Miracle-dz/UniFAR-FTUs huggingface dataset:
Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex

The conserved transcription coactivator SAGA is comprised of several modules that are involved in activator binding, TBP binding, histone acetylation (HAT) and deubiquitination (DUB). Crosslinking and mass spectrometry, together with genetic and biochemical analyses, were used to determine the molecular architecture of the SAGA‐TBP complex. We find that the SAGA Taf and Taf‐like subunits form a TFIID‐like core complex at the center of SAGA that makes extensive interactions with all other SAGA modules. SAGA‐TBP binding involves a network of interactions between subunits Spt3, Spt8, Spt20, and Spt7. The HAT and DUB modules are in close proximity, and the DUB module modestly stimulates HAT function. The large activator‐binding subunit Tra1 primarily connects to the TFIID‐like core via its FAT domain. These combined results were used to derive a model for the arrangement of the SAGA subunits and its interactions with TBP. Our results provide new insight into SAGA function in gene regulation, its structural similarity with TFIID, and functional interactions between the SAGA modules.
Clumping factor B (ClfB), a new surface‐located fibrinogen‐binding adhesin of Staphylococcus aureus

The surface‐located fibrinogen‐binding protein (clumping factor; ClfA) of Staphylococcus aureus has an unusual dipeptide repeat linking the ligand binding domain to the wall‐anchored region. Southern blotting experiments revealed several other loci in the S. aureus Newman genome that hybridized to a probe comprising DNA encoding the dipeptide repeat. One of these loci is analysed here. It also encodes a fibrinogen‐binding protein, which we have called ClfB. The overall organization of ClfB is very similar to that of ClfA, and the proteins have considerable sequence identity in the signal sequence and wall attachment domains. However, the A regions are only 26% identical. Recombinant biotinylated ClfB protein bound to fibrinogen in Western ligand blots. ClfB reacted with the α‐ and β‐chains of fibrinogen in the ligand blots in contrast to ClfA, which binds exclusively to the γ‐chain. Analysis of proteins released from the cell wall of S. aureus Newman by Western immunoblotting using antibody raised against the recombinant A region of ClfB identified a 124 kDa protein as the clfB gene product. This protein was detectable only on cells that were grown to the early exponential phase. It was absent from cells from late exponential phase or stationary phase cultures. Using a clfB mutant isolated by allelic replacement alone and in combination with a clfA mutation, the ClfB protein was shown to promote (i) clumping of exponential‐phase cells in a solution of fibrinogen, (ii) adherence of exponential‐phase bacteria to immobilized fibrinogen in vitro, and (iii) bacterial adherence to ex vivo human haemodialysis tubing, suggesting that it could contribute to the pathogenicity of biomaterial‐related infections. However, in wild‐type exponential‐phase S. aureus Newman cultures, ClfB activity was masked by the ClfA protein, and it did not contribute at all to interactions of cells from stationary‐phase cultures with fibrinogen. ClfB‐dependent bacterial adherence to immobilized fibrinogen was inhibited by millimolar concentrations of Ca2+ and Mn2+, which indicates that, like ClfA, ligand binding by ClfB is regulated by a low‐affinity inhibitory cation binding site.
Authentic Self-expression Breaking Them in or Eliciting Their Best? Reframing Socialization around Newcomers'

Socialization theory has focused on enculturating new employees such that they develop pride in their new organization and internalize its values. We draw on authenticity research to theorize that the initial stage of socialization leads to more effective employment relationships when it instead primarily encourages newcomers to express their personal identities. In a field experiment carried out in a large business process outsourcing company in India, we found that initial socialization focused on personal identity (emphasizing newcomers’ authentic best selves) led to greater customer satisfaction and employee retention after six months than socialization that focused on organizational identity (emphasizing the pride to be gained from organizational affiliation) or the organization’s traditional approach, which focused primarily on skills training. To confirm causation and explore the mechanisms underlying the effects, we replicated the results in a laboratory experiment in a U.S. university. We found that individuals working temporarily as part of a research team were more engaged and satisfied with their work, performed their tasks more effectively, and were less likely to quit when initial socialization focused on personal identity rather than on organizational identity or a control condition. In addition, authentic self-expression mediated these relationships. We call for a new direction in socialization theory that examines how both organizations and employees can benefit by emphasizing newcomers’ authentic best selves.
Management of Intrathoracic Benign Schwannomas of the Brachial Plexus

