Miracle-dz/UniFAR-FTUs huggingface dataset:
Ubiquitin-dependent and Ubiquitin-independent Control of Subunit Stoichiometry in the SWI/SNF Complex*

The mammalian SWI/SNF chromatin remodeling complex is a key player in multiple chromatin transactions. Core subunits of this complex, including the ATPase, Brg-1, and various Brg-1-associated factors (BAFs), work in concert to maintain a functional remodeling complex. This intra-complex regulation is supervised by protein-protein interactions, as stoichiometric levels of BAF proteins are maintained by proteasomal degradation. We show that the mechanism of BAF155-mediated stabilization of BAF57 involves blocking its ubiquitination by preventing interaction with TRIP12, an E3 ubiquitin ligase. Consequently, as opposed to complexed BAF57, whose principal lysines are unavailable for ubiquitination, uncomplexed BAF57 can be freely ubiquitinated and degraded by the proteasome. Additionally, a BAF57 mutant, which contains no lysine residues, was found to retain its ability to be stabilized by interaction with BAF155, suggesting that in addition to the ubiquitin-dependent mechanism of BAF57 degradation, there exists a ubiquitin-independent mechanism that may involve the direct interaction of BAF57 with the proteasome. We propose that this regulatory mechanism exists to ensure functional fidelity of the complex and prevent the accumulation of uncomplexed proteins, which may disrupt the normal activity of the complex.
Sperm whale behaviour indicates the use of echolocation click buzzes ‘creaks’ in prey capture

During foraging dives, sperm whales (Physeter macrocephalus) produce long series of regular clicks at 0.5–2 s intervals interspersed with rapid–click buzzes called ‘creaks’. Sound, depth and orientation recording Dtags were attached to 23 whales in the Ligurian Sea and Gulf of Mexico to test whether the behaviour of diving sperm whales supports the hypothesis that creaks are produced during prey capture. Sperm whales spent most of their bottom time within one or two depth bands, apparently feeding in vertically stratified prey layers. Creak rates were highest during the bottom phase: 99.8% of creaks were produced in the deepest 50% of dives, 57% in the deepest 15% of dives. Whales swam actively during the bottom phase, producing a mean of 12.5 depth inflections per dive. A mean of 32% of creaks produced during the bottom phase occurred within 10 s of an inflection (13 x more than chance). Sperm whales actively altered their body orientation throughout the bottom phase with significantly increased rates of change during creaks, reflecting increased manoeuvring. Sperm whales increased their bottom foraging time when creak rates were higher. These results all strongly support the hypothesis that creaks are an echolocation signal adapted for foraging, analogous to terminal buzzes in taxonomically diverse echolocating species.
Frequent Mutation of the PIK3CA Gene in Ovarian and Breast Cancers

Purpose: Activation of the phosphatidylinositol 3-kinase (PI3K)-AKT pathway, resulting in increased cell proliferation, survival, and motility, is believed to play an oncogenic role in many cancer types. The PIK3CA gene encodes the p110α catalytic subunit of PI3K, and is amplified in some ovarian cancers, whereas the AKT2 gene is amplified in some ovarian, breast, and pancreatic cancers. Recently, in a mutational screen of eight PI3K genes and eight PI3K-like genes, PIK3CA was found to be the only gene affected by somatic mutations, which were observed frequently in gastrointestinal and brain cancers. Here, we test whether PIK3CA is subject to mutation in ovarian and breast cancers. Experimental Design: Exons 9 and 20, encoding the highly conserved helical and kinase domains of PIK3CA, were subjected to sequence analysis in 198 advanced stage epithelial ovarian carcinomas and 72 invasive breast carcinomas (48 of ductal histology and 24 of lobular histology). Results: Somatic missense mutations were observed in 24 of 198 (12%) ovarian carcinomas, and in 13 of 72 (18%) breast carcinomas. Conclusions: These data indicate that mutations of PIK3CA play an oncogenic role in substantial fractions of ovarian and breast carcinomas, and in consideration of mutation of other components of the PI3K-AKT pathway in both tumor types, confirm the major oncogenic role of this pathway in ovarian and breast carcinomas.
Comment on "A Semi-Empirical Approach to Projecting Future Sea-Level Rise"

