. The demonstration that immobilized astroglial membranes support neural migration suggests that astroglial receptor systems, in combination with glial fiber geometry, promote CNS neural migration. Moreover, granule neurons migrated rapidly on LAM fibers, moved relatively slowly on FN fibers, and not at all on COLL fibers. Antibody perturbation analyses suggested that, whereas astrotactin provides the neural receptor for migration on astroglial membranes, integrin beta 1 provides the neural receptor for migration on LAM fibers. These results suggest that multiple receptor systems support CNS neural migration.
Comprehending annotations on object-oriented programs using fractional permissions

Fractional permissions are a general system for managing access to mutable state. We show how fractional permissions can give semantics to a regimen of annotations including "unique," "non-null," "read-only," ownership, and method effects. The unification supports new annotations: "unique-write" and "from". We also develop a model of object invariants in the presence of inheritance using "nesting," an extension of "adoption. "
Substitution, Risk Aversion, Taste Shocks, and Equity Premia

This paper investigates the testable restrictions on the time-series behavior of equity premia implied by a representative agent model whose stateand time-non-separable preferences are subject to taste shocks. The model nests stateand time-separable preferences with and without taste shocks as special cases. Empirically, the linearized Euler equations are estimated through Kalman ltering, allowing for conditional heteroscedasticity via a common factor GARCH process. With or without conditional heteroscedasticity, (i) the hypothesis that preferences are separable cannot be rejected, (ii) taste shocks inuences are statistically signi cant, and (iii) taste shocks yield reasonable estimates of the coe cient of relative risk aversion. This last result occurs because taste shocks reproduce the large observed equity premium by shifting weight away from consumption risk in favor to taste risk.
Seeing with Sound? Exploring Different Characteristics of a Visual-to-Auditory Sensory Substitution Device

Sensory substitution devices convert live visual images into auditory signals, for example with a web camera (to record the images), a computer (to perform the conversion) and headphones (to listen to the sounds). In a series of three experiments, the performance of one such device (‘The vOICe’) was assessed under various conditions on blindfolded sighted participants. The main task that we used involved identifying and locating objects placed on a table by holding a webcam (like a flashlight) or wearing it on the head (like a miner's light). Identifying objects on a table was easier with a hand-held device, but locating the objects was easier with a head-mounted device. Brightness converted into loudness was less effective than the reverse contrast (dark being loud), suggesting that performance under these conditions (natural indoor lighting, novice users) is related more to the properties of the auditory signal (ie the amount of noise in it) than the cross-modal association between loudness and brightness. Individual differences in musical memory (detecting pitch changes in two sequences of notes) was related to the time taken to identify or recognise objects, but individual differences in self-reported vividness of visual imagery did not reliably predict performance across the experiments. In general, the results suggest that the auditory characteristics of the device may be more important for initial learning than visual associations.
Discretization from data streams: applications to histograms and data mining

In this paper we propose a new method to perform incremental discretization. The basic idea is to perform the task in two layers. The first layer receives the sequence of input data and keeps some statistics on the data using many more intervals than required. Based on the statistics stored by the first layer, the second layer creates the final discretization. The proposed architecture processes streaming examples in a single scan, in constant time and space even for infinite sequences of examples. We experimentally demonstrate that incremental discretization is able to maintain the performance of learning algorithms in comparison to a batch discretization. The proposed method is much more appropriate in incremental learning, and in problems where data flows continuously, as in most of the recent data mining applications.
Detection of diffuse interstellar bands in M 31

Aims. We investigate the diffuse interstellar band (DIB) spectrum in the interstellar medium of M 31. Methods. The DEIMOS spectrograph of the W. M. Keck observatory was used to make optical spectroscopic observations of two supergiant stars, MAG 63885 and MAG 70817, in the vicinity of the OB78 association in M 31 where the metallicity is approximately equal to solar. Results. The $\lambda\lambda$5780, 5797, 6203, 6283 and 6613 DIBs are detected in both sightlines at velocities matching the M 31 interstellar Na I absorption. The spectra are classified and interstellar reddenings are derived for both stars. Diffuse interstellar band (DIB) equivalent widths and radial velocities are presented. Conclusions. The spectrum of DIBs observed in M 31 towards MAG 63885 is found to be similar to that observed in the Milky Way. Towards MAG 70817 the DIB equivalent widths per unit reddening are about three times the Galactic average. Compared to observations elsewhere in the Universe, relative to reddening the M 31 ISM in the vicinity of OB78 is apparently a highly favourable environment for the formation of DIB carriers.
Interest rate pass-through and financial crises: do switching regimes matter? the case of Argentina

The dynamic relationship between a money market (interbank) rate and different short-term lending rates is analysed by measuring the pass-through process between these rates in the Argentinean banking system. Neither linear single-equation modelling nor linear multi-equation systems capture efficiently this relationship. The presence of several episodes of financial crises alters the speed and degree of response to shocks in the interbank rate. Thus, a Markov switching VAR model shows that under normal financial conditions short-run stickiness is higher for those rates on loans with higher credit risk. But it also shows that when there is a high-volatility scenario, the pass-through increases considerably for all interest rates. The MSIAH(2)-VAR(1) identifies correctly periods of financial distress (in which regime switch occurs).
The role of memory updating in shallow native and opaque second language learning