Primary tumours of the brachial plexus are rare entities. They usually present as extrathoracic masses located in the supraclavicular region. This report describes two cases of benign schwannomas arising from the brachial plexus with an intrathoracic growth. In the first case the tumour was completely intrathoracic and it was hardly removed through a standard posterolateral thoracotomy. In the second case the tumour presented as a cervicomediastinal lesion and it was resected through a one-stage combined supraclavicular incision followed by left video-assisted thoracoscopic surgery. A brachial plexus tumour should be suspected not only in patients with a supraclavicular or cervicomediastinal mass but also in those with intrathoracic apical lesions. A preoperative magnetic resonance imaging study of brachial plexus should be performed in such cases in order to plan the correct surgical approach.
Neutral and acid retinyl ester hydrolases associated with rat liver microsomes: relationships to microsomal cholesteryl ester hydrolases.

We recently reported the presence of a neutral, bile salt-independent retinyl ester hydrolase (REH) activity in rat liver microsomes and showed that it was distinct from the previously studied bile salt-dependent REH and from nonspecific carboxylesterases (Harrison, E. H., and M. Z. Gad. 1989. J. Biol. Chem. 264: 17142-17147). We have now further characterized the hydrolysis of retinyl esters by liver microsomes and have compared the observed activities with those catalyzing the hydrolysis of cholesteryl esters. Microsomes and microsomal subfractions enriched in plasma membranes and endosomes catalyze the hydrolysis of retinyl esters at both neutral and acid pH. The acid and neutral REH enzyme activities can be distinguished from one another on the basis of selective inhibition by metal ions and by irreversible, active site-directed serine esterase inhibitors. The same preparations also catalyze the hydrolysis of cholesteryl esters at both acid and neutral pH. However, the enzyme(s) responsible for the neutral REH activity can be clearly responsible for the neutral REH activity can be clearly differentiated from the neutral cholesteryl ester hydrolase(s) on the basis of differential stability, sensitivity to proteolysis, and sensitivity to active site-directed reagents. These results suggest that the neutral, bile salt-independent REH is relatively specific for the hydrolysis of retinyl esters and thus may play an important physiological role in hepatic vitamin A metabolism. In contrast to the neutral hydrolases, the activities responsible for hydrolysis of retinyl esters and cholesterol esters at acid pH are similar in their responses to the treatments mentioned above. Thus, a single microsomal acid hydrolase may catalyze the hydrolysis of both types of ester. (ABSTRACT TRUNCATED AT 250 WORDS)
Graphene Single Crystals: Size and Morphology Engineering

Recently developed chemical vapor deposition (CVD) is considered as an effective way to large‐area and high‐quality graphene preparation due to its ultra‐low cost, high controllability, and high scalability. However, CVD‐grown graphene film is polycrystalline, and composed of numerous grains separated by grain boundaries, which are detrimental to graphene‐based electronics. Intensive investigations have been inspired on the controlled growth of graphene single crystals with the absence of intrinsic defects. As the two most concerned parameters, the size and morphology serve critical roles in affecting properties and understanding the growth mechanism of graphene crystals. Therefore, a precise tuning of the size and morphology will be of great significance in scale‐up graphene production and wide applications. Here, recent advances in the synthesis of graphene single crystals on both metals and dielectric substrates by the CVD method are discussed. The review mainly covers the size and morphology engineering of graphene single crystals. Furthermore, recent progress in the growth mechanism and device applications of graphene single crystals are presented. Finally, the opportunities and challenges are discussed.
Langerhans cells cross-present antigen derived from skin