Rahmstorf (Reports, 19 January 2007, p. 368) presented an approach for predicting sea-level rise based on a proposed linear relationship between global mean surface temperature and the rate of global mean sea-level change. We find no such linear relationship. Although we agree that there is considerable uncertainty in the prediction of future sea-level rise, this approach does not meaningfully contribute to quantifying that uncertainty.
The active force–length relationship is invisible during extensive eccentric contractions in skinned skeletal muscle fibres

In contrast to experimentally observed progressive forces in eccentric contractions, cross-bridge and sliding-filament theories of muscle contraction predict that varying myofilament overlap will lead to increases and decreases in active force during eccentric contractions. Non-cross-bridge contributions potentially explain the progressive total forces. However, it is not clear whether underlying abrupt changes in the slope of the nonlinear force–length relationship are visible in long isokinetic stretches, and in which proportion cross-bridges and non-cross-bridges contribute to muscle force. Here, we show that maximally activated single skinned rat muscle fibres behave (almost across the entire working range) like linear springs. The force slope is about three times the maximum isometric force per optimal length. Cross-bridge and non-cross-bridge contributions to the muscle force were investigated using an actomyosin inhibitor. The experiments revealed a nonlinear progressive contribution of non-cross-bridge forces and suggest a nonlinear cross-bridge contribution similar to the active force–length relationship (though with increased optimal length and maximum isometric force). The linear muscle behaviour might significantly reduce the control effort. Moreover, the observed slight increase in slope with initial length is in accordance with current models attributing the non-cross-bridge force to titin.
Regulation of the proneural gene achaete by helix-loop-helix proteins

The Achaete (Ac) protein, a transcriptional regulator of the basic-helix-loop-helix (bHLH) type, confers upon ectodermal cells the ability to become neural precursors. Its temporally and spatially regulated expression, together with that of the related Scute (Sc) protein, helps define the pattern of Drosophila melanogaster sensory organs. We have examined the transcriptional control of the ac gene and shown, using in vivo assays, that several E-boxes, putative interacting sites for bHLH proteins, present in the ac promoter are most important for ac regulation. They most likely mediate ac self-stimulation and sc trans-activation. We also demonstrate that ac transcription is negatively regulated in vivo by the gene extramacrochaetae (emc) in a manner dependent on Ac and Sc products. emc encodes an HLH protein that lacks the basic region and presumably antagonizes Ac and Sc function by sequestering these proteins in complexes unable to interact with DNA. Our results strongly support the model of negative regulation of emc on ac and sc transcription through titration of their products. As currently thought, this seems accomplished by heterodimerization via the HLH domain, because an amino acid substitution in this region abolishes the emc antagonistic effect both in vitro and in vivo.
Electrophysiological characterization of different types of neurons recorded in vivo in the motor cortex of the cat. I. Patterns of firing activity and synaptic responses.

1. Patterns of firing activity and characteristics of antidromic and synaptic responses to stimulation of the pyramidal tract at peduncular level [peduncular pyramidal tract (PP)] and the ventrolateral thalamic nucleus (VL) were studied in neurons of area 4 gamma of the motor cortex of awake, chronic cats using intracellular microelectrode techniques. The results offer a new functional classification of neocortical neurons based on electrophysiological properties of the 640 recorded cells. 2. Four classes of neurons were distinguished: (class i) inactivating bursting (ib) neurons (n = 60) including fast antidromic response PP (fPP) (n = 0), slow antidromic response PP (sPP) (n = 11), and no antidromic response PP cells (nPP) (n = 49); (class ii) noninactivating bursting (nib) neurons (n = 79), including fPP (n = 23), sPP (n = 0), and nPP cells (n = 56); (class iii) fast-spiking (fsp) neurons (n = 56), including fPP (n = 0), sPP (n = 0), and nPP cells (n = 56); and (class iv) regular-spiking (rsp) neurons (n = 445), including fPP (n = 96), sPP (n = 38), and nPP cells (n = 311). (Neurons in each classification were further separated by their antidromic responses to PP stimulation: fast PP (fPP) slow PP (sPP), or nPP cells, the latter not responding antidromically to electrical stimulation of the peduncle. ) 3. Recurrent monosynaptic excitatory postsynaptic potentials (EPSPs) followed antidromic spikes elicited by PP stimulation in most (96%) fPP but much fewer (24%) sPP cells. In fPP cells, it was possible to separate the PP EPSPs into two monosynaptic EPSP components that were generated by other fPP and sPP cells, respectively. VL stimulation evoked monosynaptic EPSPs in 100% of fPP cells (vs. 63% of sPP cells) and antidromic action potentials in 16% of fPP cells (vs. 12% of sPP cells). 4. Firing activity consisted of single spike discharges in most PP cells; however, noninactivating bursting was observed in 19% of fPP cells, and inactivating bursting was observed in 23% of sPP cells (see below). In 18% of ib and 11% of nib/nPP neurons, VL stimulation elicited antidromic action potentials. Other bursting neurons proved to be PP cells with characteristic differences in axonal conduction velocity (see above). All PP cells among the nib cells were fPP, and all PP cells among the ib cells were sPP cells. All fsp neurons were found to be nPP cells, and none could be activated antidromically by VL stimulation. Thus the fsp pattern of discharge distinguished a unique class of nPP cells. (ABSTRACT TRUNCATED AT 400 WORDS)
Dynamic Models versus Frailty Models for Recurrent Event Data