The current study investigates the relation between working memory updating and second language learning (L2) outcomes in typically-developing fourth grade children. Our primary aim was to replicate and extend previous findings on the relationship between updating and low-level reading skills, i.e. fluency. Our second objective was to examine possible updating transfer effects across languages, from the native language (L1) to L2 learning. The languages considered have different orthographic features; shallow for L1 (Italian), and opaque for L2 (English). Mediation analyses were tested using the bootstrapping method; we found that updating was directly related to reading fluency in L2 learning. Moreover, we showed evidence of the mediating role of L1 fluency in the relation between memory updating and L2 fluency. Our findings suggest that updating processes may act at a low level for reading, and are potentially independent from specific language features, both for opaque and regular orthographies.
Analyzing and Re ning an Architectural Style

Architectural styles have been introduced in 1] in order to classify and analyze software architectures. In that paper, Z was used as a notation to specify and study architectural styles, however some problems remained open concerning speciication and analysis of their behavioral properties. We use a new operational semantics to describe and analyze an architectural style of distributed systems. We introduce three reenements of a \Message Router" style, useful to describe distributed applications like e-mail or news systems; we also formalize and prove some properties of the style and, henceforth, of derived software architectures.
An Open Benchmark Suite for Evaluating Computer Architecture on Bioinformatics and Life Science Applications

In this paper, we propose BIOPERF, a definitive benchmark suite of representative applications from the biology and life sciences community, where the codes are carefully selected to span a breadth of algorithms and performance char- acteristics. The BIOPERF suite is available from www.bioperf. org and includes benchmark source code, input datasets of various sizes, and information for compiling and using the benchmarks. We include parallel codes where available. I. INTRODUCTION
Rotary ultrasonic milling of C/SiC composites fabricated using chemical vapor infiltration and needling technique

Carbon fiber reinforced silicon carbide (C/SiC) has a widespread application in the aerospace industry owing to its superior properties like hardness, wear resistance, low density and heat resistant. However, poor characteristics of conventional machining of C/SiC composite has impoverished its utility in space and military applications. To overcome this problem, a new method of rotary ultrasonic milling has been used for machining the composites with a varying material density which have been prepared using chemical vapor infiltration (CVI) and needling technique available at Indian space research organization. Different response characteristics were studied with different machining parameters namely material density, feed rate, and axial depth of cut. The pragmatic results revealed that maximum average change in the surface roughness is 6.08 μm for 1.74 g cm−3, 50 mm min−1, and 0.01 mm whereas material removal rate decreases by 33.29%, 66.57%, and 66.82% on increasing the material density from 1.74 to 2.46 g cm−3, feed rate from 50 to 200 mm min−1 and axial depth of cut from 0.01 to 0.04 mm respectively. Furthermore, it is apparent from tool wear study that wear reduces as the material density is decreased. Subsequently, morphological examination revealed that SiC was uniformly distributed throughout the sample and very less gap present inside the structure and energy dispersive spectroscopy confirms the presence of carbon (45.77%) and silicon (54.23%) in the fabricated composites.
Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus

ABSTRACT Acyl-homoserine lactones (acyl-HSLs) serve as dedicated cell-to-cell signaling molecules in many species of the classProteobacteria. We have addressed the question of whether these compounds can be degraded biologically. A motile, rod-shaped bacterium was isolated from soil based upon its ability to utilizeN-(3-oxohexanoyl)-l-homoserine lactone as the sole source of energy and nitrogen. The bacterium was classified as a strain of Variovorax paradoxus. TheV. paradoxus isolate was capable of growth on all of the acyl-HSLs tested. The molar growth yields correlated with the length of the acyl group. HSL, a product of acyl-HSL metabolism, was used as a nitrogen source, but not as an energy source. Cleavage and partial mineralization of the HSL ring were demonstrated by using radiolabeled substrate. This study indicates that some strains of V. paradoxus degrade and grow on acyl-HSL signals as the sole energy and nitrogen sources. This study provides clues about the metabolic pathway of acyl-HSL degradation by V. paradoxus.
Suppressor of Cytokine Signaling-3 Is Recruited to the Activated Granulocyte-Colony Stimulating Factor Receptor and Modulates its Signal Transduction1

G-CSF is a polypeptide growth factor used in treatment following chemotherapy. G-CSF regulates granulopoiesis and acts on its target cells by inducing homodimerization of the G-CSFR, thereby activating intracellular signaling cascades. The G-CSFR encompasses four tyrosine motifs on its cytoplasmic tail that have been shown to recruit a number of regulatory proteins. Suppressor of cytokine signaling 3 (SOCS-3), also referred to as cytokine-inducible Src homolgy 2-containing protein 3, is a member of a recently discovered family of feedback inhibitors that have been shown to inhibit the Janus kinase/STAT pathway. In this study, we demonstrate that human SOCS-3 is rapidly induced by G-CSF in polymorphonuclear neutrophils as well as in the myeloid precursor cell line U937 and that SOCS-3 negatively regulates G-CSFR-mediated STAT activation. Most importantly, we show that SOCS-3 is recruited to the G-CSFR in a phosphorylation-dependent manner and we identify phosphotyrosine (pY)729 as the major recruitment site for SOCS-3. Furthermore, we demonstrate that SOCS-3 directly binds to this pY motif. Surface plasmon resonance analysis reveals a dissociation constant (KD) for this interaction of around 2.8 μM. These findings strongly suggest that the recruitment of SOCS-3 to pY729 is important for the modulation of G-CSFR-mediated signal transduction by SOCS-3.