Dendritic cells (DC) efficiently cross-present exogenous antigen on MHC class I molecules to CD8+ T cells. However, little is known about cross-presentation by Langerhans cells (LC), the DCs of the epidermis. Therefore, we investigated this issue in detail. Isolated murine LCs were able to cross-present soluble ovalbumin protein on MHC-class I molecules to antigen-specific CD8+ T cells, albeit less potently than the CD8+ DC subsets from spleen. Furthermore, LCs cross-presented cell-associated ovalbumin peptide and protein expressed by neighboring keratinocytes. Use of transporter associated with antigen processing (TAP-1)-deficient mice suggested a TAP-dependent pathway. Similar observations were made with migratory LC. Antigen expressed in the epidermis was ingested by LCs during migration from the epidermis and presented to antigen-specific T cells in vitro. Cross-presentation of ovalbumin protein by LCs induced IFN-γ production and cytotoxicity in antigen-specific CD8+ T cells. Additionally, epicutaneous application of ovalbumin protein induced in vivo proliferation of OT-I T cells in the draining lymph nodes; this was markedly enhanced when antigen was applied to inflamed, barrier-disrupted skin. Thus, LCs cross-present exogenous antigen to CD8+ T cells and induce effector functions, like cytokine production and cytotoxicity, and may thereby critically contribute in epicutaneous vaccination approaches.
Distinct Functions of the Unique C Terminus of LAP2α in Cell Proliferation and Nuclear Assembly*

The non-membrane-bound lamina-associated polypeptide 2 isoform, LAP2α, forms nucleoskeletal structures with A-type lamins and interacts with chromosomes in a cell cycle-dependent manner. LAP2α contains a LEM (LAP2, emerin, and MAN1) domain in the constant N terminus that binds to chromosomal barrier-to-autointegration factor, and a C-terminal unique region that is essential for chromosome binding. Here we show that C-terminal LAP2α fragment efficiently bound to mitotic chromosomes and inhibited assembly of endogenous LAP2α, nuclear membranes, and lamins A/C inin vitro nuclear assembly assays. Full-length recombinant LAP2α, which bound to chromosomes, and N-terminal fragment, which did not bind, had no effect on assembly. This suggested an essential role for the LAP2α C terminus in chromosome association and for the N-terminal LEM domain in subsequent assembly stages. In vivo analysis upon transient expression of GFP-tagged LAP2α fragments confirmed that, unlike the N-terminal fragment, the C-terminal fragment was able to bind to chromosomes during mitosis, if expressed weakly. At higher expression levels, C-terminal LAP2α fragment and full-length protein led to cell cycle arrest in interphase and apoptosis, as shown by fluorescence-activated cell sorter analysis, time lapse microscopy, and BrdUrd incorporation assays. These data indicated distinct functions of LAP2α in cell cycle progression during interphase and in nuclear reassembly during mitosis.
The Absolute Magnitude of RR Lyrae Stars Derived from the Hipparcos Catalogue

The present determination of the absolute magnitude MV(RR) of RR Lyrae stars is twofold, relying upon Hipparcos proper motions and trigonometric parallaxes separately. First, applying the statistical parallax method to the proper motions, we find ⟨ MV(RR)⟩ = 0.69±0.10 for 99 halo RR Lyrae stars with ⟨ [Fe/H]⟩ = -1.58. Second, applying the Lutz-Kelker correction to the RR Lyrae HIP 95497 with the most accurately measured parallax, we obtain MV(RR) = (0.58–0.68)+0.28−0.31 at [Fe/H] = -1.6. Furthermore, allowing full use of low-accuracy and negative parallaxes, as well 125 RR Lyrae stars with -2.49 ≤ [Fe/H] ≤ 0.07, the maximum likelihood estimation yields the relation MV(RR) = (0.59 ± 0.37) + (0.20 ± 0.63)([Fe/H] + 1.60), which formally agrees with the recent preferred relation. The same estimation again yields ⟨ MV(RR)⟩ = 0.65±0.33 for the 99 halo RR Lyrae stars. Although the formal errors in the latter three parallax estimates are rather large, all four results suggest the fainter absolute magnitude, MV(RR) ≈ 0.6-0.7 at [Fe/H] = -1.6. The present results still provide the lower limit on the age of the universe that is inconsistent with a flat, matter-dominated universe and current estimates of the Hubble constant.
Identification and characterization of repopulating spermatogonial stem cells from the adult human testis.