— R ecurrent event data is a special type of multivariate survival data. Dynamic and frailty models are one of the approaches that dealt with this kind of data. A comparison between these two models is studied using the empirical standard deviation of the standardized martingale residual processes as a way of assessing the fit of the two models based on the Aalen additive regression model. Here we found both approaches took heterogeneity into account and produce residual standard deviations close to each other both in the simulation study and in the real data set.
Depression and Parenting by Nonoffending Mothers of Children Who Experienced Sexual Abuse

Parenting may be one mechanism by which depression in nonoffending mothers impacts child emotional and behavioral adjustment after sexual abuse. This study examined the relationship between self-reported maternal depression and parenting behaviors by nonoffending mothers of children who experienced sexual abuse. The participants were 204 nonoffending biological mother–child pairs recruited from a clinic providing services for children who experienced sexual abuse. The mothers completed pretreatment self-report measures of demographic information, depression, and parenting behaviors. Children (7 to 17 years) completed a measure of mothers’ parenting behaviors. Mothers with clinically high levels of self-reported depression employed more inconsistent parenting behavior and provided poorer monitoring/supervision of their children than mothers without clinically high levels of self-reported depression. Implications for clinical practice and future research are discussed.
DSSS Signal Parameter Detection and PN Sequence Estimation Based on SOFM Neural Network

Having not the a prior knowledge about the DSSS signal in the non-cooperation condition, we utilize a self-organizing feature map (SOFM) neural network algorithm to detection and identify the PN sequence. A new method that is suit DSSS signal is proposed according the Kohonen rule in SOFM theory. Utilizing the characteristic based on non-supervised learning rule, the blind algorithm can estimation the PN sequence in low SNR. The computer simulation and experiment test demonstrated that the algorithm is effective. Comparing the traditional slip-correlation method, the SOFM algorithm's BER and implementation complexity is lower
A Cellular MicroRNA Facilitates Regulatory T Lymphocyte Development by Targeting the FOXP3 Promoter TATA-Box Motif

The CD4+CD25+FOXP3+ regulatory T cells (Tregs) mediate immunological self-tolerance and suppress various immune responses. FOXP3 is a key transcriptional factor for the generation and development of Tregs. Its expression is regulated by various cytokines including TGF-β, IL-2, and IL-10. It is important to further identify the regulatory factors for Tregs. Given that many microRNAs (miRNAs) could specifically interact with the core promoter region and specifically enhance the transcription of many target genes, we searched for any possible miRNA(s) targeting the core promoter region of the FOXP3 gene. We found that miR-4281, an miRNA specifically expressed in hominids, can potently and specifically upregulate FOXP3 expression by directly interacting with the TATA-box motif in the human FOXP3 promoter. Consequently, miR-4281 significantly accelerated the differentiation of human naive cells to induced Tregs (iTregs) that possess immune suppressor functions and weaken the development of graft-versus-host disease in a humanized mouse model. Interestingly, iTregs induced by the combination of TGF-β, IL-2, and chemically synthesized miR-4281 were more stable and functional than those induced by TGF-β and IL-2 alone. Moreover, we found that the IL-2/STAT5 signal transduction upregulates FOXP3 expression not only through the classical pathway, but also by enhancing the expression of the miR-4281 precursor gene (SNCB) and, correspondingly, miR-4281. This study reveals a novel mechanism regulating FOXP3 expression and human iTreg development and, therefore, offers a new therapeutic target to manipulate immunosuppressive system.
EMARE: an email-based mobile agent runtime environment for information retrieval on the Internet

Most of current information retrieval systems are deployed on high-speed network and high-power environment. For those great increasingly popular mobile devices with low-speed network and low-power environment, to intensively retrieve the information on the Internet is difficult. In this paper, we propose a framework named EMARE (stand for E-mail based mobile agent runtime environment) to solve the difficulty. EMARE provides users to retrieve desired information via mobile devices over the Internet. The mobile device can be a mobile phone, PDA, or handheld PC. Take advantage of the compatibility of the e-mail protocol, EMARE can be uniformly accessed by those versatile devices. Furthermore, we, in the proposed framework, also utilize mobile agent technologies to enhance the ability of mobile devices. The experiments show that EMARE is an ideal mobile computing framework with cost-effective communications, unified user interface, and ease-of-deployment features.
hisT is part of a multigene operon in Escherichia coli K-12

The Escherichia coli K-12 hisT gene has been cloned, and its organization and expression have been analyzed on multicopy plasmids. The hisT gene, which encodes tRNA pseudouridine synthase I (PSUI), was isolated on a Clarke-Carbon plasmid known to contain the purF gene. The presence of the hisT gene on this plasmid was suggested by its ability to restore both production of PSUI enzymatic activity and suppression of amber mutations in a hisT mutant strain. A 2.3-kilobase HindIII-ClaI restriction fragment containing the hisT gene was subcloned into plasmid pBR322, and the resulting plasmid (designated psi 300) was mapped with restriction enzymes. Complementation analysis with different kinds of hisT mutations and tRNA structural analysis confirmed that plasmid psi 300 contained the hisT structural gene. Enzyme assays showed that plasmid psi 300 overproduced PSUI activity by ca. 20-fold compared with the wild-type level. Subclones containing restriction fragments from plasmid psi 300 inserted downstream from the lac promoter established that the hisT gene is oriented from the HindIII site toward the ClaI site. Other subclones and derivatives of plasmid psi 300 containing insertion or deletion mutations were constructed and assayed for production of PSUI activity and production of proteins in minicells. These experiments showed that: (i) the proximal 1.3-kilobase HindIII-BssHII restriction fragment contains a promoter for the hisT gene and encodes a 45,000-dalton polypeptide that is not PSUI; (ii) the distal 1.0-kilobase BssHII-ClaI restriction fragment encodes the 31,000-dalton PSUI polypeptide; (iii) the 45,000-dalton polypeptide is synthesized in an approximately eightfold excess compared with PSUI; and (iv) synthesis of the two polypeptides is coupled, suggesting that the two genes are part of an operon. Insertion of mini-Mu d1 (lac Km) phage into plasmid psi 300 confirmed that the hisT gene is the downstream gene in the operon.
Adaptive Genetic Algorithm Based Artificial Neural Network for Software Defect Prediction By Racharla

To meet the requirement of an efficient software defect prediction,in this paper an evolutionary computing based neural network learning scheme has been developed that alleviates the existing Artificial Neural Network (ANN) limitations such as local minima and convergence issues. To achieve optimal software defect prediction, in this paper, Adaptive-Genetic Algorithm (A-GA) based ANN learning and weightestimation scheme has been developed. Unlike conventional GA, in this paper we have used adaptive crossover and mutation probability parameter that alleviates the issue of disruption towards optimal solution. We have used object oriented software metrics, CK metrics for fault prediction and the proposed Evolutionary Computing Based Hybrid Neural Network (HENN)algorithm has been examined for performance in terms of accuracy, precision, recall, F-measure, completeness etc, where it has performed better as compared to major existing schemes. The proposed scheme exhibited 97.99% prediction accuracy while ensuring optimal precision, F-
Issue report on business adoption of Microsoft Passport

Purpose – The purpose of this paper is to examine the feasibility and desirability of using the Microsoft Passport service for client authentication and authorization. It aims to present the business benefits of using Microsoft Passport, an overview (logical) description of the work involved in adopting Microsoft Passport into a business site, and a functional description of how Microsoft Passport works in conceptual terms.Design/methodology/approach – An analysis of the level of business adoption of passport is then presented.Findings – The paper concludes that business adoption of Microsoft Passport appears to be losing ground due to lack of trust, control, and privacy; and the proliferation of other identity management paradigms. This issue report is prepared from the perspective of a business analyst and is pitched in terminology suitable for a business audience.Practical implications – This work provides organisations investigating the feasibility/desirability of using the Microsoft Passport, a funda.
[Value of percutaneous core needle biopsy in the investigation of a suspected bone tumor].