BACKGROUND This study was conducted to identify and characterize repopulating spermatogonial stem cells (SSCs) in the adult human testes. METHODS Testes biopsies from obstructive azoospermic patients and normal segments of human testicular tissue were used. Flow cytometry, real-time PCR and immunohistochemical analysis were performed. Purified human spermatogonia were transplanted into busulfan-treated recipient mouse testes and integrated cells were detected by human nuclear protein antibody co-localized with stem cell and germ cell markers. RESULTS Testicular biopsies collected from obstructive azoospermic men showed similar morphology and distribution of markers to the normal human testes. Flow cytometry showed distinct populations of stage-specific embryonic antigen-4 (SSEA-4), CD49f and CD90 positive cells in the adult human testes. SSEA-4 (+) cells showed high expression levels of SSC-specific genes and high levels of telomerase activity. Extensive colonization of human cells in the mouse testes indicates the presence of highly enriched populations of SSCs in the SSEA-4 (+) sorted cells. All the HNP (+) cells in the mouse testes were positive for germ cell marker dead box mRNA helicase and only half of them were dimly positive for c-kit. In addition, subpopulations of human spermatogonia that colonized mouse testes were positively stained for CD49f, GPR-125, Nanog and Oct-4 indicating the existence of population of cells among human spermatogonia with SSC and pluripotent characteristics. CONCLUSIONS This study clearly demonstrates that repopulating human SSCs have phenotypic characteristics of SSEA-4(+), CD49f(+), GPR-125(+)and c-Kit (neg/low). The results have direct implications for enrichment of human spermatogonia for further culture and germ cell differentiation studies.
I. Thresholds and Principal Components Analysis in Healthy Men and Women

Gustatory testing using the whole-mouth method was performed in 123 healthy young male and female subjects. The average thresholds for detection and recognition of the four basic tastes were not greatly different from the normal thresholds previously reported in Japan: a 0.0165 M solution of sucrose for sweet taste, a 0.0316 M solution of table salt for salty taste, a 0.000743 M solution of tartaric acid for sour taste and a 0.0000203 M solution of quinine hydrochloride for bitter taste. These results indicate that the whole-mouth gustatory test procedure employed in this study may be useful for evaluating gustatory function clinically. Principal components analysis conermed that sweet, salty, sour and bitter are indeed the four basic tastes and revealed that the sensation of taste is detected before the speciec taste is recognized, regardless of the speciec taste tested. Key words: multivariate analysis, taste sensation, whole-mouth gustatory test.
The epidemiology of tuberculosis in Europe

Tuberculosis (TB) continues to be one of the most devastating and widespread infections in the world. It is estimated that in 2004 there were 8.9 million new cases of TB globally.1 In general, children make up only a small proportion of cases, but in some high-incidence countries up to 15% of all TB cases occur in children.2 In June 2005 the World Health Organization (WHO) approved a new Stop TB Strategy with the aim of dramatically reducing the global burden of TB by 2015.3 Their intention is to cure at least 85% of sputum smear-positive cases and reduce the prevalence of and deaths due to TB by 50% relative to the rates in 1990. The WHO Global tuberculosis control report shows that the greatest burden of TB is in sub-Saharan Africa and Asia, with TB case notifications in the WHO European Region constituting less than 10% of worldwide notifications.1 While notifications are an excellent source of information on adult disease, an accurate description of the burden of TB in children is very difficult to obtain. The WHO notification criteria include only cases that are sputum smear positive. Fewer than 15% of children with culture-proven TB will be sputum smear positive, with the result that only a small percentage of children with TB will be represented in the data. The quality of information provided to the WHO can also vary and in many countries surveillance data are often unreliable due to poor diagnostic facilities and reporting systems. Because of these issues the International Union Against Tuberculosis and Lung Disease has stated that reliable information on the incidence of TB in childhood can only be obtained in developed countries, which have better diagnostic and reporting systems.4 In Europe there is a huge disparity in the rates of …
Toward information sharing: benefit and risk access control (BARAC)

This paper describes an access control model, called BARAC, that is based on balancing risks of information disclosure with benefits of information sharing. The model configuration associates risk and benefit vectors with every read and update transaction. An allowed transactions graph captures allowed transactions and flow paths that can be used to carry out the transactions. The total system is required to be profitable, in that the total system benefit must overweigh the total system risk; and the allowed transaction graph is required to be optimal, in that its profit cannot be improved by adding transactions or removing transactions. Both the system configuration and the allowed transaction graph can be dynamically modified, while preserving the required properties. The dynamic modifications are done in the scope of hierarchies of tasks and responsible parties, that control the task structure and risk budget allocation to tasks
Dynamic Recurrent Neural Network for Biped Robot Equilibrium Control: Preliminary Results

The purpose of the research addressed in this paper is to develop a real time neural control algorithm for the balance of a biped robot. Our approach is based on dynamic recurrent neural networks and dynamic backpropagation through time algorithm. The neural architecture and its learning process are validated on the control of the ROBIAN biped torso. The neural controller described is trained to compensate, by the torso’s joint motions, applied external perturbations. The algorithm is embedded in the real time electronic unit of the robot and online learning is achieved. The learning behavior and the control performances are the preliminary results presented in this paper. These experimental results show the ability and efficiency of the proposed approach.
Prenatal detection of neuroblastoma: a ten-year experience from the Dana-Farber Cancer Institute and Children's Hospital.

OBJECTIVES To assess the relative frequency of, the clinical and pathological correlates in, and the prognosis of the subset of infants with neuroblastoma who were identified initially by prenatal ultrasonography. DESIGN Retrospective review of all patients with neuroblastoma evaluated between 1982 and 1992. SETTING Large, urban, tertiary care children's hospital in Boston, Massachusetts. PATIENTS Eleven infants with neuroblastoma initially detected with prenatal sonograms were identified. RESULTS Nine patients had adrenal tumors; two had thoracic paraspinal tumors. Typical diagnostic evidence for neuroblastoma including a palpable abdominal mass and elevations in urinary catecholamines were not commonly seen postnatally. These patients had multiple favorable prognostic indicators including low stage of disease (10/11), favorable biological markers including cellular DNA content (5/5) and N-myc oncogene copy number (5/5), and histopathology suggestive for neuroblastoma in situ (7/11). All patients were treated by surgical resection. One patient exhibited progression of disease postoperatively, but demonstrated a complete clinical response to multiagent chemotherapy. Overall survival in our population was excellent with no deaths seen at a mean follow-up of 37 months (range 3 to 120 months). CONCLUSIONS Patients with neuroblastoma identified by prenatal ultrasonography generally, although not exclusively, follow a clinically favorable course in which surgical resection is curative. Chemotherapy is not indicated unless substantial progression of disease occurs.
3D Model Acquisition by Tracking 2D Wireframes

This paper presents a semi-automatic wireframe acquisition system. The system uses real-time (25Hz) tracking of a user specified 2D wireframe and intermittent camera pose parameters to accumulate 3D position information. The 2D tracking framework enables the application of model-based constraints in an intuitive way which interacts naturally with the Kalman filter formulation used. In particular, this is used to introduce feedback from the current 3D shape estimate to improve the robustness of the 2D tracking. The scheme allows wireframe models of simple edge based objects to be built in around 5 minutes.