PURPOSE To Determine the value of percutaneous core needle biopsy in the investigation of a suspected bone neoplasm. MATERIAL AND METHODS We performed a retrospective study of 91 core needle biopsies performed between May 1995 and October 2001. Patients were excluded if they had a known primary carcinoma or if an infection was suspected by clinical, physical or laboratory findings. The results were correlated to the analysis of the surgical piece or, for the 28 patients who did not undergo surgery, to the clinical evolution over more than 12 months. RESULTS The final diagnosis was metastasis in 29 cases, primary bone tumor in 36 cases and benign lesions in 25 cases. Sensitivity was 92.3% and specificity was 97.4%. For primary malignant bone tumors, results respected histology features and grade in 79.2%. In cases of mistake, because of the correlation of these results to the clinical and radiological context, the treatment of the bony malignant lesions were adapted in 95.8% of cases. Only one major complication was reported in these 91 biopsies. CONCLUSION First intention core needle biopsy, confronted with radio-clinical context seems to have a place in the evaluation of bone lesions when a tumor is suspected. This technique, less expensive than an open biopsy and with fewer complications, is best performed as part of a multidisciplinary approach with the surgeon's collaboration.
Antiperlecan Antibodies Are Novel Accelerators of Immune‐Mediated Vascular Injury

Acute vascular rejection (AVR) is characterized by immune‐mediated vascular injury and heightened endothelial cell (EC) apoptosis. We reported previously that apoptotic ECs release a bioactive C‐terminal fragment of perlecan referred to as LG3. Here, we tested the possibility that LG3 behaves as a neoantigen, fuelling the production of anti‐LG3 antibodies of potential importance in regulating allograft vascular injury. We performed a case–control study in which we compared anti‐LG3 IgG titers in kidney transplant recipients with AVR (n = 15) versus those with acute tubulo‐interstitial rejection (ATIR) (n = 15) or stable graft function (n = 30). Patients who experienced AVR had elevated anti‐LG3 titers pre and posttransplantation compared to subjects with ATIR or stable graft function (p < 0.05 for both mediators). Elevated pretransplant anti‐LG3 titers (OR: 4.62, 95% CI: 1.08–19.72) and pretransplant donor‐specific antibodies (DSA) (OR 4.79, 95% CI: 1.03–22.19) were both independently associated with AVR. To address the functional role of anti‐LG3 antibodies in AVR, we turned to passive transfer of anti‐LG3 antibodies in an animal model of vascular rejection based on orthotopic aortic transplantation between fully MHC‐mismatched mice. Neointima formation, C4d deposition and allograft inflammation were significantly increased in recipients of an ischemic aortic allograft passively transferred with anti‐LG3 antibodies. Collectively, these data identify anti‐LG3 antibodies as novel accelerators of immune‐mediated vascular injury and obliterative remodeling.
Immunoprotection of rat islet xenografts by cotransplantation with sertoli cells and a single injection of antilymphocyte serum1

Background. Islet transplantation has become a clinical reality; however, before it can be extended to young juvenile diabetics an unlimited supply of tissue is needed and the use of chronic immunosuppression should be eliminated. This study was designed to determine whether Sertoli cells can immunoprotect islet xenografts. Methods. Lewis rat islets were cotransplanted with Balb/c Sertoli cells in diabetic Balb/c mice treated with one injection of anti-mouse lymphocyte serum (ALS). Results. When islets were transplanted alone, in combination with Sertoli cells, or in combination with ALS, mean graft survival times were 10.9±0.8, 14.0±1.2, or 12.2±0.7, respectively. When islets were combined with Sertoli cells and ALS, mean graft survival time increased to 64.9±8.1. Conclusions. Sertoli cells are able to prolong the survival of islet xenografts when combined with ALS, thereby supporting their use as a means to immunoprotect cellular grafts such as islets for the treatment of type 1 diabetes.